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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: Thu Oct 10 11:34:24 2024

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