5ZRF

Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
A	0005524	molecular_function	ATP binding
A	0006259	biological_process	DNA metabolic process
A	0006265	biological_process	DNA topological change
B	0003677	molecular_function	DNA binding
B	0003918	molecular_function	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
B	0005524	molecular_function	ATP binding
B	0006259	biological_process	DNA metabolic process
B	0006265	biological_process	DNA topological change

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue MG A 1301

Chain	Residue
A	ASP557
A	ASP559
A	HOH1462
A	HOH1496
A	HOH1577
C	HOH102

---

site_id	AC2
Number of Residues	2
Details	binding site for residue MG A 1302

Chain	Residue
A	ASN867
A	GLY868

---

site_id	AC3
Number of Residues	4
Details	binding site for residue MG B 1301

Chain	Residue
B	GLY868
B	HOH1557
E	HOH101
B	ASN867

---

site_id	AC4
Number of Residues	6
Details	binding site for residue MG B 1302

Chain	Residue
B	ASP557
B	ASP559
B	HOH1424
B	HOH1531
E	HOH104
E	HOH114

---

site_id	AC5
Number of Residues	12
Details	binding site for residue EVP D 101

Chain	Residue
B	GLY478
B	ASP479
B	ARG503
B	GLN778
B	MET782
D	DA12
D	DG13
D	HOH505
D	HOH510
E	DC8
F	IU9
F	DG10

---

site_id	AC6
Number of Residues	1
Details	binding site for residue MG D 102

Chain	Residue
D	HOH507

---

site_id	AC7
Number of Residues	12
Details	binding site for residue EVP F 1301

Chain	Residue
A	GLY478
A	ASP479
A	ARG503
A	MET782
C	DC8
C	HOH107
D	IU9
D	DG10
F	DA12
F	DG13
F	HOH1404
F	HOH1417

---

site_id	AC8
Number of Residues	4
Details	binding site for residue MG F 1302

Chain	Residue
A	HOH1604
F	HOH1402
F	HOH1409
F	HOH1415

---

site_id	AC9
Number of Residues	8
Details	binding site for Di-nucleotide IU D 9 and DG D 10

Chain	Residue
A	ASP479
B	ARG820
B	TYR821
D	DC11
F	DG10
F	DC11
F	DA12
F	EVP1301

---

site_id	AD1
Number of Residues	14
Details	binding site for Di-nucleotide DC D 14 and IU D 15

Chain	Residue
B	LYS505
B	ILE506
B	LEU507
B	ASN508
B	GLN516
B	HIS564
D	DG13
D	DC16
D	HOH503
D	HOH506
D	HOH513
E	DG5
E	DA6
E	DG7

---

site_id	AD2
Number of Residues	20
Details	binding site for Di-nucleotide IU D 15 and DC D 16

Chain	Residue
B	ILE506
B	LEU507
B	ASN508
B	HIS564
B	PHE669
B	ILE872
B	GLY873
B	THR874
B	HOH1406
D	DC14
D	DG17
D	HOH503
D	HOH504
D	HOH506
D	HOH508
D	HOH513
E	DC4
E	DG5
E	DA6
E	DG7

---

site_id	AD3
Number of Residues	12
Details	binding site for Di-nucleotide DC D 19 and IU D 20

Chain	Residue
E	DA1
E	DG2
A	ASP897
A	LEU899
B	LYS879
B	THR1010
B	LEU1011
B	THR1012
B	ASN1014
D	DG18
D	HOH501
D	HOH502

---

site_id	AD4
Number of Residues	8
Details	binding site for Di-nucleotide IU F 9 and DG F 10

Chain	Residue
A	TYR821
B	ASP479
D	DG10
D	DC11
D	DA12
D	EVP101
F	DC11
F	HOH1401

---

site_id	AD5
Number of Residues	15
Details	binding site for Di-nucleotide DC F 14 and IU F 15

Chain	Residue
A	LYS505
A	ILE506
A	LEU507
A	ASN508
A	GLN516
A	HIS564
C	DG5
C	DA6
C	DG7
F	DG13
F	DC16
F	HOH1405
F	HOH1406
F	HOH1418
F	HOH1419

---

site_id	AD6
Number of Residues	20
Details	binding site for Di-nucleotide IU F 15 and DC F 16

Chain	Residue
A	ILE506
A	LEU507
A	ASN508
A	HIS564
A	PHE669
A	ILE872
A	GLY873
A	THR874
A	HOH1407
C	DG5
C	DA6
C	DG7
F	DC14
F	DG17
F	HOH1403
F	HOH1405
F	HOH1406
F	HOH1412
F	HOH1418
F	HOH1419

---

site_id	AD7
Number of Residues	9
Details	binding site for Di-nucleotide DC F 19 and IU F 20

Chain	Residue
A	LYS879
A	THR1010
A	LEU1011
A	THR1012
A	ASN1014
A	SER1015
C	DA1
C	DG2
F	DG18

---

Functional Information from PROSITE/UniProt

site_id	PS00177
Number of Residues	9
Details	TOPOISOMERASE_II DNA topoisomerase II signature. LTEGDSAKS

Chain	Residue	Details
A	LEU475-SER483

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: O-(5'-phospho-DNA)-tyrosine intermediate => ECO:0000255|PROSITE-ProRule:PRU01384, ECO:0000269|PubMed:21778401

Chain	Residue	Details
A	TYR821
B	TYR821

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00995

Chain	Residue	Details
A	GLU477
B	GLU477

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00995, ECO:0000269|PubMed:21778401

Chain	Residue	Details
A	ASP557
A	ASP559
B	ASP557
B	ASP559

---

site_id	SWS_FT_FI4
Number of Residues	12
Details	SITE: Interaction with DNA

Chain	Residue	Details
A	LYS505
B	LYS678
B	LYS739
B	TRP947
A	ASN508
A	ARG677
A	LYS678
A	LYS739
A	TRP947
B	LYS505
B	ASN508
B	ARG677

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	SITE: Interaction with DNA => ECO:0000255|PROSITE-ProRule:PRU00995

Chain	Residue	Details
A	TYR773
B	TYR773

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	SITE: Transition state stabilizer

Chain	Residue	Details
A	ARG820
B	ARG820

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Important for DNA bending; intercalates between base pairs of target DNA

Chain	Residue	Details
A	ILE872
B	ILE872

---

site_id	SWS_FT_FI8
Number of Residues	14
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
A	LYS595
B	LYS630
B	LYS641
B	LYS671
B	LYS707
B	LYS1087
A	LYS630
A	LYS641
A	LYS671
A	LYS707
A	LYS1087
B	LYS595

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:25772364, ECO:0007744|PubMed:28112733

Chain	Residue	Details
A	LYS600
A	LYS638
B	LYS600
B	LYS638

---