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: Sat Dec 12 13:02:15 2020

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