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Platinum in PDB 6qe9: The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands

Enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands

All present enzymatic activity of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands:
3.1.27.5;

Protein crystallography data

The structure of The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands, PDB code: 6qe9 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) 22.89 / 2.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.005, 30.655, 68.680, 90.00, 92.97, 90.00
R / Rfree (%) 17.7 / 25.4

Platinum Binding Sites:

The binding sites of Platinum atom in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands (pdb code 6qe9). 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 the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands, PDB code: 6qe9:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 6qe9

Go back to Platinum Binding Sites List in 6qe9
Platinum binding site 1 out of 2 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands


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 the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:40.0
occ:0.60
 PT A:J9H202 0.0 40.0 0.6
NE2 A:HIS105 2.1 34.5 1.0
CP A:J9H202 2.5 19.5 0.6
CE1 A:HIS105 3.0 32.2 1.0
CD2 A:HIS105 3.1 30.4 1.0
C21 A:J9H202 3.1 20.0 0.6
C22 A:J9H202 3.1 18.9 0.6
ND1 A:HIS105 4.1 31.9 1.0
CG A:HIS105 4.1 28.4 1.0
CG2 A:THR78 4.3 36.0 1.0
O A:HOH304 4.5 45.0 1.0

Platinum binding site 2 out of 2 in 6qe9

Go back to Platinum Binding Sites List in 6qe9
Platinum binding site 2 out of 2 in the The X-Ray Structure of the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands


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 the Adduct Formed in the Reaction Between Bovine Pancreatic Ribonuclease and Complex I, A Pentacoordinate Pt(II) Compound Containing 2,9-Dimethyl-1,10-Phenanthroline, Dimethylfumarate, Methyl and Iodine As Ligands within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt201

b:74.7
occ:0.40
 PT B:J9H201 0.0 74.7 0.4
N1 B:J9H201 1.7 57.1 0.4
NE2 B:HIS105 2.1 40.9 1.0
N10 B:J9H201 2.2 59.5 0.4
C1A B:J9H201 2.5 56.8 0.4
C2 B:J9H201 2.7 52.9 0.4
C10 B:J9H201 2.7 58.1 0.4
C22 B:J9H201 2.9 12.1 0.4
CE1 B:HIS105 3.0 36.4 1.0
CP B:J9H201 3.1 46.1 0.4
C21 B:J9H201 3.1 12.7 0.4
C2A B:J9H201 3.2 51.5 0.4
CD2 B:HIS105 3.2 36.7 1.0
C9 B:J9H201 3.4 58.1 0.4
C4A B:J9H201 3.8 54.6 0.4
C9A B:J9H201 3.9 57.4 0.4
C3 B:J9H201 3.9 53.0 0.4
C6A B:J9H201 4.1 56.8 0.4
ND1 B:HIS105 4.1 38.1 1.0
CG B:HIS105 4.3 36.1 1.0
O B:HOH331 4.4 45.5 1.0
C4 B:J9H201 4.4 54.0 0.4
CG2 B:THR78 4.5 36.4 1.0
C8 B:J9H201 4.6 60.3 0.4
C7 B:J9H201 4.8 57.4 0.4
C5 B:J9H201 4.9 54.5 0.4
C6 B:J9H201 5.0 54.2 0.4

Reference:

G.Ferraro, T.Marzo, M.E.Cucciolito, F.Ruffo, L.Messori, A.Merlino. Reaction with Proteins of A Five-Coordinate Platinum(II) Compound. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 30691130
DOI: 10.3390/IJMS20030520
Page generated: Wed Dec 16 02:05:39 2020

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