Atomistry » Platinum » PDB 5djl-5t7l » 5e5e
Atomistry »
  Platinum »
    PDB 5djl-5t7l »
      5e5e »

Platinum in PDB 5e5e: X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3)

Enzymatic activity of X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3)

All present enzymatic activity of X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3):
3.1.27.5;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3), PDB code: 5e5e was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.50 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.398, 32.768, 72.540, 90.00, 89.82, 90.00
R / Rfree (%) 19.2 / 25.4

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3) (pdb code 5e5e). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 2 binding sites of Platinum where determined in the X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3), PDB code: 5e5e:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 5e5e

Go back to Platinum Binding Sites List in 5e5e
Platinum binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3)


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 in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:62.2
occ:0.50
 NE2 A:HIS105 2.3 29.9 1.0
CE1 A:HIS105 3.0 26.3 1.0
O A:HOH365 3.3 46.0 1.0
CD2 A:HIS105 3.3 28.0 1.0
ND1 A:HIS105 4.1 29.0 1.0
CG A:HIS105 4.3 28.4 1.0

Platinum binding site 2 out of 2 in 5e5e

Go back to Platinum Binding Sites List in 5e5e
Platinum binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3)


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 in the Reaction Between Rnase A and A Neutral Organometallic Derivative [Pt(Pbi)(Me)(Dmso)], Pbi=2- (2'-Pyridil)Benzimidazole (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:64.0
occ:0.40
 ND1 A:HIS119 2.3 23.8 0.5
ND1 A:HIS119 2.9 22.6 0.5
CE1 A:HIS119 3.2 25.4 0.5
CG A:HIS119 3.4 23.8 0.5
CG A:HIS119 3.7 23.6 0.5
CB A:HIS119 3.7 23.3 0.5
CB A:HIS119 3.7 24.0 0.5
CE1 A:HIS119 3.9 23.5 0.5
O A:HOH374 3.9 51.5 1.0
O A:HOH324 4.3 40.4 1.0
CA A:HIS119 4.3 22.4 0.5
CA A:HIS119 4.3 21.9 0.5
NE2 A:HIS119 4.4 22.5 0.5
CD2 A:HIS119 4.5 23.3 0.5
O A:PHE120 4.6 23.5 1.0
N A:PHE120 4.6 21.9 1.0
O A:HOH315 4.8 32.7 1.0
CD2 A:HIS119 4.8 23.4 0.5
C A:HIS119 4.9 23.5 0.5
NE2 A:HIS119 4.9 24.2 0.5

Reference:

M.Serratrice, L.Maiore, A.Zucca, S.Stoccoro, I.Landini, E.Mini, L.Massai, G.Ferraro, A.Merlino, L.Messori, M.A.Cinellu. Cytotoxic Properties of A New Organometallic Platinum(II) Complex and Its Gold(I) Heterobimetallic Derivatives. Dalton Trans V. 45 579 2015.
ISSN: ESSN 1477-9234
PubMed: 26609781
DOI: 10.1039/C5DT02714D
Page generated: Wed Dec 16 02:05:13 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