Platinum in PDB 8c64: Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking

The structure of Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking, PDB code: 8c64 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)	34.14 / 2.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.97, 65.67, 23.56, 90, 90, 90
R / Rfree (%)	17.9 / 23.2

The structure of Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Platinum atom in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking (pdb code 8c64). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking, PDB code: 8c64:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking


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 Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt101 b:62.3 occ:0.15 N7 A:DG10 2.2 66.7 1.0 O6 A:DG10 2.8 70.5 1.0 C5 A:DG10 3.0 51.2 1.0 C6 A:DG10 3.2 52.8 1.0 C8 A:DG10 3.4 60.6 1.0 C5 A:DC9 3.9 52.1 1.0 C6 A:DC9 4.2 54.8 1.0 C4 A:DG10 4.3 48.4 1.0 N9 A:DG10 4.4 57.8 1.0 C4 A:DC9 4.5 47.9 1.0 N1 A:DG10 4.6 46.5 1.0 O A:HOH203 4.9 49.4 1.0 N4 A:DC9 4.9 52.1 1.0 N1 A:DC9 4.9 43.8 1.0 O6 B:DG14 5.0 42.7 1.0

Platinum binding site 2 out of 3 in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking


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 Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt102 b:66.4 occ:0.25 PT1 A:A6R102 0.0 66.4 0.2 N7 A:DG2 2.1 54.7 1.0 AS1 A:A6R102 2.3 54.4 0.2 C8 A:DG2 3.0 52.1 1.0 C5 A:DG2 3.2 53.4 1.0 N4 A:DC3 3.4 51.6 1.0 O6 A:DG2 3.6 53.5 1.0 C6 A:DG2 3.8 53.6 1.0 C6 A:DC1 3.9 74.6 1.0 N1 A:DC1 4.0 73.4 1.0 O6 B:DG22 4.0 38.3 1.0 C2' A:DC1 4.0 64.8 1.0 C5 A:DC1 4.2 65.7 1.0 N9 A:DG2 4.2 59.4 1.0 C4 A:DC3 4.3 48.0 1.0 C2 A:DC1 4.3 60.3 1.0 C4 A:DG2 4.4 58.3 1.0 C1' A:DC1 4.4 63.1 1.0 C4 A:DC1 4.5 61.5 1.0 N3 A:DC1 4.6 49.2 1.0 OP2 A:DG2 4.7 79.4 1.0 C5 A:DC3 4.8 53.2 1.0 O2 A:DC1 4.9 60.7 1.0 C6 B:DG22 5.0 45.6 1.0

Platinum binding site 3 out of 3 in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking


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 Arsenoplatin-1/B-Dna Adduct Obtained Upon 48 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt101 b:86.9 occ:0.40 N7 B:DG14 2.1 57.0 1.0 C8 B:DG14 3.0 57.2 1.0 C5 B:DG14 3.2 47.2 1.0 O6 B:DG14 3.6 42.7 1.0 N4 B:DC15 3.8 56.4 1.0 C6 B:DG14 3.8 45.4 1.0 C6 B:DC13 4.0 62.1 1.0 O6 A:DG10 4.1 70.5 1.0 N1 B:DC13 4.2 60.8 1.0 C2' B:DC13 4.2 59.8 1.0 N9 B:DG14 4.2 49.3 1.0 C4 B:DG14 4.3 49.5 1.0 C4 B:DC15 4.4 51.1 1.0 C1' B:DC13 4.4 61.6 1.0 C5 B:DC13 4.5 65.7 1.0 C2 B:DC13 4.7 64.5 1.0 C6 A:DG10 4.9 52.8 1.0 C5 B:DC15 4.9 50.5 1.0 N3 B:DC15 5.0 49.9 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