2NVQ

RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0001172	biological_process	RNA-templated transcription
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0003968	molecular_function	RNA-directed RNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005665	cellular_component	RNA polymerase II, core complex
A	0005739	cellular_component	mitochondrion
A	0006351	biological_process	DNA-templated transcription
A	0006366	biological_process	transcription by RNA polymerase II
A	0006367	biological_process	transcription initiation at RNA polymerase II promoter
A	0006368	biological_process	transcription elongation by RNA polymerase II
A	0008270	molecular_function	zinc ion binding
A	0010494	cellular_component	cytoplasmic stress granule
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0019985	biological_process	translesion synthesis
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0042789	biological_process	mRNA transcription by RNA polymerase II
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0001172	biological_process	RNA-templated transcription
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003729	molecular_function	mRNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0003968	molecular_function	RNA-directed RNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005665	cellular_component	RNA polymerase II, core complex
B	0005739	cellular_component	mitochondrion
B	0006351	biological_process	DNA-templated transcription
B	0006366	biological_process	transcription by RNA polymerase II
B	0006367	biological_process	transcription initiation at RNA polymerase II promoter
B	0006368	biological_process	transcription elongation by RNA polymerase II
B	0008270	molecular_function	zinc ion binding
B	0010494	cellular_component	cytoplasmic stress granule
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0032549	molecular_function	ribonucleoside binding
B	0034062	molecular_function	5'-3' RNA polymerase activity
B	0046872	molecular_function	metal ion binding
C	0000428	cellular_component	DNA-directed RNA polymerase complex
C	0001172	biological_process	RNA-templated transcription
C	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0003968	molecular_function	RNA-directed RNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005665	cellular_component	RNA polymerase II, core complex
C	0006351	biological_process	DNA-templated transcription
C	0006366	biological_process	transcription by RNA polymerase II
C	0006367	biological_process	transcription initiation at RNA polymerase II promoter
C	0006368	biological_process	transcription elongation by RNA polymerase II
C	0006369	biological_process	termination of RNA polymerase II transcription
C	0008270	molecular_function	zinc ion binding
C	0046872	molecular_function	metal ion binding
C	0046983	molecular_function	protein dimerization activity
C	0055029	cellular_component	nuclear DNA-directed RNA polymerase complex
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0001172	biological_process	RNA-templated transcription
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0003968	molecular_function	RNA-directed RNA polymerase activity
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005665	cellular_component	RNA polymerase II, core complex
E	0005666	cellular_component	RNA polymerase III complex
E	0005736	cellular_component	RNA polymerase I complex
E	0006351	biological_process	DNA-templated transcription
E	0006360	biological_process	transcription by RNA polymerase I
E	0006361	biological_process	transcription initiation at RNA polymerase I promoter
E	0006362	biological_process	transcription elongation by RNA polymerase I
E	0006363	biological_process	termination of RNA polymerase I transcription
E	0006366	biological_process	transcription by RNA polymerase II
E	0006367	biological_process	transcription initiation at RNA polymerase II promoter
E	0006368	biological_process	transcription elongation by RNA polymerase II
E	0006383	biological_process	transcription by RNA polymerase III
E	0006384	biological_process	transcription initiation at RNA polymerase III promoter
E	0006386	biological_process	termination of RNA polymerase III transcription
E	0042254	biological_process	ribosome biogenesis
E	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
E	0042797	biological_process	tRNA transcription by RNA polymerase III
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0001172	biological_process	RNA-templated transcription
F	0003677	molecular_function	DNA binding
F	0003899	molecular_function	DNA-directed RNA polymerase activity
F	0003968	molecular_function	RNA-directed RNA polymerase activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005665	cellular_component	RNA polymerase II, core complex
F	0005666	cellular_component	RNA polymerase III complex
F	0005736	cellular_component	RNA polymerase I complex
F	0005737	cellular_component	cytoplasm
F	0006351	biological_process	DNA-templated transcription
F	0006360	biological_process	transcription by RNA polymerase I
F	0006361	biological_process	transcription initiation at RNA polymerase I promoter
F	0006362	biological_process	transcription elongation by RNA polymerase I
F	0006363	biological_process	termination of RNA polymerase I transcription
F	0006366	biological_process	transcription by RNA polymerase II
F	0006367	biological_process	transcription initiation at RNA polymerase II promoter
F	0006368	biological_process	transcription elongation by RNA polymerase II
F	0006383	biological_process	transcription by RNA polymerase III
F	0006384	biological_process	transcription initiation at RNA polymerase III promoter
F	0006386	biological_process	termination of RNA polymerase III transcription
F	0042254	biological_process	ribosome biogenesis
F	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
F	0042797	biological_process	tRNA transcription by RNA polymerase III
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0001172	biological_process	RNA-templated transcription
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0003968	molecular_function	RNA-directed RNA polymerase activity
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005665	cellular_component	RNA polymerase II, core complex
H	0005666	cellular_component	RNA polymerase III complex
H	0005736	cellular_component	RNA polymerase I complex
H	0006351	biological_process	DNA-templated transcription
H	0006360	biological_process	transcription by RNA polymerase I
H	0006361	biological_process	transcription initiation at RNA polymerase I promoter
H	0006362	biological_process	transcription elongation by RNA polymerase I
H	0006363	biological_process	termination of RNA polymerase I transcription
H	0006366	biological_process	transcription by RNA polymerase II
H	0006367	biological_process	transcription initiation at RNA polymerase II promoter
H	0006368	biological_process	transcription elongation by RNA polymerase II
H	0006383	biological_process	transcription by RNA polymerase III
H	0006384	biological_process	transcription initiation at RNA polymerase III promoter
H	0006386	biological_process	termination of RNA polymerase III transcription
H	0042254	biological_process	ribosome biogenesis
H	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
H	0042797	biological_process	tRNA transcription by RNA polymerase III
I	0000428	cellular_component	DNA-directed RNA polymerase complex
I	0001172	biological_process	RNA-templated transcription
I	0001193	biological_process	maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II
I	0003676	molecular_function	nucleic acid binding
I	0003899	molecular_function	DNA-directed RNA polymerase activity
I	0003968	molecular_function	RNA-directed RNA polymerase activity
I	0005515	molecular_function	protein binding
I	0005634	cellular_component	nucleus
I	0005665	cellular_component	RNA polymerase II, core complex
I	0005730	cellular_component	nucleolus
I	0006281	biological_process	DNA repair
I	0006283	biological_process	transcription-coupled nucleotide-excision repair
I	0006351	biological_process	DNA-templated transcription
I	0006366	biological_process	transcription by RNA polymerase II
I	0006367	biological_process	transcription initiation at RNA polymerase II promoter
I	0006368	biological_process	transcription elongation by RNA polymerase II
I	0006974	biological_process	DNA damage response
I	0008270	molecular_function	zinc ion binding
I	0046872	molecular_function	metal ion binding
J	0000428	cellular_component	DNA-directed RNA polymerase complex
J	0001172	biological_process	RNA-templated transcription
J	0003677	molecular_function	DNA binding
J	0003899	molecular_function	DNA-directed RNA polymerase activity
J	0003968	molecular_function	RNA-directed RNA polymerase activity
J	0005515	molecular_function	protein binding
J	0005634	cellular_component	nucleus
J	0005654	cellular_component	nucleoplasm
J	0005665	cellular_component	RNA polymerase II, core complex
J	0005666	cellular_component	RNA polymerase III complex
J	0005730	cellular_component	nucleolus
J	0005736	cellular_component	RNA polymerase I complex
J	0006351	biological_process	DNA-templated transcription
J	0006360	biological_process	transcription by RNA polymerase I
J	0006361	biological_process	transcription initiation at RNA polymerase I promoter
J	0006362	biological_process	transcription elongation by RNA polymerase I
J	0006363	biological_process	termination of RNA polymerase I transcription
J	0006366	biological_process	transcription by RNA polymerase II
J	0006367	biological_process	transcription initiation at RNA polymerase II promoter
J	0006368	biological_process	transcription elongation by RNA polymerase II
J	0006383	biological_process	transcription by RNA polymerase III
J	0006384	biological_process	transcription initiation at RNA polymerase III promoter
J	0006386	biological_process	termination of RNA polymerase III transcription
J	0008270	molecular_function	zinc ion binding
J	0042254	biological_process	ribosome biogenesis
J	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
J	0042797	biological_process	tRNA transcription by RNA polymerase III
J	0046872	molecular_function	metal ion binding
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0001172	biological_process	RNA-templated transcription
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0003968	molecular_function	RNA-directed RNA polymerase activity
K	0005515	molecular_function	protein binding
K	0005634	cellular_component	nucleus
K	0005665	cellular_component	RNA polymerase II, core complex
K	0006351	biological_process	DNA-templated transcription
K	0006366	biological_process	transcription by RNA polymerase II
K	0006367	biological_process	transcription initiation at RNA polymerase II promoter
K	0006368	biological_process	transcription elongation by RNA polymerase II
K	0006369	biological_process	termination of RNA polymerase II transcription
K	0046983	molecular_function	protein dimerization activity
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0001172	biological_process	RNA-templated transcription
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0003968	molecular_function	RNA-directed RNA polymerase activity
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005665	cellular_component	RNA polymerase II, core complex
L	0005666	cellular_component	RNA polymerase III complex
L	0005730	cellular_component	nucleolus
L	0005736	cellular_component	RNA polymerase I complex
L	0005737	cellular_component	cytoplasm
L	0005777	cellular_component	peroxisome
L	0006351	biological_process	DNA-templated transcription
L	0006360	biological_process	transcription by RNA polymerase I
L	0006361	biological_process	transcription initiation at RNA polymerase I promoter
L	0006362	biological_process	transcription elongation by RNA polymerase I
L	0006363	biological_process	termination of RNA polymerase I transcription
L	0006366	biological_process	transcription by RNA polymerase II
L	0006367	biological_process	transcription initiation at RNA polymerase II promoter
L	0006368	biological_process	transcription elongation by RNA polymerase II
L	0006383	biological_process	transcription by RNA polymerase III
L	0006384	biological_process	transcription initiation at RNA polymerase III promoter
L	0006386	biological_process	termination of RNA polymerase III transcription
L	0008270	molecular_function	zinc ion binding
L	0042254	biological_process	ribosome biogenesis
L	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
L	0042797	biological_process	tRNA transcription by RNA polymerase III
L	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1734

Chain	Residue
A	CYS107
A	CYS110
A	CYS148
A	CYS167

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1735

Chain	Residue
A	CYS67
A	CYS70
A	CYS77
A	HIS80

---

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN B 1307

Chain	Residue
B	CYS1166
B	CYS1182
B	CYS1185
B	ASN1187
B	CYS1163

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN C 319

Chain	Residue
C	CYS86
C	CYS88
C	HIS91
C	CYS92
C	CYS95

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN I 203

Chain	Residue
I	CYS7
I	CYS10
I	CYS29
I	CYS32

---

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN I 204

Chain	Residue
I	CYS75
I	CYS78
I	CYS103
I	CYS106
I	HIS108

---

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN J 101

Chain	Residue
J	CYS7
J	CYS10
J	ARG43
J	CYS45
J	CYS46

---

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN L 105

Chain	Residue
L	CYS31
L	CYS34
L	SER36
L	CYS48
L	CYS51

---

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 2001

Chain	Residue
A	ASP481
A	ASP483
A	ASP485
R	A10
T	DUT29

---

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 2002

Chain	Residue
A	ASP481
A	ASP483
B	ASP837
B	ARG1020
T	DUT29

---

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DUT T 29

Chain	Residue
A	ARG446
A	ASP481
A	ASP483
A	LYS752
A	MG2001
A	MG2002
B	ARG766
B	LYS987
B	SER1019
B	ARG1020
R	A10
T	DA18

---

Functional Information from PROSITE/UniProt

site_id	PS00115
Number of Residues	7
Details	RNA_POL_II_REPEAT Eukaryotic RNA polymerase II heptapeptide repeat. YSPTSPA

Chain	Residue	Details
A	TYR1549-ALA1555
A	TYR1612-SER1618
A	TYR1619-SER1625
A	TYR1626-SER1632
A	TYR1633-SER1639
A	TYR1640-SER1646
A	TYR1647-SER1653
A	TYR1654-ALA1660
A	TYR1661-SER1667
A	TYR1668-SER1674
A	TYR1675-SER1681
A	TYR1556-SER1562
A	TYR1682-SER1688
A	TYR1689-ASN1695
A	TYR1696-SER1702
A	TYR1563-SER1569
A	TYR1570-SER1576
A	TYR1577-SER1583
A	TYR1584-SER1590
A	TYR1591-SER1597
A	TYR1598-SER1604
A	TYR1605-SER1611

---

site_id	PS00446
Number of Residues	41
Details	RNA_POL_D_30KD RNA polymerases D / 30 to 40 Kd subunits signature. NSLRRvmiaeiptlAidsVevetNtTvlaDEfIAhRLGLIP

Chain	Residue	Details
C	ASN31-PRO71

---

site_id	PS00466
Number of Residues	36
Details	ZF_TFIIS_1 Zinc finger TFIIS-type signature. CpkChsrenvffqSQQRRkDTSmvlffvCls...CshiF

Chain	Residue	Details
I	CYS75-PHE110

---

site_id	PS01030
Number of Residues	27
Details	RNA_POL_M_15KD RNA polymerases M / 15 Kd subunits signature. FCRDCNNMLypredkennrllfeCrtC

Chain	Residue	Details
I	PHE6-CYS32

---

site_id	PS01110
Number of Residues	14
Details	RNA_POL_H_23KD RNA polymerases H / 23 Kd subunits signature. HELVPKHirLssDE

Chain	Residue	Details
E	HIS147-GLU160

---

site_id	PS01111
Number of Residues	15
Details	RNA_POL_K_14KD RNA polymerases K / 14 to 18 Kd subunits signature. TkYErARiLGtRAlQ

Chain	Residue	Details
F	THR86-GLN100

---

site_id	PS01112
Number of Residues	10
Details	RNA_POL_N_8KD RNA polymerases N / 8 Kd subunits signature. IVPVrCFSCG

Chain	Residue	Details
J	ILE2-GLY11

---

site_id	PS01154
Number of Residues	32
Details	RNA_POL_L_13KD RNA polymerases L / 13 to 16 Kd subunits signature. FekEdHTLgNlIraeLlndrkVlfaaYkveHP

Chain	Residue	Details
K	PHE35-PRO66

---

site_id	PS01166
Number of Residues	13
Details	RNA_POL_BETA RNA polymerases beta chain signature. GdKFASrHGQKGT

Chain	Residue	Details
B	GLY977-THR989

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Region: {"description":"Lid loop"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	17
Details	Region: {"description":"Rudder loop"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	Region: {"description":"Bridging helix"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	11
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23151482","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25652824","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4BBR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V1M","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	5
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	42
Details	Zinc finger: {"description":"C4-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	11
Details	Region: {"description":"Fork loop 1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	13
Details	Binding site: {}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17330950","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	21
Details	Region: {"description":"Leucine-zipper"}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	23
Details	Region: {"description":"Non-specific ssDNA binding","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"PubMed","id":"22814378","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	25
Details	Zinc finger: {"description":"C4-type","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	40
Details	Zinc finger: {"description":"TFIIS-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00472","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10145","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11313498","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11805306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11313499","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00472","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11313498","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11805306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11313499","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15537538","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1TWF","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	1
Details	M-CSA 788

Chain

Residue

Details

---