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

Enzymatic activity of 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;

Protein crystallography data

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

Platinum Binding Sites:

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 4ot4

Go back to Platinum Binding Sites List in 4ot4
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 4ot4

Go back to Platinum Binding Sites List in 4ot4
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 4ot4

Go back to Platinum Binding Sites List in 4ot4
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

Reference:

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
Page generated: Wed Dec 16 02:04:56 2020

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