Atomistry » Platinum » PDB 5v6i-7kem » 6goj
Atomistry »
  Platinum »
    PDB 5v6i-7kem »
      6goj »

Platinum in PDB 6goj: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation, PDB code: 6goj 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) 55.23 / 2.25
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.108, 78.108, 37.172, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 27.9

Other elements in 6goj:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Platinum Binding Sites:

The binding sites of Platinum atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation (pdb code 6goj). 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 Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation, PDB code: 6goj:
Jump to Platinum binding site number: 1; 2;

Platinum binding site 1 out of 2 in 6goj

Go back to Platinum Binding Sites List in 6goj
Platinum binding site 1 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation


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 Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt201

b:50.2
occ:0.45
O A:HOH371 2.4 36.1 0.5
CL A:CL206 2.4 31.3 0.5
ND1 A:HIS15 2.4 38.9 1.0
CE1 A:HIS15 3.2 39.2 1.0
CG A:HIS15 3.3 34.1 1.0
CB A:HIS15 3.6 32.0 1.0
CA A:HIS15 3.7 32.8 1.0
O A:HIS15 4.2 28.8 1.0
O A:HOH370 4.2 47.9 1.0
NE2 A:HIS15 4.3 39.2 1.0
CD2 A:HIS15 4.4 36.3 1.0
C A:HIS15 4.4 30.4 1.0
CG2 A:THR89 4.5 24.5 1.0
O A:HOH314 4.7 44.2 1.0
N A:HIS15 4.8 34.1 1.0
OG1 A:THR89 4.9 24.0 1.0
OD1 A:ASN93 4.9 39.1 1.0
O A:ARG14 4.9 32.4 0.5
O A:ARG14 4.9 32.8 0.5

Platinum binding site 2 out of 2 in 6goj

Go back to Platinum Binding Sites List in 6goj
Platinum binding site 2 out of 2 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation


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 Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt202

b:52.2
occ:0.30
CL A:CL205 2.4 34.1 0.3
NH2 A:ARG14 2.5 38.2 0.5
NE2 A:HIS15 2.6 39.2 1.0
CD2 A:HIS15 3.4 36.3 1.0
CE1 A:HIS15 3.6 39.2 1.0
CZ A:ARG14 3.8 37.5 0.5
CB A:ALA11 4.5 26.4 1.0
OD2 A:ASP87 4.5 45.4 1.0
CG1 A:ILE88 4.5 30.7 1.0
NH1 A:ARG14 4.5 37.6 0.5
CG A:HIS15 4.6 34.1 1.0
NE A:ARG14 4.6 39.0 0.5
ND1 A:HIS15 4.7 38.9 1.0
CD A:ARG14 4.7 39.4 0.5
CG A:ASP87 4.8 36.2 1.0
OD1 A:ASP87 4.8 33.2 1.0
N A:ILE88 4.9 26.9 1.0
CA A:ALA11 5.0 25.3 1.0
O A:ALA11 5.0 24.5 1.0

Reference:

G.Ferraro, A.M.Mansour, A.Merlino. Exploring the Interactions Between Model Proteins and Pd(II) or Pt(II) Compounds Bearing Charged N,N-Pyridylbenzimidazole Bidentate Ligands By X-Ray Crystallography. Dalton Trans V. 47 10130 2018.
ISSN: ESSN 1477-9234
PubMed: 30004541
DOI: 10.1039/C8DT01663A
Page generated: Wed Dec 16 02:05:35 2020

Last articles

Zn in 7NN0
Zn in 7NIO
Zn in 7LUP
Zn in 7M1Y
Zn in 7LO4
Zn in 7KWO
Zn in 7KJY
Zn in 7KCQ
Zn in 7KC2
Zn in 7KCB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy