Platinum in PDB 8ri3: Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking

The structure of Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking, PDB code: 8ri3 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)	34.40 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.56, 40.39, 65.67, 90, 90, 90
R / Rfree (%)	21.6 / 25.7

The structure of Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Platinum atom in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking (pdb code 8ri3). 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 Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking, PDB code: 8ri3:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days 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 7 Days of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt102 b:54.0 occ:0.30 N A:NH3103 2.0 20.9 0.3 N7 A:DG10 2.2 15.4 1.0 O A:HOH232 2.6 39.5 1.0 O B:HOH225 2.9 33.4 1.0 O A:HOH228 3.0 29.7 1.0 C5 A:DG10 3.1 12.9 1.0 C8 A:DG10 3.1 15.4 1.0 O6 A:DG10 3.4 13.3 1.0 C6 A:DG10 3.6 12.2 1.0 N9 A:DG10 4.2 15.4 1.0 C4 A:DG10 4.2 12.9 1.0 O A:HOH236 4.4 26.9 1.0 O A:HOH202 4.4 40.5 1.0 O6 B:DG14 4.6 13.7 1.0 C5 A:DC9 4.7 12.5 1.0 N4 A:DC11 4.7 14.2 1.0 O A:HOH240 4.9 36.4 1.0 C6 A:DC9 4.9 13.3 1.0 N1 A:DG10 4.9 11.8 1.0

Platinum binding site 2 out of 3 in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days 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 Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt104 b:51.8 occ:0.30 N A:NH3105 1.8 31.9 0.3 N7 A:DG4 1.9 19.8 1.0 CL A:CL106 2.1 26.5 0.3 C8 A:DG4 2.5 16.0 1.0 O A:HOH207 2.8 35.3 1.0 C5 A:DG4 3.0 16.3 1.0 N6 A:DA5 3.4 14.4 1.0 N9 A:DG4 3.6 17.4 1.0 C6 A:DG4 3.8 15.7 1.0 C4 A:DG4 3.8 17.1 1.0 O6 A:DG4 3.9 20.3 1.0 N7 A:DA5 4.0 16.3 1.0 C6 A:DA5 4.2 13.3 1.0 C5 A:DA5 4.4 14.5 1.0 O B:HOH207 4.7 31.1 1.0 O B:HOH203 4.8 29.8 1.0 C1' A:DG4 4.8 22.5 1.0 C2' A:DC3 4.9 19.5 1.0 C2' A:DG4 4.9 25.1 1.0 N1 A:DG4 5.0 15.0 1.0

Platinum binding site 3 out of 3 in the Crystal Structure of Transplatin/B-Dna Adduct Obtained Upon 7 Days 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 Transplatin/B-Dna Adduct Obtained Upon 7 Days of Soaking within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt101 b:27.0 occ:0.25 N B:NH3102 2.0 18.5 0.2 O B:HOH222 2.6 38.8 1.0 N7 B:DG16 2.7 14.1 1.0 O B:HOH224 3.2 31.1 1.0 C8 B:DG16 3.5 14.5 1.0 C5 B:DG16 3.7 11.6 1.0 O A:HOH206 3.8 22.3 1.0 O6 B:DG16 3.8 10.5 1.0 O B:HOH214 4.0 35.3 1.0 C6 B:DG16 4.1 11.3 1.0 N6 B:DA17 4.3 10.0 1.0 C6 B:DC15 4.4 15.1 1.0 OP2 B:DG16 4.4 19.3 1.0 C5 B:DC15 4.5 15.4 1.0 N9 B:DG16 4.7 13.4 1.0 C4 B:DG16 4.8 12.6 1.0 N1 B:DC15 4.9 14.6 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 V. 53 3476 2024.
ISSN: ESSN 1477-9234
PubMed: 38270175
DOI: 10.1039/D3DT04302A