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Platinum in PDB 4ddb: Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5

Enzymatic activity of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5

All present enzymatic activity of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5:
3.2.1.17;

Protein crystallography data

The structure of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5, PDB code: 4ddb was solved by S.W.Tanley, A.M.Schreurs, L.M.Kroon-Batenburg, J.Meredith, R.Prendergast, D.Walsh, P.Bryant, C.Levy, J.R.Helliwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.16 / 3.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.641, 79.641, 37.018, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 28

Other elements in 4ddb:

The structure of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5 (pdb code 4ddb). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5, PDB code: 4ddb:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 4ddb

Go back to Platinum Binding Sites List in 4ddb
Platinum binding site 1 out of 2 in the Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:92.1
occ:1.00
PT1 A:CPT201 0.0 92.1 1.0
N1 A:CPT201 2.0 83.5 1.0
C1 A:DMS211 2.1 47.6 1.0
NE2 A:HIS15 2.4 34.6 1.0
CL1 A:CPT201 2.4 73.7 1.0
CL2 A:CPT201 2.4 85.6 1.0
CD2 A:HIS15 3.2 33.8 1.0
NH1 A:ARG14 3.4 46.6 1.0
CE1 A:HIS15 3.4 35.2 1.0
S A:DMS211 3.8 49.0 1.0
CZ A:ARG14 4.1 46.4 1.0
CD A:ARG14 4.2 43.3 1.0
C2 A:DMS211 4.3 45.2 1.0
OD2 A:ASP87 4.4 26.8 1.0
NE A:ARG14 4.4 45.4 1.0
CG A:HIS15 4.5 33.4 1.0
ND1 A:HIS15 4.5 34.1 1.0
OG1 A:THR89 4.5 25.4 1.0
CG A:ASP87 4.6 25.0 1.0
O A:DMS211 4.6 44.8 1.0
OD1 A:ASP87 4.7 24.0 1.0
N A:ILE88 4.8 21.2 1.0
NH2 A:ARG14 5.0 47.0 1.0

Platinum binding site 2 out of 2 in 4ddb

Go back to Platinum Binding Sites List in 4ddb
Platinum binding site 2 out of 2 in the Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Eval Processed Hewl, Cisplatin Dmso Paratone pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:65.8
occ:1.00
PT1 A:CPT202 0.0 65.8 1.0
N2 A:CPT202 2.0 59.1 1.0
N1 A:CPT202 2.0 59.5 1.0
CL1 A:CPT202 2.4 60.4 1.0
ND1 A:HIS15 2.5 34.1 1.0
CE1 A:HIS15 3.1 35.2 1.0
CG A:HIS15 3.4 33.4 1.0
O A:DMS211 3.7 44.8 1.0
CA A:HIS15 3.8 33.6 1.0
CB A:HIS15 4.0 32.5 1.0
NE2 A:HIS15 4.0 34.6 1.0
CD2 A:HIS15 4.2 33.8 1.0
S A:DMS211 4.3 49.0 1.0
O A:ARG14 4.4 37.4 1.0
O A:HIS15 4.5 32.6 1.0
C A:HIS15 4.5 33.0 1.0
S A:DMS209 4.6 50.0 1.0
C1 A:DMS211 4.6 47.6 1.0
C2 A:DMS209 4.6 46.6 1.0
N A:HIS15 4.7 34.2 1.0
CG2 A:THR89 4.7 25.0 1.0
C A:ARG14 4.8 36.1 1.0
OG1 A:THR89 4.9 25.4 1.0
O A:DMS209 5.0 48.8 1.0

Reference:

S.W.Tanley, A.M.Schreurs, L.M.Kroon-Batenburg, J.Meredith, R.Prendergast, D.Walsh, P.Bryant, C.Levy, J.R.Helliwell. Structural Studies of the Effect That Dimethyl Sulfoxide (Dmso) Has on Cisplatin and Carboplatin Binding to Histidine in A Protein. Acta Crystallogr.,Sect.D V. 68 601 2012.
ISSN: ISSN 0907-4449
PubMed: 22525758
DOI: 10.1107/S0907444912006907
Page generated: Wed Dec 16 02:04:41 2020

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