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Platinum in PDB 5gwi: Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

Enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R

All present enzymatic activity of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R:
5.99.1.3;

Protein crystallography data

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R, PDB code: 5gwi 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) 29.72 / 2.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 79.788, 176.966, 94.528, 90.00, 112.30, 90.00
R / Rfree (%) 21.4 / 25.3

Other elements in 5gwi:

The structure of Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms
Chlorine (Cl) 8 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R (pdb code 5gwi). 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 E7873R, PDB code: 5gwi:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 5gwi

Go back to Platinum Binding Sites List in 5gwi
Platinum binding site 1 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


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 E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1301

b:83.6
occ:0.50
 PT A:N2R1301 0.0 83.6 0.5
PT1 A:N2N1302 0.2 85.3 0.5
N13 A:N2N1302 1.9 83.1 0.5
N09 A:N2R1301 2.0 82.6 0.5
N13 A:N2R1301 2.0 82.8 0.5
N09 A:N2N1302 2.0 84.3 0.5
CL1 A:N2N1302 2.3 50.3 0.5
CL1 A:N2R1301 2.3 55.6 0.5
CL2 A:N2R1301 2.3 0.8 0.5
CL2 A:N2N1302 2.4 0.3 0.5
C02 A:N2N1302 2.7 75.8 0.5
C10 A:N2N1302 2.8 77.5 0.5
C10 A:N2R1301 2.8 77.5 0.5
C02 A:N2R1301 2.9 73.0 0.5
CE A:MET782 3.9 71.0 1.0
C21 A:N2N1302 4.1 73.2 0.5
CG A:MET782 4.2 68.0 1.0
NE2 A:GLN778 4.2 64.8 1.0
C21 A:N2R1301 4.2 73.8 0.5
SD A:MET782 4.3 0.0 1.0
CG A:GLN778 4.5 46.7 1.0
C20 A:N2R1301 4.7 66.1 0.5
CD A:GLN778 4.8 67.3 1.0
C20 A:N2N1302 4.9 65.2 0.5
CG A:PRO819 4.9 41.9 1.0
O A:GLN778 5.0 37.6 1.0

Platinum binding site 2 out of 4 in 5gwi

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Platinum binding site 2 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


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 E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1302

b:85.3
occ:0.50
 PT1 A:N2N1302 0.0 85.3 0.5
PT A:N2R1301 0.2 83.6 0.5
N09 A:N2R1301 2.0 82.6 0.5
N09 A:N2N1302 2.0 84.3 0.5
N13 A:N2N1302 2.0 83.1 0.5
N13 A:N2R1301 2.1 82.8 0.5
CL2 A:N2R1301 2.2 0.8 0.5
CL1 A:N2N1302 2.3 50.3 0.5
CL2 A:N2N1302 2.3 0.3 0.5
CL1 A:N2R1301 2.3 55.6 0.5
C10 A:N2N1302 2.8 77.5 0.5
C02 A:N2N1302 2.8 75.8 0.5
C10 A:N2R1301 2.9 77.5 0.5
C02 A:N2R1301 3.0 73.0 0.5
CE A:MET782 4.0 71.0 1.0
C21 A:N2N1302 4.2 73.2 0.5
CG A:MET782 4.2 68.0 1.0
SD A:MET782 4.3 0.0 1.0
C21 A:N2R1301 4.3 73.8 0.5
NE2 A:GLN778 4.4 64.8 1.0
CG A:GLN778 4.6 46.7 1.0
C20 A:N2R1301 4.8 66.1 0.5
CG A:PRO819 4.8 41.9 1.0
CD A:GLN778 4.9 67.3 1.0
C20 A:N2N1302 5.0 65.2 0.5

Platinum binding site 3 out of 4 in 5gwi

Go back to Platinum Binding Sites List in 5gwi
Platinum binding site 3 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


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 E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1301

b:66.9
occ:0.50
 PT B:N2R1301 0.0 66.9 0.5
PT1 B:N2N1302 0.4 96.0 0.5
N13 B:N2N1302 1.9 79.8 0.5
N09 B:N2N1302 2.0 75.3 0.5
N09 B:N2R1301 2.0 74.0 0.5
N13 B:N2R1301 2.0 77.8 0.5
CL1 B:N2R1301 2.3 55.1 0.5
CL2 B:N2R1301 2.3 0.3 0.5
CL1 B:N2N1302 2.4 53.0 0.5
CL2 B:N2N1302 2.4 0.1 0.5
C02 B:N2N1302 2.6 69.6 0.5
C10 B:N2N1302 2.7 70.2 0.5
C10 B:N2R1301 2.9 70.5 0.5
C02 B:N2R1301 2.9 66.4 0.5
CE B:MET782 3.8 67.9 1.0
CG B:MET782 4.1 48.5 1.0
C21 B:N2N1302 4.1 63.9 0.5
SD B:MET782 4.2 0.1 1.0
C21 B:N2R1301 4.2 64.0 0.5
NE2 B:GLN778 4.3 51.4 1.0
CG B:GLN778 4.4 52.5 1.0
CD B:GLN778 4.8 59.8 1.0
C20 B:N2R1301 4.8 54.8 0.5
O19 B:N2R1301 4.8 59.6 0.5
C20 B:N2N1302 4.9 54.7 0.5
O19 B:N2N1302 4.9 59.6 0.5
O B:GLN778 5.0 37.6 1.0

Platinum binding site 4 out of 4 in 5gwi

Go back to Platinum Binding Sites List in 5gwi
Platinum binding site 4 out of 4 in the Structure of A Human Topoisomerase Iibeta Fragment in Complex with Dna and E7873R


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 E7873R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt1302

b:96.0
occ:0.50
 PT1 B:N2N1302 0.0 96.0 0.5
PT B:N2R1301 0.4 66.9 0.5
N09 B:N2N1302 2.0 75.3 0.5
N13 B:N2N1302 2.0 79.8 0.5
N09 B:N2R1301 2.1 74.0 0.5
N13 B:N2R1301 2.2 77.8 0.5
CL2 B:N2R1301 2.2 0.3 0.5
CL1 B:N2N1302 2.3 53.0 0.5
CL2 B:N2N1302 2.3 0.1 0.5
CL1 B:N2R1301 2.3 55.1 0.5
C10 B:N2N1302 2.8 70.2 0.5
C02 B:N2N1302 2.8 69.6 0.5
C02 B:N2R1301 2.9 66.4 0.5
C10 B:N2R1301 2.9 70.5 0.5
CE B:MET782 4.1 67.9 1.0
C21 B:N2N1302 4.2 63.9 0.5
CG B:MET782 4.3 48.5 1.0
C21 B:N2R1301 4.4 64.0 0.5
SD B:MET782 4.4 0.1 1.0
CG B:GLN778 4.7 52.5 1.0
NE2 B:GLN778 4.7 51.4 1.0
CD B:PRO819 4.7 41.4 1.0
CG B:PRO819 4.9 46.9 1.0
C20 B:N2R1301 5.0 54.8 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 11:34:51 2024

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