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Platinum in PDB 4yeo: Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement

Enzymatic activity of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement

All present enzymatic activity of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement:
3.2.1.17;

Protein crystallography data

The structure of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement, PDB code: 4yeo was solved by I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.26 / 0.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 26.998, 31.807, 34.072, 89.08, 72.00, 67.81
R / Rfree (%) 11.2 / 13.1

Other elements in 4yeo:

The structure of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement (pdb code 4yeo). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement, PDB code: 4yeo:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 4yeo

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Platinum binding site 1 out of 5 in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:5.8
occ:0.25
 PT1 A:CPT201 0.0 5.8 0.2
O A:HOH429 1.3 11.0 0.8
NE2 A:HIS15 2.0 18.0 0.6
N1 A:CPT201 2.0 7.4 0.2
CL1 A:CPT201 2.3 7.6 0.2
CL2 A:CPT201 2.3 7.7 0.2
PT A:PT202 2.4 12.7 0.2
NE2 A:HIS15 2.5 16.8 0.4
CD2 A:HIS15 2.8 15.7 0.6
CE1 A:HIS15 3.0 19.4 0.6
CD2 A:HIS15 3.1 15.3 0.4
CE1 A:HIS15 3.5 17.0 0.4
O A:HOH451 3.8 12.0 0.5
CG A:HIS15 4.0 15.9 0.6
ND1 A:HIS15 4.0 17.6 0.6
NE A:ARG14 4.0 11.6 1.0
O A:HOH451 4.1 12.3 0.5
CG A:HIS15 4.2 15.3 0.4
CB A:ARG14 4.2 8.8 1.0
CD A:ARG14 4.3 11.2 1.0
ND1 A:HIS15 4.4 17.1 0.4
O A:HOH430 4.4 10.7 0.8
O A:HOH497 4.8 21.7 1.0
OG1 A:THR89 4.9 10.6 1.0
CG A:ARG14 4.9 9.8 1.0

Platinum binding site 2 out of 5 in 4yeo

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Platinum binding site 2 out of 5 in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:12.7
occ:0.20
 N1 A:CPT201 0.4 7.4 0.2
PT1 A:CPT201 2.4 5.8 0.2
NE2 A:HIS15 2.4 16.8 0.4
NE2 A:HIS15 2.8 18.0 0.6
CE1 A:HIS15 3.1 17.0 0.4
O A:HOH429 3.2 11.0 0.8
CL1 A:CPT201 3.3 7.6 0.2
CE1 A:HIS15 3.6 19.4 0.6
CD2 A:HIS15 3.6 15.7 0.6
O A:HOH446 3.6 31.2 1.0
O A:HOH508 3.7 11.7 1.0
CD2 A:HIS15 3.7 15.3 0.4
NE A:ARG14 4.3 11.6 1.0
ND1 A:HIS15 4.3 17.1 0.4
OG1 A:THR89 4.3 10.6 1.0
NH2 A:ARG14 4.6 13.1 1.0
ND1 A:HIS15 4.6 17.6 0.6
CG A:HIS15 4.6 15.3 0.4
O A:HOH451 4.7 12.0 0.5
CG A:HIS15 4.7 15.9 0.6
CL2 A:CPT201 4.7 7.7 0.2
CB A:ALA11 4.8 5.5 1.0
O A:HOH442 4.8 24.4 1.0
O A:HOH304 4.9 13.0 1.0
CZ A:ARG14 4.9 11.3 1.0
O A:ALA11 4.9 6.2 1.0

Platinum binding site 3 out of 5 in 4yeo

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Platinum binding site 3 out of 5 in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt203

b:14.7
occ:0.25
 O A:HOH430 1.7 10.7 0.8
ND1 A:HIS15 2.9 17.6 0.6
O A:HOH407 3.5 5.5 0.5
CG A:HIS15 3.5 15.9 0.6
CB A:HIS15 3.5 13.2 0.6
CB A:HIS15 3.5 13.3 0.4
CA A:HIS15 3.8 11.0 1.0
CE1 A:HIS15 3.8 19.4 0.6
CG A:HIS15 3.8 15.3 0.4
OD1 A:ASN93 3.9 11.9 0.7
O A:HOH414 3.9 26.7 1.0
O A:HOH384 3.9 26.2 1.0
O A:HIS15 4.0 15.0 1.0
ND1 A:HIS15 4.0 17.1 0.4
NZ A:LYS96 4.3 10.7 1.0
C A:HIS15 4.3 10.8 1.0
CD2 A:HIS15 4.5 15.7 0.6
CG2 A:THR89 4.6 9.0 1.0
NE2 A:HIS15 4.7 18.0 0.6
CD2 A:HIS15 4.7 15.3 0.4
CE1 A:HIS15 4.8 17.0 0.4
CG A:ASN93 4.9 8.9 0.7

Platinum binding site 4 out of 5 in 4yeo

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Platinum binding site 4 out of 5 in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt204

b:10.8
occ:0.08
 O2 A:NO3210 1.5 13.6 0.9
NZ A:LYS116 1.7 5.5 0.3
NZ A:LYS116 2.0 7.4 0.7
N A:NO3210 2.2 10.3 0.9
O1 A:NO3210 2.4 7.6 0.9
CE A:LYS116 2.8 5.3 0.3
O A:HOH327 3.1 14.3 0.5
CE A:LYS116 3.1 7.2 0.7
O3 A:NO3210 3.3 15.2 0.9
CD A:LYS116 3.3 6.6 0.7
CD A:LYS116 4.0 5.9 0.3
O A:HOH325 4.1 19.0 1.0
O A:HOH466 4.2 22.6 1.0
CD A:ARG112 4.4 16.3 1.0
CB A:ARG112 4.6 11.0 1.0
CG A:ARG112 4.6 13.7 1.0
O A:ARG112 4.8 10.8 1.0
CG A:LYS116 4.8 7.3 0.7
OD1 A:ASN106 5.0 16.1 0.5

Platinum binding site 5 out of 5 in 4yeo

Go back to Platinum Binding Sites List in 4yeo
Platinum binding site 5 out of 5 in the Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Triclinic Hewl Co-Crystallised with Cisplatin, Studied at A Data Collection Temperature of 150K - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt205

b:13.1
occ:0.17
 N A:LYS1 2.3 6.7 1.0
O A:HOH361 3.0 21.4 1.0
OG A:SER86 3.1 9.9 0.4
O A:HOH423 3.1 28.4 1.0
CA A:LYS1 3.2 6.0 1.0
O A:HOH511 3.4 29.3 1.0
O A:HOH469 3.5 7.9 1.0
O A:HOH445 3.6 26.7 1.0
CB A:LYS1 3.7 6.4 1.0
O A:HOH315 4.0 8.2 1.0
OE1 A:GLN41 4.1 8.0 1.0
OG1 A:THR40 4.1 5.2 1.0
CD A:GLN41 4.1 6.9 1.0
CB A:SER86 4.3 8.2 0.4
CG A:GLN41 4.3 5.7 1.0
CB A:SER86 4.5 9.1 0.6
C A:LYS1 4.5 5.7 1.0
NE2 A:GLN41 4.7 8.7 1.0
O A:LYS1 5.0 6.7 1.0

Reference:

I.G.Shabalin, Z.Dauter, M.Jaskolski, W.Minor, A.Wlodawer. Crystallography and Chemistry Should Always Go Together: A Cautionary Tale of Protein Complexes with Cisplatin and Carboplatin To Be Published.
Page generated: Mon Aug 18 23:47:41 2025

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