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Platinum 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 / Rfree (%) 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
Chlorine (Cl) 4 atoms

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 4 binding sites of Platinum where determined in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873S, PDB code: 5gwj:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 5gwj

Go back to Platinum Binding Sites List in 5gwj
Platinum 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 Platinum with other atoms in the Pt 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:Pt1301

b:1.0
occ:0.50
 PT A:N2S1301 0.0 1.0 0.5
PT A:N2W1302 0.1 0.2 0.5
N28 A:N2W1302 1.9 62.5 0.5
N28 A:N2S1301 2.0 62.5 0.5
N24 A:N2S1301 2.0 91.0 0.5
N24 A:N2W1302 2.0 91.2 0.5
SD A:MET782 2.3 0.4 1.0
CL A:N2S1301 2.3 0.2 0.5
CL A:N2W1302 2.4 0.1 0.5
CE A:MET782 2.5 0.3 1.0
C22 A:N2S1301 2.7 71.4 0.5
C23 A:N2S1301 2.8 76.4 0.5
C23 A:N2W1302 2.8 77.4 0.5
C22 A:N2W1302 2.8 75.6 0.5
CG A:MET782 3.3 62.5 1.0
C21 A:N2W1302 3.9 64.5 0.5
C21 A:N2S1301 4.1 64.7 0.5
CB A:MET782 4.5 38.7 1.0
NE2 A:GLN778 4.9 70.4 1.0
C20 A:N2W1302 5.0 52.3 0.5
C20 A:N2S1301 5.0 52.4 0.5

Platinum binding site 2 out of 4 in 5gwj

Go back to Platinum Binding Sites List in 5gwj
Platinum 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 Platinum with other atoms in the Pt 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:Pt1302

b:0.2
occ:0.50
 PT A:N2W1302 0.0 0.2 0.5
PT A:N2S1301 0.1 1.0 0.5
N24 A:N2S1301 2.0 91.0 0.5
N28 A:N2W1302 2.0 62.5 0.5
N24 A:N2W1302 2.0 91.2 0.5
N28 A:N2S1301 2.0 62.5 0.5
CL A:N2S1301 2.3 0.2 0.5
SD A:MET782 2.3 0.4 1.0
CL A:N2W1302 2.3 0.1 0.5
CE A:MET782 2.5 0.3 1.0
C22 A:N2S1301 2.7 71.4 0.5
C23 A:N2S1301 2.8 76.4 0.5
C23 A:N2W1302 2.8 77.4 0.5
C22 A:N2W1302 2.9 75.6 0.5
CG A:MET782 3.4 62.5 1.0
C21 A:N2W1302 3.9 64.5 0.5
C21 A:N2S1301 4.1 64.7 0.5
CB A:MET782 4.5 38.7 1.0
NE2 A:GLN778 4.9 70.4 1.0
C20 A:N2W1302 5.0 52.3 0.5
C20 A:N2S1301 5.0 52.4 0.5

Platinum binding site 3 out of 4 in 5gwj

Go back to Platinum Binding Sites List in 5gwj
Platinum 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 Platinum with other atoms in the Pt 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:Pt1301

b:0.6
occ:0.50
 PT B:N2S1301 0.0 0.6 0.5
PT B:N2W1302 0.1 0.7 0.5
N28 B:N2W1302 1.9 68.4 0.5
N28 B:N2S1301 2.0 67.9 0.5
N24 B:N2S1301 2.0 90.8 0.5
N24 B:N2W1302 2.0 91.2 0.5
SD B:MET782 2.3 0.8 1.0
CL B:N2S1301 2.3 98.2 0.5
CL B:N2W1302 2.4 97.0 0.5
C22 B:N2S1301 2.6 71.5 0.5
C23 B:N2S1301 2.8 76.3 0.5
C22 B:N2W1302 2.8 74.7 0.5
C23 B:N2W1302 2.8 76.0 0.5
CE B:MET782 3.3 87.4 1.0
C21 B:N2W1302 3.6 60.8 0.5
CG B:MET782 3.7 79.7 1.0
C21 B:N2S1301 4.1 61.2 0.5
NE2 B:GLN778 4.3 76.8 1.0
CB B:MET782 4.7 63.7 1.0
C20 B:N2S1301 5.0 51.7 0.5
C20 B:N2W1302 5.0 51.6 0.5

Platinum binding site 4 out of 4 in 5gwj

Go back to Platinum Binding Sites List in 5gwj
Platinum 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 Platinum with other atoms in the Pt 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:Pt1302

b:0.7
occ:0.50
 PT B:N2W1302 0.0 0.7 0.5
PT B:N2S1301 0.1 0.6 0.5
N28 B:N2W1302 2.0 68.4 0.5
N24 B:N2S1301 2.0 90.8 0.5
N24 B:N2W1302 2.0 91.2 0.5
N28 B:N2S1301 2.0 67.9 0.5
CL B:N2S1301 2.3 98.2 0.5
SD B:MET782 2.3 0.8 1.0
CL B:N2W1302 2.3 97.0 0.5
C22 B:N2S1301 2.6 71.5 0.5
C23 B:N2S1301 2.8 76.3 0.5
C22 B:N2W1302 2.8 74.7 0.5
C23 B:N2W1302 2.8 76.0 0.5
CE B:MET782 3.3 87.4 1.0
C21 B:N2W1302 3.6 60.8 0.5
CG B:MET782 3.7 79.7 1.0
C21 B:N2S1301 4.1 61.2 0.5
NE2 B:GLN778 4.2 76.8 1.0
CB B:MET782 4.7 63.7 1.0
C20 B:N2S1301 5.0 51.7 0.5
C20 B:N2W1302 5.0 51.6 0.5

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: Thu Oct 10 11:35:13 2024

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