Iodine in PDB 5zqf: Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221

Enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221

All present enzymatic activity of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221:
5.99.1.3;

Protein crystallography data

The structure of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221, PDB code: 5zqf was solved by S.F.Chen, Y.R.Wang, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	19.90 / 3.87
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	94.990, 94.990, 231.486, 90.00, 90.00, 120.00
*R / R_free (%)*	20.3 / 24.7

Other elements in 5zqf:

The structure of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221 (pdb code 5zqf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221, PDB code: 5zqf:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 5zqf

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Iodine Binding Sites List in 5zqf

Iodine binding site 1 out of 2 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:I15 b:0.1 occ:1.00	I5	C:IU15	0.0	0.1	1.0
	C5	C:IU15	2.1	0.0	1.0
	C4	C:IU15	3.2	0.3	1.0
	C6	C:IU15	3.2	0.3	1.0
	O4	C:IU15	3.3	0.3	1.0
	N4	C:DC16	3.7	0.4	1.0
	C6	C:DC14	3.9	0.2	1.0
	OP2	C:IU15	4.0	91.3	1.0
	C5	C:DC14	4.0	0.5	1.0
	N1	C:DC14	4.3	0.6	1.0
	C2'	C:DC14	4.4	0.2	1.0
	C4	C:DC14	4.4	0.9	1.0
	N3	C:IU15	4.5	0.3	1.0
	N1	C:IU15	4.5	0.3	1.0
	C3'	C:DC14	4.6	0.5	1.0
	C4	C:DC16	4.7	0.9	1.0
	O6	B:DG5	4.7	0.3	1.0
	C2	C:DC14	4.7	0.6	1.0
	N3	C:DC14	4.8	0.7	1.0
	C1'	C:DC14	4.9	0.9	1.0

Iodine binding site 2 out of 2 in 5zqf

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Iodine Binding Sites List in 5zqf

Iodine binding site 2 out of 2 in the Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Human Topoisomerase II Beta in Complex with 5- Iodouridine-Containing-Dna in Space Group P3221 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:I20 b:0.3 occ:1.00	I5	C:IU20	0.0	0.3	1.0
	C5	C:IU20	2.1	0.5	1.0
	C6	C:IU20	3.1	0.2	1.0
	C4	C:IU20	3.2	0.9	1.0
	O4	C:IU20	3.3	0.6	1.0
	C2'	C:DC19	4.1	0.3	1.0
	C6	C:DC19	4.2	0.6	1.0
	C5	C:DC19	4.4	0.6	1.0
	N1	C:DC19	4.5	0.9	1.0
	N1	C:IU20	4.5	0.6	1.0
	N3	C:IU20	4.5	0.9	1.0
	C1'	C:DC19	4.9	0.6	1.0
	C4	C:DC19	4.9	0.7	1.0
	C2	C:DC19	5.0	0.0	1.0

Reference:

S.F.Chen, N.L.Huang, J.H.Lin, C.C.Wu, Y.R.Wang, Y.J.Yu, M.K.Gilson, N.L.Chan. Structural Insights Into the Gating of Dna Passage By the Topoisomerase II Dna-Gate. Nat Commun V. 9 3085 2018.
ISSN: ESSN 2041-1723
PubMed: 30082834
DOI: 10.1038/S41467-018-05406-Y

Page generated: Fri Aug 8 20:52:23 2025

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