Atomistry » Platinum » PDB 5v6i-7bd7 » 6qe9
Atomistry »
  Platinum »
    PDB 5v6i-7bd7 »
      6qe9 »

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy