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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: Thu Oct 10 11:44:58 2024

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