Chlorine in PDB 5gwj: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S, PDB code: 5gwj was solved by Y.R.Wang, S.F.Chen, C.C.Wu, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.68 / 2.57
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	80.178, 176.990, 94.414, 90.00, 111.50, 90.00
*R / R_free (%)*	18.3 / 22.6

Other elements in 5gwj:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Platinum	(Pt)	4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S (pdb code 5gwj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S, PDB code: 5gwj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5gwj

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Chlorine Binding Sites List in 5gwj

Chlorine binding site 1 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl1301 b:0.2 occ:0.50	CL	A:N2S1301	0.0	0.2	0.5
	CL	A:N2W1302	0.1	0.1	0.5
	PT	A:N2W1302	2.3	0.2	0.5
	PT	A:N2S1301	2.3	1.0	0.5
	N24	A:N2W1302	2.9	91.2	0.5
	N24	A:N2S1301	3.0	91.0	0.5
	SD	A:MET782	3.1	0.4	1.0
	CE	A:MET782	3.4	0.3	1.0
	C23	A:N2S1301	4.2	76.4	0.5
	C23	A:N2W1302	4.2	77.4	0.5
	N28	A:N2W1302	4.3	62.5	0.5
	N28	A:N2S1301	4.3	62.5	0.5
	C22	A:N2S1301	4.7	71.4	0.5
	CG	A:MET782	4.8	62.5	1.0
	C22	A:N2W1302	4.9	75.6	0.5

Chlorine binding site 2 out of 4 in 5gwj

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Chlorine Binding Sites List in 5gwj

Chlorine binding site 2 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl1302 b:0.1 occ:0.50	CL	A:N2W1302	0.0	0.1	0.5
	CL	A:N2S1301	0.1	0.2	0.5
	PT	A:N2W1302	2.3	0.2	0.5
	PT	A:N2S1301	2.4	1.0	0.5
	N24	A:N2W1302	3.0	91.2	0.5
	N24	A:N2S1301	3.1	91.0	0.5
	SD	A:MET782	3.1	0.4	1.0
	CE	A:MET782	3.4	0.3	1.0
	C23	A:N2S1301	4.3	76.4	0.5
	N28	A:N2W1302	4.3	62.5	0.5
	C23	A:N2W1302	4.3	77.4	0.5
	N28	A:N2S1301	4.3	62.5	0.5
	C22	A:N2S1301	4.7	71.4	0.5
	CG	A:MET782	4.8	62.5	1.0
	C22	A:N2W1302	5.0	75.6	0.5

Chlorine binding site 3 out of 4 in 5gwj

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Chlorine Binding Sites List in 5gwj

Chlorine binding site 3 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl1301 b:98.2 occ:0.50	CL	B:N2S1301	0.0	98.2	0.5
	CL	B:N2W1302	0.3	97.0	0.5
	PT	B:N2W1302	2.3	0.7	0.5
	PT	B:N2S1301	2.3	0.6	0.5
	N24	B:N2W1302	2.8	91.2	0.5
	N24	B:N2S1301	3.1	90.8	0.5
	SD	B:MET782	3.4	0.8	1.0
	N28	B:N2W1302	4.2	68.4	0.5
	C23	B:N2W1302	4.2	76.0	0.5
	N28	B:N2S1301	4.3	67.9	0.5
	C23	B:N2S1301	4.3	76.3	0.5
	C22	B:N2S1301	4.6	71.5	0.5
	CE	B:MET782	4.7	87.4	1.0
	CG	B:MET782	4.8	79.7	1.0
	NE2	B:GLN778	4.8	76.8	1.0
	C22	B:N2W1302	4.9	74.7	0.5

Chlorine binding site 4 out of 4 in 5gwj

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Chlorine Binding Sites List in 5gwj

Chlorine binding site 4 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Cl1302 b:97.0 occ:0.50	CL	B:N2W1302	0.0	97.0	0.5
	CL	B:N2S1301	0.3	98.2	0.5
	PT	B:N2W1302	2.3	0.7	0.5
	PT	B:N2S1301	2.4	0.6	0.5
	N24	B:N2W1302	3.0	91.2	0.5
	N24	B:N2S1301	3.2	90.8	0.5
	SD	B:MET782	3.3	0.8	1.0
	N28	B:N2W1302	4.3	68.4	0.5
	N28	B:N2S1301	4.3	67.9	0.5
	C23	B:N2W1302	4.4	76.0	0.5
	C23	B:N2S1301	4.5	76.3	0.5
	CE	B:MET782	4.6	87.4	1.0
	CG	B:MET782	4.6	79.7	1.0
	C22	B:N2S1301	4.7	71.5	0.5
	NE2	B:GLN778	4.7	76.8	1.0
	C22	B:N2W1302	4.9	74.7	0.5
	CA	B:MET782	5.0	27.5	1.0

Reference:

Y.R.Wang, S.F.Chen, C.C.Wu, Y.W.Liao, T.S.Lin, K.T.Liu, Y.S.Chen, T.K.Li, T.C.Chien, N.L.Chan. Producing Irreversible Topoisomerase II-Mediated Dna Breaks By Site-Specific Pt(II)-Methionine Coordination Chemistry Nucleic Acids Res. V. 45 10861 2017.
ISSN: ESSN 1362-4962
PubMed: 28977631
DOI: 10.1093/NAR/GKX742

Page generated: Fri Jul 26 08:37:10 2024

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