Platinum in PDB 8c62: Crystal Structure of Cisplatin/B-Dna Adduct

The structure of Crystal Structure of Cisplatin/B-Dna Adduct, PDB code: 8c62 was solved by R.Troisi, G.Tito, G.Ferraro, F.Sica, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.17 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	24.725, 41.001, 66.483, 90, 90, 90
R / Rfree (%)	23.1 / 26.6

The binding sites of Platinum atom in the Crystal Structure of Cisplatin/B-Dna Adduct (pdb code 8c62). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 4 binding sites of Platinum where determined in the Crystal Structure of Cisplatin/B-Dna Adduct, PDB code: 8c62:
Jump to Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in the Crystal Structure of Cisplatin/B-Dna Adduct


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 Cisplatin/B-Dna Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt101 b:84.1 occ:0.50 N7 A:DG10 2.2 51.0 1.0 C8 A:DG10 3.0 49.7 1.0 C5 A:DG10 3.3 48.6 1.0 O6 A:DG10 3.7 45.2 1.0 C6 A:DG10 3.9 45.8 1.0 N9 A:DG10 4.2 51.2 1.0 C4 A:DG10 4.4 46.8 1.0 C5 A:DC9 4.7 49.3 1.0 C6 A:DC9 4.7 50.1 1.0 O6 B:DG14 4.9 43.0 1.0

Platinum binding site 2 out of 4 in the Crystal Structure of Cisplatin/B-Dna Adduct


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 Cisplatin/B-Dna Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt102 b:78.8 occ:0.60 N7 A:DG4 2.2 53.7 1.0 C5 A:DG4 3.2 49.9 1.0 C8 A:DG4 3.2 52.9 1.0 O6 A:DG4 3.4 46.9 1.0 C6 A:DG4 3.7 48.0 1.0 C6 A:DC3 3.9 41.0 1.0 C5 A:DC3 4.0 41.2 1.0 C2' A:DC3 4.4 50.3 1.0 C4 A:DG4 4.4 49.6 1.0 N9 A:DG4 4.4 52.2 1.0 N1 A:DC3 4.6 41.7 1.0 N6 A:DA5 4.6 40.2 1.0 C4 A:DC3 4.8 38.7 1.0 O4 B:DT20 4.9 45.3 1.0

Platinum binding site 3 out of 4 in the Crystal Structure of Cisplatin/B-Dna Adduct


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 Cisplatin/B-Dna Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt101 b:71.8 occ:0.50 N7 B:DG16 2.2 46.3 1.0 C8 B:DG16 3.1 46.6 1.0 C5 B:DG16 3.3 43.6 1.0 O6 B:DG16 3.7 40.6 1.0 C6 B:DG16 3.9 42.3 1.0 N6 B:DA17 4.3 39.6 1.0 N9 B:DG16 4.3 46.9 1.0 C6 B:DC15 4.4 38.2 1.0 C4 B:DG16 4.4 45.8 1.0 C5 B:DC15 4.5 37.0 1.0 OP2 B:DG16 4.6 51.4 1.0 C2' B:DC15 4.7 46.3 1.0 N1 B:DC15 4.9 42.2 1.0

Platinum binding site 4 out of 4 in the Crystal Structure of Cisplatin/B-Dna Adduct


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 Cisplatin/B-Dna Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt102 b:85.5 occ:0.65 N7 B:DG22 2.2 59.5 1.0 C8 B:DG22 3.2 60.5 1.0 C5 B:DG22 3.2 54.8 1.0 O6 B:DG22 3.5 47.5 1.0 C6 B:DG22 3.7 49.8 1.0 C5 B:DC21 4.4 50.0 1.0 N9 B:DG22 4.4 60.3 1.0 C4 B:DG22 4.4 56.6 1.0 C6 B:DC21 4.5 50.0 1.0 O6 A:DG2 4.7 41.0 1.0 N4 B:DC23 4.8 46.0 1.0 C4 B:DC21 5.0 48.0 1.0

R.Troisi, G.Tito, G.Ferraro, F.Sica, L.Massai, A.Geri, D.Cirri, L.Messori, A.Merlino. On the Mechanism of Action of Arsenoplatins: Arsenoplatin-1 Binding to A B-Dna Dodecamer Dalton Trans 2024.
ISSN: ESSN 1477-9234
DOI: 10.1039/D3DT04302A