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Palladium in PDB 6goi: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(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 Pd(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 Pd(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 Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation, PDB code: 6goi 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) 55.47 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.443, 78.443, 37.385, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 24.2

Other elements in 6goi:

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

Chlorine (Cl) 2 atoms

Palladium Binding Sites:

The binding sites of Palladium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation (pdb code 6goi). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 2 binding sites of Palladium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation, PDB code: 6goi:
Jump to Palladium binding site number: 1; 2;

Palladium binding site 1 out of 2 in 6goi

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


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd407

b:54.2
occ:0.20
 NE2 A:HIS15 2.2 31.9 1.0
O A:HOH580 2.3 28.5 0.8
O A:HOH563 2.9 42.7 0.8
CE1 A:HIS15 3.0 33.2 1.0
NH1 A:ARG14 3.0 60.8 1.0
CD2 A:HIS15 3.3 30.9 1.0
OD1 A:ASP87 3.5 32.0 1.0
OG1 A:THR89 4.1 23.0 1.0
N A:ILE88 4.1 22.4 1.0
CG1 A:ILE88 4.2 23.5 1.0
ND1 A:HIS15 4.2 32.8 1.0
CG A:ASP87 4.2 38.3 1.0
CZ A:ARG14 4.3 57.1 1.0
CG A:HIS15 4.3 30.1 1.0
N A:THR89 4.6 21.6 1.0
CA A:ASP87 4.7 28.3 1.0
OD2 A:ASP87 4.8 48.0 1.0
C A:ASP87 4.8 24.6 1.0
CA A:ILE88 4.9 22.8 1.0
NH2 A:ARG14 4.9 58.9 1.0

Palladium binding site 2 out of 2 in 6goi

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


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pd(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pd408

b:34.7
occ:0.70
 ND1 A:HIS15 2.3 32.8 1.0
S A:DMS411 2.4 32.0 0.7
CL A:CL410 2.4 41.3 0.7
CL A:CL409 2.4 21.6 0.7
O A:DMS411 2.5 43.4 0.7
CG A:HIS15 3.2 30.1 1.0
C1 A:DMS411 3.2 36.0 0.7
CB A:HIS15 3.4 27.4 1.0
CE1 A:HIS15 3.4 33.2 1.0
CA A:HIS15 3.5 29.1 1.0
C2 A:DMS411 4.0 38.4 0.7
O A:HIS15 4.0 28.3 1.0
O A:HOH575 4.1 44.3 1.0
C A:HIS15 4.2 27.2 1.0
CD2 A:HIS15 4.4 30.9 1.0
NE2 A:HIS15 4.4 31.9 1.0
N A:HIS15 4.6 32.4 1.0
CG2 A:THR89 4.6 23.0 1.0
O A:ARG14 4.8 33.9 1.0
OD1 A:ASN93 4.8 53.8 1.0
OG1 A:THR89 4.9 23.0 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 10:22:46 2024

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