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Chlorine 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:

Platinum (Pt) 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 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 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 Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Triphenylphosphonium Cation, PDB code: 6goj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6goj

Go back to Chlorine Binding Sites List in 6goj
Chlorine 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 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 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:Cl205

b:34.1
occ:0.30
 PT A:PT202 2.4 52.2 0.3
N A:ILE88 3.3 26.9 1.0
O A:HOH327 3.4 38.9 1.0
CG1 A:ILE88 3.6 30.7 1.0
CA A:ASP87 3.8 30.2 1.0
O A:SER86 4.0 26.8 1.0
C A:ASP87 4.1 28.3 1.0
NE2 A:HIS15 4.1 39.2 1.0
CZ A:PHE3 4.2 28.2 1.0
CG2 A:ILE88 4.2 30.0 1.0
CB A:ILE88 4.2 29.8 1.0
CD1 A:ILE88 4.2 33.5 1.0
CB A:ALA11 4.2 26.4 1.0
CA A:ILE88 4.3 27.8 1.0
CG A:ASP87 4.4 36.2 1.0
OD1 A:ASP87 4.6 33.2 1.0
OD2 A:ASP87 4.6 45.4 1.0
CB A:ASP87 4.6 33.0 1.0
CD2 A:HIS15 4.7 36.3 1.0
CE2 A:PHE3 4.7 26.9 1.0
N A:ASP87 4.8 27.0 1.0
C A:SER86 4.8 27.3 1.0
NH2 A:ARG14 4.8 38.2 0.5

Chlorine binding site 2 out of 2 in 6goj

Go back to Chlorine Binding Sites List in 6goj
Chlorine 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 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 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:Cl206

b:31.3
occ:0.45
 PT A:PT201 2.4 50.2 0.5
OD1 A:ASN93 2.9 39.1 1.0
ND1 A:HIS15 3.0 38.9 1.0
CG A:ASN93 3.7 35.8 1.0
O A:THR89 3.7 26.4 1.0
CB A:HIS15 3.7 32.0 1.0
CG A:HIS15 3.7 34.1 1.0
CG2 A:THR89 3.7 24.5 1.0
CG1 A:VAL92 3.8 25.2 1.0
CE1 A:HIS15 4.0 39.2 1.0
CB A:VAL92 4.0 24.3 1.0
O A:HIS15 4.0 28.8 1.0
ND2 A:ASN93 4.0 39.0 1.0
O A:HOH370 4.1 47.9 1.0
CA A:THR89 4.2 23.9 1.0
C A:THR89 4.4 23.8 1.0
N A:ASN93 4.4 26.0 1.0
CA A:HIS15 4.4 32.8 1.0
CB A:THR89 4.5 24.0 1.0
NZ A:LYS96 4.6 26.3 1.0
C A:HIS15 4.7 30.4 1.0
O A:HOH371 4.7 36.1 0.5
OG1 A:THR89 4.8 24.0 1.0
CB A:ASN93 4.8 30.9 1.0
CA A:ASN93 4.9 27.0 1.0
CD2 A:HIS15 4.9 36.3 1.0
CG2 A:VAL92 4.9 24.5 1.0
C A:VAL92 4.9 24.8 1.0
NE2 A:HIS15 5.0 39.2 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 Oct 28 13:28:38 2020

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