Platinum in PDB 8c63: Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 H of Soaking

The structure of Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 H of Soaking, PDB code: 8c63 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)	34.64 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.51, 40.73, 65.85, 90, 90, 90
R / Rfree (%)	23.8 / 26.1

The structure of Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 H of Soaking also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Platinum atom in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 H of Soaking (pdb code 8c63). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 H of Soaking, PDB code: 8c63:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 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 4 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt101 b:57.9 occ:0.20 N7 A:DG10 2.2 25.6 1.0 O A:HOH207 3.0 42.4 0.8 C8 A:DG10 3.2 27.0 1.0 C4 B:A6R101 3.2 40.0 0.2 C5 A:DG10 3.3 24.8 1.0 O6 A:DG10 3.5 24.1 1.0 C6 A:DG10 3.7 22.7 1.0 C3 B:A6R101 3.9 40.0 0.2 C5 A:DC9 4.0 24.4 1.0 C6 A:DC9 4.1 24.3 1.0 O2 B:A6R101 4.2 42.9 0.2 N9 A:DG10 4.4 26.9 1.0 C4 A:DG10 4.4 24.2 1.0 C4 A:DC9 4.7 23.7 1.0 N2 B:A6R101 4.7 38.9 0.2 N1 A:DC9 4.8 24.6 1.0 O A:HOH222 4.9 41.3 1.0

Platinum binding site 2 out of 2 in the Crystal Structure of Arsenoplatin-1/B-Dna Adduct Obtained Upon 4 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 4 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt101 b:39.3 occ:0.20 PT1 B:A6R101 0.0 39.3 0.2 N7 B:DG14 2.0 29.8 1.0 N1 B:A6R101 2.0 40.3 0.2 N2 B:A6R101 2.0 38.9 0.2 AS1 B:A6R101 2.3 44.1 0.2 C8 B:DG14 2.7 31.3 1.0 C1 B:A6R101 2.9 41.6 0.2 C3 B:A6R101 2.9 40.0 0.2 O1 B:A6R101 3.0 42.9 0.2 O2 B:A6R101 3.1 42.9 0.2 C5 B:DG14 3.2 28.0 1.0 O3 B:A6R101 3.5 43.5 0.2 O4 B:A6R101 3.6 45.2 0.2 C2' B:DC13 3.6 44.8 1.0 N4 B:DC15 3.7 27.7 1.0 O6 B:DG14 3.8 28.6 1.0 C6 B:DG14 3.9 26.7 1.0 O B:HOH216 3.9 49.0 1.0 N9 B:DG14 4.0 30.9 1.0 C4 B:DG14 4.2 29.8 1.0 C6 B:DC13 4.2 37.2 1.0 C2 B:A6R101 4.3 42.3 0.2 N1 B:DC13 4.3 37.1 1.0 C4 B:A6R101 4.3 40.0 0.2 C4 B:DC15 4.3 26.1 1.0 O6 A:DG10 4.4 24.1 1.0 O A:HOH207 4.4 42.4 0.8 C1' B:DC13 4.5 40.1 1.0 C5 B:DC13 4.7 38.3 1.0 C5 B:DC15 4.8 28.9 1.0 C2 B:DC13 4.8 35.2 1.0 C3' B:DC13 4.9 48.7 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