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Platinum in PDB 3re0: Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin

Enzymatic activity of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin

All present enzymatic activity of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin, PDB code: 3re0 was solved by I.Bertini, O.Blazevits, V.Calderone, M.Jaifei, M.Vieru, I.Amori, M.Cozzolino, M.T.Carri, L.Banci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.32 / 2.28
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.412, 34.805, 115.225, 90.00, 112.28, 90.00
R / Rfree (%) 20.9 / 29

Other elements in 3re0:

The structure of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin (pdb code 3re0). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin, PDB code: 3re0:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 3re0

Go back to Platinum Binding Sites List in 3re0
Platinum binding site 1 out of 5 in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:54.2
occ:0.40
PT1 B:CPT201 0.0 54.2 0.4
N2 B:CPT201 2.0 56.6 0.4
N1 B:CPT201 2.0 46.2 0.4
SG A:CYS111 2.2 50.3 1.0
CL2 B:CPT201 2.4 59.7 0.4
N2 B:CPT201 2.8 66.6 0.4
CB A:CYS111 3.2 45.0 1.0
CB A:ILE113 4.2 27.2 1.0
CL2 B:CPT201 4.3 53.7 0.4
PT1 B:CPT201 4.5 72.5 0.4
O A:ILE113 4.6 25.8 1.0
CA A:CYS111 4.6 40.1 1.0
O A:LEU106 4.6 44.6 1.0
CG1 A:ILE113 4.7 30.4 1.0
N A:ILE113 4.8 26.3 1.0
C A:CYS111 5.0 32.5 1.0
CG2 A:ILE113 5.0 28.6 1.0

Platinum binding site 2 out of 5 in 3re0

Go back to Platinum Binding Sites List in 3re0
Platinum binding site 2 out of 5 in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:72.5
occ:0.40
PT1 B:CPT201 0.0 72.5 0.4
N2 B:CPT201 2.0 66.6 0.4
N1 B:CPT201 2.0 59.4 0.4
SG B:CYS111 2.2 43.4 1.0
CL2 B:CPT201 2.4 53.7 0.4
N2 B:CPT201 2.8 56.6 0.4
CB B:CYS111 3.0 44.2 1.0
O B:ILE113 4.3 30.3 1.0
CA B:CYS111 4.4 41.9 1.0
CB B:ILE113 4.5 27.4 1.0
PT1 B:CPT201 4.5 54.2 0.4
O B:GLY108 4.6 67.0 1.0
N1 B:CPT201 4.6 46.2 0.4
C B:CYS111 4.7 35.7 1.0
O B:CYS111 4.9 32.3 1.0
N B:ILE113 4.9 30.4 1.0
O B:LEU106 5.0 45.0 1.0
CG2 B:ILE113 5.0 26.2 1.0

Platinum binding site 3 out of 5 in 3re0

Go back to Platinum Binding Sites List in 3re0
Platinum binding site 3 out of 5 in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt202

b:82.6
occ:0.60
PT1 B:CPT202 0.0 82.6 0.6
N1 B:CPT202 2.0 69.7 0.6
N2 B:CPT202 2.1 80.5 0.6
CL2 B:CPT202 2.4 63.9 0.6
OD1 B:ASP109 2.9 94.6 1.0
CG B:ASP109 3.1 91.2 1.0
OD2 B:ASP109 3.5 86.6 1.0
CB B:ASP109 3.8 82.2 1.0
CA B:ASP109 4.8 74.5 1.0

Platinum binding site 4 out of 5 in 3re0

Go back to Platinum Binding Sites List in 3re0
Platinum binding site 4 out of 5 in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt201

b:55.4
occ:0.40
PT1 C:CPT201 0.0 55.4 0.4
N2 C:CPT201 2.0 48.5 0.4
N1 C:CPT201 2.0 46.0 0.4
SG C:CYS111 2.2 52.6 1.0
CL2 C:CPT201 2.4 37.4 0.4
CB C:CYS111 2.9 46.9 1.0
N2 C:CPT201 3.4 67.3 0.4
CB C:ILE113 4.3 41.6 1.0
CA C:CYS111 4.3 48.1 1.0
O C:ILE113 4.4 32.5 1.0
C C:CYS111 4.5 41.4 1.0
N1 C:CPT201 4.6 56.4 0.4
O C:GLY108 4.7 66.0 1.0
N C:ILE113 4.7 34.6 1.0
O C:CYS111 4.7 44.9 1.0
PT1 C:CPT201 4.7 72.7 0.4
CD1 C:ILE113 4.8 46.3 1.0
CA C:ILE113 4.9 36.5 1.0
CA C:SER107 4.9 43.9 1.0

Platinum binding site 5 out of 5 in 3re0

Go back to Platinum Binding Sites List in 3re0
Platinum binding site 5 out of 5 in the Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of Human Apo Cu,Zn Superoxide Dismutase (SOD1) Complexed with Cisplatin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pt201

b:72.7
occ:0.40
PT1 C:CPT201 0.0 72.7 0.4
N1 C:CPT201 2.0 56.4 0.4
N2 C:CPT201 2.0 67.3 0.4
SG D:CYS111 2.4 50.2 1.0
CL2 C:CPT201 2.4 57.9 0.4
N2 C:CPT201 3.1 48.5 0.4
CB D:CYS111 3.3 43.1 1.0
CB D:ILE113 4.3 37.3 1.0
CG1 D:ILE113 4.4 38.6 1.0
O D:ILE113 4.5 32.9 1.0
CA D:SER107 4.6 45.0 1.0
CL2 C:CPT201 4.6 37.4 0.4
CA D:CYS111 4.7 42.8 1.0
PT1 C:CPT201 4.7 55.4 0.4
O D:LEU106 4.9 49.1 1.0
N D:ILE113 5.0 34.5 1.0

Reference:

L.Banci, I.Bertini, O.Blazevits, V.Calderone, F.Cantini, J.Mao, A.Trapananti, M.Vieru, I.Amori, M.Cozzolino, M.T.Carri. Interaction of Cisplatin with Human Superoxide Dismutase. J.Am.Chem.Soc. V. 134 7009 2012.
ISSN: ISSN 0002-7863
PubMed: 22471402
DOI: 10.1021/JA211591N
Page generated: Wed Dec 16 02:04:20 2020

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