Platinum in PDB 8ri5: Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 48 H of Soaking

The structure of Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 48 H of Soaking, PDB code: 8ri5 was solved by G.Tito, R.Troisi, 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)	25.45 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.474, 40.221, 65.676, 90, 90, 90
R / Rfree (%)	19 / 23

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

Magnesium

(Mg)

1 atom

The binding sites of Platinum atom in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 48 H of Soaking (pdb code 8ri5). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total only one binding site of Platinum was determined in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 48 H of Soaking, PDB code: 8ri5:

Platinum binding site 1 out of 1 in the Crystal Structure of Transplatin/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 Transplatin/B-Dna Adduct Obtained Upon 48 H of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt102 b:38.8 occ:0.20 N7 B:DG16 2.4 16.5 1.0 N B:NH3101 2.5 9.3 0.2 O B:HOH231 3.0 33.4 1.0 O B:HOH203 3.1 40.8 1.0 O B:HOH215 3.2 47.8 1.0 C8 B:DG16 3.3 17.7 1.0 C5 B:DG16 3.5 14.3 1.0 O6 B:DG16 3.8 14.7 1.0 O B:HOH204 3.8 27.8 1.0 O B:HOH224 4.0 34.6 1.0 C6 B:DG16 4.0 14.5 1.0 N6 B:DA17 4.3 14.9 1.0 C6 B:DC15 4.4 17.5 1.0 C5 B:DC15 4.4 18.8 1.0 OP2 B:DG16 4.5 23.7 1.0 N9 B:DG16 4.5 17.4 1.0 C4 B:DG16 4.6 15.7 1.0 N1 B:DC15 4.9 17.5 1.0 C4 B:DC15 4.9 17.3 1.0 O B:HOH213 5.0 32.7 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
PubMed: 38270175
DOI: 10.1039/D3DT04302A