4AYB

RNAP at 3.2Ang

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0000428	cellular_component	DNA-directed RNA polymerase complex
A	0003677	molecular_function	DNA binding
A	0003899	molecular_function	DNA-directed RNA polymerase activity
A	0005737	cellular_component	cytoplasm
A	0006351	biological_process	DNA-templated transcription
A	0008270	molecular_function	zinc ion binding
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0034062	molecular_function	5'-3' RNA polymerase activity
A	0046872	molecular_function	metal ion binding
B	0000428	cellular_component	DNA-directed RNA polymerase complex
B	0003677	molecular_function	DNA binding
B	0003899	molecular_function	DNA-directed RNA polymerase activity
B	0005737	cellular_component	cytoplasm
B	0006351	biological_process	DNA-templated transcription
B	0008270	molecular_function	zinc ion binding
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	0003677	molecular_function	DNA binding
C	0003899	molecular_function	DNA-directed RNA polymerase activity
C	0005737	cellular_component	cytoplasm
C	0006351	biological_process	DNA-templated transcription
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0034062	molecular_function	5'-3' RNA polymerase activity
D	0000428	cellular_component	DNA-directed RNA polymerase complex
D	0003677	molecular_function	DNA binding
D	0003899	molecular_function	DNA-directed RNA polymerase activity
D	0005737	cellular_component	cytoplasm
D	0006351	biological_process	DNA-templated transcription
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0034062	molecular_function	5'-3' RNA polymerase activity
D	0046872	molecular_function	metal ion binding
D	0046983	molecular_function	protein dimerization activity
D	0051536	molecular_function	iron-sulfur cluster binding
D	0051538	molecular_function	3 iron, 4 sulfur cluster binding
E	0000428	cellular_component	DNA-directed RNA polymerase complex
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003899	molecular_function	DNA-directed RNA polymerase activity
E	0005737	cellular_component	cytoplasm
E	0006351	biological_process	DNA-templated transcription
E	0006352	biological_process	DNA-templated transcription initiation
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
F	0000166	molecular_function	nucleotide binding
F	0000428	cellular_component	DNA-directed RNA polymerase complex
F	0003899	molecular_function	DNA-directed RNA polymerase activity
F	0005737	cellular_component	cytoplasm
F	0006351	biological_process	DNA-templated transcription
F	0006352	biological_process	DNA-templated transcription initiation
F	0016740	molecular_function	transferase activity
F	0016779	molecular_function	nucleotidyltransferase activity
F	0030880	cellular_component	RNA polymerase complex
G	0000428	cellular_component	DNA-directed RNA polymerase complex
G	0003899	molecular_function	DNA-directed RNA polymerase activity
G	0005737	cellular_component	cytoplasm
G	0006351	biological_process	DNA-templated transcription
G	0016740	molecular_function	transferase activity
G	0016779	molecular_function	nucleotidyltransferase activity
H	0000428	cellular_component	DNA-directed RNA polymerase complex
H	0003677	molecular_function	DNA binding
H	0003899	molecular_function	DNA-directed RNA polymerase activity
H	0005737	cellular_component	cytoplasm
H	0006351	biological_process	DNA-templated transcription
H	0006362	biological_process	transcription elongation by RNA polymerase I
H	0006366	biological_process	transcription by RNA polymerase II
H	0016740	molecular_function	transferase activity
H	0016779	molecular_function	nucleotidyltransferase activity
H	0034062	molecular_function	5'-3' RNA polymerase activity
H	0042797	biological_process	tRNA transcription by RNA polymerase III
K	0000428	cellular_component	DNA-directed RNA polymerase complex
K	0003677	molecular_function	DNA binding
K	0003899	molecular_function	DNA-directed RNA polymerase activity
K	0005737	cellular_component	cytoplasm
K	0006351	biological_process	DNA-templated transcription
K	0006360	biological_process	transcription by RNA polymerase I
K	0006366	biological_process	transcription by RNA polymerase II
K	0016740	molecular_function	transferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0034062	molecular_function	5'-3' RNA polymerase activity
K	0042797	biological_process	tRNA transcription by RNA polymerase III
L	0000428	cellular_component	DNA-directed RNA polymerase complex
L	0003677	molecular_function	DNA binding
L	0003899	molecular_function	DNA-directed RNA polymerase activity
L	0005737	cellular_component	cytoplasm
L	0006351	biological_process	DNA-templated transcription
L	0016740	molecular_function	transferase activity
L	0016779	molecular_function	nucleotidyltransferase activity
L	0034062	molecular_function	5'-3' RNA polymerase activity
L	0046983	molecular_function	protein dimerization activity
N	0000428	cellular_component	DNA-directed RNA polymerase complex
N	0003677	molecular_function	DNA binding
N	0003899	molecular_function	DNA-directed RNA polymerase activity
N	0005737	cellular_component	cytoplasm
N	0006351	biological_process	DNA-templated transcription
N	0008270	molecular_function	zinc ion binding
N	0016740	molecular_function	transferase activity
N	0016779	molecular_function	nucleotidyltransferase activity
N	0034062	molecular_function	5'-3' RNA polymerase activity
N	0046872	molecular_function	metal ion binding
P	0000428	cellular_component	DNA-directed RNA polymerase complex
P	0003677	molecular_function	DNA binding
P	0003899	molecular_function	DNA-directed RNA polymerase activity
P	0005737	cellular_component	cytoplasm
P	0006351	biological_process	DNA-templated transcription
P	0008270	molecular_function	zinc ion binding
P	0016740	molecular_function	transferase activity
P	0016779	molecular_function	nucleotidyltransferase activity
P	0034062	molecular_function	5'-3' RNA polymerase activity
P	0046872	molecular_function	metal ion binding
Q	0000428	cellular_component	DNA-directed RNA polymerase complex
Q	0003677	molecular_function	DNA binding
Q	0003899	molecular_function	DNA-directed RNA polymerase activity
Q	0005737	cellular_component	cytoplasm
Q	0016740	molecular_function	transferase activity
Q	0016779	molecular_function	nucleotidyltransferase activity
Q	0070063	molecular_function	RNA polymerase binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1880

Chain	Residue
A	CYS58
A	CYS61
A	CYS68
A	HIS71

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN A 1881

Chain	Residue
A	CYS98
A	CYS101
A	CYS146
A	CYS149

---

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ZN A 1882

Chain	Residue
A	THR488
C	GLU80
A	HIS426

---

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ZN A 1883

Chain	Residue
A	HIS237
A	ASP241

---

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 1884

Chain	Residue
A	ASP456
A	ASP458
A	ASP460

---

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN B 2126

Chain	Residue
B	CYS1064
B	CYS1067
B	CYS1082
B	HIS1085

---

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ZN B 2127

Chain	Residue
B	HIS570

---

site_id	AC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ZN B 2128

Chain	Residue
B	HIS696
B	HIS997

---

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE ZN C 1395

Chain	Residue
C	HIS353

---

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 D 1264

Chain	Residue
D	CYS183
D	PRO184
D	GLU185
D	VAL187
D	PHE188
D	CYS203
D	CYS206
D	GLU207
D	CYS209
D	ILE219

---

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ZN N 1066

Chain	Residue
N	CYS7
N	CYS10
N	CYS44
N	CYS45

---

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ZN P 1049

Chain	Residue
P	CYS9
P	THR12
P	CYS26
P	TYR28
P	CYS29

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
D	ASN26-PRO66

---

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

Chain	Residue	Details
H	HIS14-GLU27

---

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

Chain	Residue	Details
K	THR28-GLN42

---

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

Chain	Residue	Details
N	MET2-GLY11

---

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

Chain	Residue	Details
L	ILE17-PRO48

---

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

Chain	Residue	Details
B	GLY878-VAL890

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	64
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22848102","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00863","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P11512","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00320","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00250","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00250","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00250","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00615","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00615","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19419240","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2WAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WB1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2Y0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4AYB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4V8S","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---