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Platinum 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:

Chlorine (Cl) 3 atoms

Platinum Binding Sites:

The binding sites of Platinum 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 Platinum atom.
In total 4 binding sites of Platinum 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 Platinum binding site number: 1; 2; 3; 4;

Platinum binding site 1 out of 4 in 6goh

Go back to Platinum Binding Sites List in 6goh
Platinum binding site 1 out of 4 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 Platinum with other atoms in the Pt 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:Pt203

b:53.7
occ:0.40
NE2 A:HIS15 2.1 41.9 1.0
CL A:CL205 2.4 28.2 0.4
O A:HOH333 2.4 36.4 0.4
S A:DMS202 2.7 29.6 0.6
CE1 A:HIS15 2.8 47.1 1.0
OD1 A:ASP87 3.2 48.5 1.0
CD2 A:HIS15 3.3 42.7 1.0
C2 A:DMS202 3.5 30.6 0.6
OG1 A:THR89 3.6 37.4 1.0
C1 A:DMS202 3.7 30.9 0.6
O A:DMS202 3.7 35.4 0.6
ND1 A:HIS15 4.0 46.8 1.0
CG A:ASP87 4.1 49.4 1.0
CG A:HIS15 4.3 41.7 1.0
OD2 A:ASP87 4.4 50.6 1.0
N A:THR89 4.8 34.3 1.0
N A:ILE88 4.9 38.2 1.0
CB A:THR89 4.9 33.8 1.0
CG1 A:ILE88 5.0 39.4 1.0

Platinum binding site 2 out of 4 in 6goh

Go back to Platinum Binding Sites List in 6goh
Platinum binding site 2 out of 4 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 Platinum with other atoms in the Pt 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:Pt204

b:62.5
occ:0.20
O A:HOH303 2.2 45.1 0.2
O A:HOH368 2.4 48.6 0.2
ND1 A:HIS15 3.0 46.8 1.0
CE1 A:HIS15 3.8 47.1 1.0
CG A:HIS15 4.0 41.7 1.0
O A:HIS15 4.0 34.2 1.0
CA A:HIS15 4.1 39.6 1.0
CB A:HIS15 4.2 39.6 1.0
ND2 A:ASN93 4.2 50.1 1.0
C A:HIS15 4.5 36.5 1.0
CG2 A:THR89 4.6 33.0 1.0
NZ A:LYS96 4.7 43.7 1.0
O A:HOH334 4.7 47.6 1.0
NE2 A:HIS15 5.0 41.9 1.0

Platinum binding site 3 out of 4 in 6goh

Go back to Platinum Binding Sites List in 6goh
Platinum binding site 3 out of 4 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 Platinum with other atoms in the Pt 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:Pt206

b:46.8
occ:0.25
PT A:F7T206 0.0 46.8 0.2
NAQ A:F7T206 2.0 38.7 0.2
NAL A:F7T206 2.0 39.3 0.2
CL2 A:F7T206 2.4 31.7 0.2
CAG A:F7T206 2.8 40.1 0.2
CAH A:F7T206 2.8 39.3 0.2
CAI A:F7T206 3.1 38.2 0.2
CAA A:F7T206 3.3 39.2 0.2
CAG A:F7T207 3.6 37.8 0.2
NE A:ARG5 3.6 35.6 1.0
CAH A:F7T207 3.8 38.4 0.2
CD A:ARG5 3.8 34.3 1.0
NAL A:F7T207 3.8 38.8 0.2
CAF A:F7T206 4.0 39.7 0.2
NAM A:F7T206 4.0 40.2 0.2
NAQ A:F7T207 4.0 39.6 0.2
CAR A:F7T206 4.1 38.8 0.2
NAM A:F7T207 4.2 37.4 0.2
CAB A:F7T206 4.2 39.4 0.2
PT A:F7T207 4.3 48.6 0.2
CAR A:F7T207 4.3 38.4 0.2
CAA A:F7T207 4.3 38.1 0.2
CAK A:F7T206 4.4 38.3 0.2
CB A:ARG5 4.4 34.0 1.0
CAB A:F7T207 4.5 37.8 0.2
O A:HOH353 4.5 49.7 1.0
CAN A:F7T207 4.6 37.5 0.2
CG A:ARG5 4.8 33.4 1.0
CAJ A:F7T206 4.8 38.2 0.2
CZ A:ARG5 4.8 39.4 1.0
CAI A:F7T207 4.8 38.7 0.2
CAJ A:F7T207 5.0 38.1 0.2

Platinum binding site 4 out of 4 in 6goh

Go back to Platinum Binding Sites List in 6goh
Platinum binding site 4 out of 4 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 Platinum with other atoms in the Pt binding site number 4 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:Pt207

b:48.6
occ:0.25
PT A:F7T207 0.0 48.6 0.2
NAL A:F7T207 2.0 38.8 0.2
NAQ A:F7T207 2.0 39.6 0.2
CAG A:F7T207 2.8 37.8 0.2
CAH A:F7T207 2.8 38.4 0.2
CAI A:F7T207 3.1 38.7 0.2
CAA A:F7T207 3.1 38.1 0.2
CAG A:F7T206 3.7 40.1 0.2
CAF A:F7T207 3.7 37.6 0.2
CAH A:F7T206 3.7 39.3 0.2
NAQ A:F7T206 3.8 38.7 0.2
NAL A:F7T206 3.9 39.3 0.2
NAM A:F7T207 4.0 37.4 0.2
CAB A:F7T207 4.1 37.8 0.2
CAR A:F7T207 4.2 38.4 0.2
PT A:F7T206 4.3 46.8 0.2
CAA A:F7T206 4.4 39.2 0.2
CAK A:F7T207 4.4 38.3 0.2
NAM A:F7T206 4.4 40.2 0.2
CAI A:F7T206 4.4 38.2 0.2
CAR A:F7T206 4.5 38.8 0.2
CAB A:F7T206 4.7 39.4 0.2
CAJ A:F7T207 4.8 38.1 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: Wed Dec 16 02:05:35 2020

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