Atomistry » Chlorine » PDB 6ggo-6gos » 6goi
Atomistry »
  Chlorine »
    PDB 6ggo-6gos »
      6goi »

Chlorine 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:

Palladium (Pd) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6goi

Go back to Chlorine Binding Sites List in 6goi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl409

b:21.6
occ:0.70
 PD A:PD408 2.4 34.7 0.7
OD1 A:ASN93 2.9 53.8 1.0
CL A:CL410 3.3 41.3 0.7
ND1 A:HIS15 3.4 32.8 1.0
CB A:HIS15 3.6 27.4 1.0
CG1 A:VAL92 3.8 26.8 1.0
CG A:HIS15 3.8 30.1 1.0
CG A:ASN93 3.8 40.4 1.0
O A:THR89 3.9 21.9 1.0
O A:HIS15 3.9 28.3 1.0
CG2 A:THR89 4.0 23.0 1.0
CB A:VAL92 4.0 24.9 1.0
N A:ASN93 4.1 23.2 1.0
NZ A:LYS96 4.2 25.6 1.0
CA A:HIS15 4.3 29.1 1.0
CA A:THR89 4.3 22.3 1.0
CE1 A:HIS15 4.4 33.2 1.0
CA A:ASN93 4.5 26.3 1.0
C A:THR89 4.6 22.5 1.0
C A:HIS15 4.6 27.2 1.0
ND2 A:ASN93 4.6 47.5 1.0
CB A:ASN93 4.6 32.7 1.0
CB A:THR89 4.7 22.1 1.0
C A:VAL92 4.7 23.3 1.0
O A:DMS411 4.7 43.4 0.7
S A:DMS411 4.7 32.0 0.7
OG1 A:THR89 4.9 23.0 1.0
CD2 A:HIS15 4.9 30.9 1.0
CA A:VAL92 5.0 21.9 1.0

Chlorine binding site 2 out of 2 in 6goi

Go back to Chlorine Binding Sites List in 6goi
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl410

b:41.3
occ:0.70
 PD A:PD408 2.4 34.7 0.7
O A:DMS411 2.7 43.4 0.7
CL A:CL409 3.3 21.6 0.7
S A:DMS411 3.4 32.0 0.7
OD1 A:ASN93 4.3 53.8 1.0
NZ A:LYS96 4.4 25.6 1.0
O A:HIS15 4.5 28.3 1.0
C2 A:DMS411 4.5 38.4 0.7
ND1 A:HIS15 4.7 32.8 1.0
C1 A:DMS411 4.8 36.0 0.7
CA A:HIS15 5.0 29.1 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: Sun Jul 28 00:04:03 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy