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Platinum in PDB 6f60: The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand

Enzymatic activity of The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand

All present enzymatic activity of The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand:
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand, PDB code: 6f60 was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.34 / 1.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.780, 32.519, 72.337, 90.00, 90.19, 90.00
R / Rfree (%) 13.8 / 19.4

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand (pdb code 6f60). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand, PDB code: 6f60:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 6f60

Go back to Platinum Binding Sites List in 6f60
Platinum binding site 1 out of 2 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:26.9
occ:0.40
 PT A:DVW202 0.0 26.9 0.4
N3 A:DVW202 1.8 31.7 0.4
NE2 A:HIS105 2.0 25.1 1.0
N1 A:DVW202 2.0 28.3 0.4
C12 A:DVW202 2.1 28.5 0.4
N10 A:DVW202 2.2 27.1 0.4
C11 A:DVW202 2.4 30.6 0.4
C10 A:DVW202 2.6 24.0 0.4
C1A A:DVW202 2.6 29.2 0.4
C22 A:DVW202 2.7 28.8 0.4
C42 A:DVW202 2.8 29.4 0.4
CE1 A:HIS105 2.9 25.9 1.0
CD2 A:HIS105 3.0 21.0 1.0
C2 A:DVW202 3.2 29.0 0.4
C9 A:DVW202 3.4 27.6 0.4
C2A A:DVW202 3.6 39.1 0.4
N12 A:DVW202 3.9 29.6 0.4
C52 A:DVW202 4.0 30.6 0.4
C4A A:DVW202 4.0 39.5 0.4
C6A A:DVW202 4.0 32.2 0.4
ND1 A:HIS105 4.0 21.3 1.0
C9A A:DVW202 4.1 34.1 0.4
CG A:HIS105 4.1 17.5 1.0
C3 A:DVW202 4.4 33.2 0.4
C8 A:DVW202 4.6 36.5 0.4
CG2 A:THR78 4.6 27.5 1.0
C4 A:DVW202 4.7 38.4 0.4
C7 A:DVW202 4.8 40.5 0.4
CB A:DVW202 5.0 33.4 0.4

Platinum binding site 2 out of 2 in 6f60

Go back to Platinum Binding Sites List in 6f60
Platinum binding site 2 out of 2 in the The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of The X-Ray Structure of Bovine Pancreatic Ribonuclease in Complex with A Five-Coordinate Platinum(II) Compound Containing A Sugar Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:24.6
occ:0.40
 PT B:DW5201 0.0 24.6 0.4
N10 B:DW5201 2.1 35.0 0.4
C12 B:DW5201 2.1 28.8 0.4
NE2 B:HIS105 2.1 21.1 1.0
C11 B:DW5201 2.2 35.9 0.4
N1 B:DW5201 2.2 39.4 0.4
C13 B:DW5201 2.7 27.5 0.4
C10 B:DW5201 2.8 35.1 0.4
C1A B:DW5201 2.8 30.8 0.4
C9 B:DW5201 3.0 33.7 0.4
C9A B:DW5201 3.1 42.5 0.4
CE1 B:HIS105 3.1 19.9 1.0
CD2 B:HIS105 3.1 21.6 1.0
C2 B:DW5201 3.3 43.4 0.4
C2A B:DW5201 3.6 45.5 0.4
O B:HOH469 3.7 59.9 1.0
C6A B:DW5201 4.1 36.1 0.4
C4A B:DW5201 4.2 30.9 0.4
ND1 B:HIS105 4.2 18.5 1.0
CG B:HIS105 4.2 17.3 1.0
C8 B:DW5201 4.3 41.9 0.4
C3 B:DW5201 4.6 41.1 0.4
C7 B:DW5201 4.8 34.2 0.4
O B:HOH305 4.9 55.9 1.0
C4 B:DW5201 5.0 29.4 0.4

Reference:

M.E.Cucciolito, A.D'amora, G.De Feo, G.Ferraro, A.Giorgio, G.Petruk, D.M.Monti, A.Merlino, F.Ruffo. Five-Coordinate Platinum(II) Compounds Containing Sugar Ligands: Synthesis, Characterization, Cytotoxic Activity, and Interaction with Biological Macromolecules. Inorg Chem V. 57 3133 2018.
ISSN: ISSN 1520-510X
PubMed: 29509011
DOI: 10.1021/ACS.INORGCHEM.7B03118
Page generated: Thu Oct 10 11:43:05 2024

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