Platinum in PDB 4ot4: X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A:
3.1.27.5;

The structure of X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A, PDB code: 4ot4 was solved by L.Messori, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.88 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.767, 32.463, 67.575, 90.00, 93.07, 90.00
R / Rfree (%)	18.9 / 24.7

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A (pdb code 4ot4). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 3 binding sites of Platinum where determined in the X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A, PDB code: 4ot4:
Jump to Platinum binding site number: 1; 2; 3;

Platinum binding site 1 out of 3 in the X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt200 b:28.7 occ:0.75 PT1 A:CPT200 0.0 28.7 0.8 N1 A:CPT200 2.1 16.4 0.8 N2 A:CPT200 2.3 16.1 0.8 O A:HOH301 2.3 8.9 0.8 SD A:MET29 2.4 26.9 1.0 PT1 A:CPT201 3.2 46.8 0.2 CE A:MET29 3.4 26.0 1.0 CA A:MET29 3.5 26.1 1.0 CG A:MET29 3.5 27.5 1.0 CB B:ALA56 3.9 22.4 1.0 N A:MET29 3.9 27.2 1.0 O A:GLN28 3.9 28.1 1.0 CB A:MET29 4.0 26.1 1.0 C A:GLN28 4.1 26.2 1.0 O A:HOH334 4.1 27.1 0.8 N1 A:CPT201 4.1 3.3 0.2 CB A:SER32 4.2 26.2 1.0 O B:HOH321 4.6 20.8 1.0 C A:MET29 4.7 22.7 1.0 OG A:SER32 4.7 32.3 1.0 O A:MET29 4.8 20.7 1.0 CB A:GLN28 4.8 35.8 1.0 NE2 B:GLN60 4.9 19.2 1.0 O A:HOH369 4.9 33.2 1.0

Platinum binding site 2 out of 3 in the X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A within 5.0Å range: probe atom residue distance (Å) B Occ A:Pt201 b:46.8 occ:0.25 PT1 A:CPT201 0.0 46.8 0.2 SD A:MET29 2.3 26.9 1.0 N1 A:CPT201 2.3 3.3 0.2 N1 A:CPT200 2.8 16.4 0.8 PT1 A:CPT200 3.2 28.7 0.8 OD2 A:ASP14 3.3 32.7 1.0 CE A:MET29 3.4 26.0 1.0 CE1 A:TYR25 3.6 32.5 1.0 CG A:MET29 3.7 27.5 1.0 CG A:ASP14 4.0 33.4 1.0 OD1 A:ASP14 4.0 29.6 1.0 CD1 A:TYR25 4.2 33.6 1.0 CB B:ALA56 4.3 22.4 1.0 CZ A:TYR25 4.4 31.2 1.0 OH A:TYR25 4.5 27.6 1.0 OG A:SER16 4.8 47.3 1.0 O A:HOH301 4.8 8.9 0.8 O B:HOH302 4.8 22.5 1.0 N2 A:CPT200 4.8 16.1 0.8

Platinum binding site 3 out of 3 in the X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of X-Ray Structure of the Adduct Formed Between Cisplatin and Ribonuclease A within 5.0Å range: probe atom residue distance (Å) B Occ B:Pt201 b:34.9 occ:0.55 PT1 B:CPT201 0.0 34.9 0.6 N1 B:CPT201 2.4 22.0 0.6 N2 B:CPT201 2.4 16.5 0.6 SD B:MET29 2.6 27.9 1.0 NE2 B:GLN28 2.6 29.5 1.0 CG B:MET29 3.2 24.6 1.0 CD B:GLN28 3.4 32.5 1.0 OE1 B:GLN28 3.6 47.6 1.0 CE1 B:TYR25 3.7 26.2 1.0 CE B:MET29 3.8 24.6 1.0 CD1 B:TYR25 3.8 26.3 1.0 O B:HOH330 4.1 33.1 1.0 O B:HOH301 4.2 30.3 1.0 OD2 B:ASP14 4.3 27.3 1.0 CZ B:TYR25 4.7 27.8 1.0 CB B:MET29 4.7 22.8 1.0 O B:HOH303 4.8 30.8 1.0 CG B:GLN28 4.8 29.0 1.0 CG B:TYR25 4.9 30.1 1.0

L.Messori, A.Merlino. Cisplatin Binding to Proteins: Molecular Structure of the Ribonuclease A Adduct. Inorg.Chem. V. 53 3929 2014.
ISSN: ISSN 0020-1669
PubMed: 24694179
DOI: 10.1021/IC500360F