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Platinum in PDB 4rsz: The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C

Protein crystallography data

The structure of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C, PDB code: 4rsz was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 104.22 / 2.19
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 120.344, 120.344, 36.673, 90.00, 90.00, 120.00
R / Rfree (%) 23.1 / 28.2

Other elements in 4rsz:

The structure of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Chlorine (Cl) 3 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C (pdb code 4rsz). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 5 binding sites of Platinum where determined in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C, PDB code: 4rsz:
Jump to Platinum binding site number: 1; 2; 3; 4; 5;

Platinum binding site 1 out of 5 in 4rsz

Go back to Platinum Binding Sites List in 4rsz
Platinum binding site 1 out of 5 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:54.8
occ:0.50
PT1 A:CPT202 0.0 54.8 0.5
OE2 A:GLU61 1.8 64.0 1.0
N2 A:CPT202 2.0 50.6 0.5
N1 A:CPT202 2.0 47.4 0.5
SD A:MET65 2.3 60.0 1.0
CD A:GLU61 2.9 61.9 1.0
CG A:MET65 3.2 50.8 1.0
CG A:GLU61 3.5 57.2 1.0
OE2 A:GLU92 3.7 56.7 1.0
CE A:MET65 3.9 52.0 1.0
CG A:GLU92 3.9 49.5 1.0
OE1 A:GLU61 4.0 70.5 1.0
CD A:GLU92 4.3 53.6 1.0
CB A:MET65 4.4 48.5 1.0
O A:GLU61 4.9 45.5 1.0
CB A:GLU92 5.0 46.0 1.0
CB A:GLU61 5.0 51.5 1.0

Platinum binding site 2 out of 5 in 4rsz

Go back to Platinum Binding Sites List in 4rsz
Platinum binding site 2 out of 5 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt203

b:58.5
occ:0.50
PT1 B:CPT203 0.0 58.5 0.5
N1 B:CPT203 2.0 44.3 0.5
N2 B:CPT203 2.0 50.8 0.5
CL1 B:CPT203 2.3 37.9 0.5
SD B:MET65 2.3 67.1 1.0
CG B:MET65 3.4 60.9 1.0
OE1 B:GLU61 4.0 75.0 1.0
CE B:MET65 4.1 67.5 1.0
CB B:GLU61 4.2 62.0 1.0
CG B:GLU92 4.4 60.7 1.0
O B:GLU61 4.5 56.2 1.0
OE1 B:GLU92 4.5 66.4 1.0
CB B:MET65 4.5 58.9 1.0
C B:GLU61 4.7 57.8 1.0
OE2 B:GLU62 4.7 72.9 1.0
CG B:GLU61 4.8 65.5 1.0
CD B:GLU61 4.9 72.2 1.0
CD B:GLU92 5.0 63.6 1.0
CA B:GLU61 5.0 57.8 1.0

Platinum binding site 3 out of 5 in 4rsz

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Platinum binding site 3 out of 5 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pt202

b:55.8
occ:0.40
PT1 D:CPT202 0.0 55.8 0.4
N2 D:CPT202 2.0 48.9 0.4
N1 D:CPT202 2.0 51.2 0.4
CL1 D:CPT202 2.2 51.3 0.4
SD D:MET65 2.2 67.6 1.0
CG D:MET65 3.2 66.9 1.0
CE D:MET65 3.9 65.0 1.0
OE1 D:GLU61 4.2 67.8 1.0
CB D:MET65 4.3 65.0 1.0
CB D:GLU61 4.3 61.9 1.0
O D:GLU61 4.3 62.7 1.0
C D:GLU61 4.6 60.5 1.0
OE1 D:GLU92 4.6 72.8 1.0
CG D:GLU92 4.6 65.3 1.0
OE1 D:GLU62 4.6 86.3 1.0
CD D:GLU62 5.0 82.5 1.0

Platinum binding site 4 out of 5 in 4rsz

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Platinum binding site 4 out of 5 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Pt202

b:65.9
occ:0.40
SD E:MET65 2.3 0.7 1.0
CG E:MET65 2.7 0.7 1.0
CB E:MET65 3.4 98.0 1.0
CE E:MET65 4.0 0.2 1.0
NH1 E:ARG91 4.3 0.1 1.0
OE2 E:GLU62 4.4 0.5 1.0
C E:MET65 4.5 91.1 1.0
CA E:MET65 4.5 91.1 1.0
N E:GLU66 4.7 89.9 1.0
CE E:LYS88 4.7 0.0 1.0
O E:MET65 4.8 91.7 1.0
O E:GLU62 5.0 87.2 1.0

Platinum binding site 5 out of 5 in 4rsz

Go back to Platinum Binding Sites List in 4rsz
Platinum binding site 5 out of 5 in the The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of The X-Ray Structure of the Primary Adduct Formed in the Reaction Between Cisplatin and Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Pt203

b:58.5
occ:0.50
PT1 F:CPT203 0.0 58.5 0.5
OE2 F:GLU61 1.8 72.2 1.0
N1 F:CPT203 2.0 51.3 0.5
SD F:MET65 2.3 79.3 1.0
CL1 F:CPT203 2.3 63.0 0.5
CD F:GLU61 3.0 69.8 1.0
CG F:MET65 3.4 69.9 1.0
OE1 F:GLU61 3.6 69.7 1.0
CE F:MET65 3.9 74.4 1.0
CG F:GLU92 3.9 69.3 1.0
OE1 F:GLU92 4.0 75.3 1.0
CG F:GLU61 4.1 69.4 1.0
CD F:GLU92 4.5 72.5 1.0
CB F:MET65 4.6 66.3 1.0
CB F:GLU61 4.8 68.1 1.0
O F:GLU61 4.8 64.2 1.0
CB F:GLU92 4.9 69.4 1.0

Reference:

G.Ferraro, L.Messori, A.Merlino. The X-Ray Structure of the Primary Adducts Formed in the Reaction Between Cisplatin and Cytochrome C Chem.Commun.(Camb.) 2014.
ISSN: ESSN 1364-548X
DOI: 10.1039/C4CC09056J
Page generated: Wed Dec 16 02:05:02 2020

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