Manganese 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:

Iodine

(I)

2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese 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 Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 5zqf

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Manganese Binding Sites List in 5zqf

Manganese 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 Manganese with other atoms in the Mn 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
A:Mn1301 b:0.6 occ:1.00	OD2	A:ASP559	1.9	0.3	1.0
	OD2	A:ASP557	2.4	0.2	1.0
	CG	A:ASP559	2.9	0.8	1.0
	OD1	A:ASP559	3.2	0.8	1.0
	CG	A:ASP557	3.2	0.4	1.0
	CB	A:ASP557	3.4	0.9	1.0
	OE2	A:GLU477	4.0	92.7	1.0
	CB	A:ASP559	4.2	0.4	1.0
	OD1	A:ASP557	4.4	0.3	1.0
	CA	A:GLY631	4.5	0.4	1.0
	O3'	B:DC8	4.5	0.6	1.0
	OP1	B:DC8	4.7	0.8	1.0
	C5'	B:DC8	4.8	0.1	1.0
	CD	A:GLU477	4.8	94.9	1.0
	N	A:GLY631	4.8	0.4	1.0
	CA	A:ASP557	4.9	0.2	1.0

Manganese binding site 2 out of 2 in 5zqf

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Manganese Binding Sites List in 5zqf

Manganese 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 Manganese with other atoms in the Mn 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
A:Mn1302 b:0.5 occ:1.00	O	A:ASN867	3.4	0.9	1.0
	O	A:SER794	3.8	78.6	1.0
	O	A:GLY868	3.9	0.2	1.0
	OP1	B:DG5	4.1	0.9	1.0
	OE1	A:GLU870	4.2	0.5	1.0
	OD1	A:ASN795	4.3	93.3	1.0
	NH1	A:ARG945	4.6	0.2	1.0
	C	A:ASN867	4.6	0.5	1.0
	C	A:GLY868	4.6	0.8	1.0
	C	A:SER794	4.7	78.4	1.0
	NH2	A:ARG945	4.9	0.8	1.0
	CD	A:GLU870	4.9	0.1	1.0
	OD1	A:ASN786	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: Tue Dec 15 04:50:03 2020

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