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Chlorine in PDB 6goh: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with A Pt(II) Complex Bearing N,N-Pyridylbenzimidazole Derivative with An Alkylated Sulphonate Side Chain

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 Sulphonate Side Chain

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 Sulphonate Side Chain:
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 Sulphonate Side Chain, PDB code: 6goh 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) 55.41 / 2.43
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.361, 78.361, 36.962, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 27.3

Other elements in 6goh:

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 Sulphonate Side Chain also contains other interesting chemical elements:

Platinum (Pt) 4 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 Sulphonate Side Chain (pdb code 6goh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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 Sulphonate Side Chain, PDB code: 6goh:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6goh

Go back to Chlorine Binding Sites List in 6goh
Chlorine binding site 1 out of 3 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 Sulphonate Side Chain


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 Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:28.2
occ:0.40
PT A:PT203 2.4 53.7 0.4
OG1 A:THR89 2.8 37.4 1.0
C2 A:DMS202 2.9 30.6 0.6
CE1 A:HIS15 3.0 47.1 1.0
NE2 A:HIS15 3.4 41.9 1.0
S A:DMS202 3.4 29.6 0.6
OD1 A:ASP87 3.7 48.5 1.0
OD2 A:ASP87 3.9 50.6 1.0
ND1 A:HIS15 4.1 46.8 1.0
CB A:THR89 4.2 33.8 1.0
CG A:ASP87 4.2 49.4 1.0
C1 A:DMS202 4.3 30.9 0.6
CG2 A:THR89 4.4 33.0 1.0
O A:DMS202 4.6 35.4 0.6
CD2 A:HIS15 4.7 42.7 1.0
O A:HOH333 4.8 36.4 0.4

Chlorine binding site 2 out of 3 in 6goh

Go back to Chlorine Binding Sites List in 6goh
Chlorine binding site 2 out of 3 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 Sulphonate Side Chain


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 Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:40.9
occ:0.25
PT A:F7T206 2.4 46.8 0.2
CL2 A:F7T206 3.1 31.7 0.2
NAQ A:F7T206 3.4 38.7 0.2
CAI A:F7T206 3.5 38.2 0.2
CAB A:F7T207 4.1 37.8 0.2
CAA A:F7T207 4.3 38.1 0.2
NAM A:F7T207 4.3 37.4 0.2
CAC A:F7T207 4.3 37.7 0.2
O A:HOH353 4.3 49.7 1.0
CAN A:F7T207 4.4 37.5 0.2
CAG A:F7T207 4.4 37.8 0.2
NAL A:F7T206 4.4 39.3 0.2
NAL A:F7T207 4.5 38.8 0.2
CAH A:F7T206 4.6 39.3 0.2
CAF A:F7T207 4.7 37.6 0.2
CB A:ARG5 4.7 34.0 1.0
CAD A:F7T207 4.8 38.0 0.2
CAK A:F7T206 4.8 38.3 0.2
CAE A:F7T207 5.0 37.5 0.2

Chlorine binding site 3 out of 3 in 6goh

Go back to Chlorine Binding Sites List in 6goh
Chlorine binding site 3 out of 3 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 Sulphonate Side Chain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 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 Sulphonate Side Chain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:31.7
occ:0.25
CL2 A:F7T206 0.0 31.7 0.2
PT A:F7T206 2.4 46.8 0.2
NAL A:F7T206 3.4 39.3 0.2
CAR A:F7T207 3.7 38.4 0.2
CAN A:F7T207 3.8 37.5 0.2
CAF A:F7T206 3.9 39.7 0.2
CAA A:F7T206 4.0 39.2 0.2
CAH A:F7T207 4.0 38.4 0.2
CAG A:F7T207 4.1 37.8 0.2
NZ A:LYS33 4.1 43.9 1.0
CE2 A:PHE38 4.1 32.8 1.0
NAM A:F7T207 4.1 37.4 0.2
CZ3 A:TRP123 4.3 35.2 1.0
CD A:ARG5 4.3 34.3 1.0
CAJ A:F7T207 4.4 38.1 0.2
NAQ A:F7T206 4.4 38.7 0.2
CB A:ARG5 4.5 34.0 1.0
CAG A:F7T206 4.6 40.1 0.2
CE A:LYS33 4.7 41.1 1.0
CD A:LYS33 4.7 38.1 1.0
CZ A:PHE38 4.7 32.6 1.0
NAQ A:F7T207 4.8 39.6 0.2
CG A:ARG5 4.8 33.4 1.0
CAB A:F7T207 4.8 37.8 0.2
NE A:ARG5 4.9 35.6 1.0
NAL A:F7T207 4.9 38.8 0.2
CAO A:F7T207 4.9 37.2 0.2

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 00:03:54 2024

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