Chlorine in PDB 6tgi: Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24

Enzymatic activity of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24

All present enzymatic activity of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24, PDB code: 6tgi was solved by L.Maso, F.Spirakis, M.Santucci, C.Simon, J.D.Docquier, G.Cruciani, M.P.Costi, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.56 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.618, 79.060, 68.207, 90.00, 131.17, 90.00
R / Rfree (%) 17.8 / 21.9

Other elements in 6tgi:

The structure of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24 also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24 (pdb code 6tgi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24, PDB code: 6tgi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6tgi

Go back to Chlorine Binding Sites List in 6tgi
Chlorine binding site 1 out of 2 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:33.8
occ:1.00
CL1 A:N8Z508 0.0 33.8 1.0
C14 A:N8Z508 1.8 32.4 1.0
C08 A:N8Z508 2.8 27.6 1.0
C12 A:N8Z508 2.8 32.8 1.0
C07 A:N8Z508 3.2 23.5 1.0
N A:ASP118 3.3 15.2 1.0
C13 A:N8Z508 3.4 35.8 1.0
N16 A:N8Z508 3.5 21.1 1.0
NE1 A:TRP87 3.5 20.3 1.0
CB A:ASP117 3.7 19.0 1.0
CB A:ASP118 3.8 16.5 1.0
CE2 A:TRP87 3.9 19.5 1.0
OD1 A:ASP118 3.9 16.5 1.0
N10 A:N8Z508 3.9 37.3 1.0
C A:ASP117 3.9 15.7 1.0
N09 A:N8Z508 3.9 30.2 1.0
N A:ASP117 3.9 15.6 1.0
O A:HOH623 4.0 23.8 1.0
CA A:ASP117 4.0 16.3 1.0
CZ2 A:TRP87 4.1 19.3 1.0
CA A:ASP118 4.1 14.1 1.0
CG A:ASP118 4.1 17.4 1.0
O A:HOH695 4.1 33.3 1.0
N04 A:N8Z508 4.1 21.1 1.0
CD1 A:TRP87 4.3 18.6 1.0
C06 A:N8Z508 4.4 25.2 1.0
N01 A:N8Z508 4.5 20.6 1.0
O A:HOH766 4.6 19.2 1.0
CB A:HIS116 4.7 13.3 1.0
C02 A:N8Z508 4.8 20.6 1.0
C A:HIS116 4.8 13.1 1.0
CD2 A:TRP87 4.8 18.5 1.0
C05 A:N8Z508 4.9 26.4 1.0
O A:ASP117 4.9 15.6 1.0
CG A:ASP117 4.9 26.2 1.0
OD2 A:ASP117 4.9 31.6 1.0

Chlorine binding site 2 out of 2 in 6tgi

Go back to Chlorine Binding Sites List in 6tgi
Chlorine binding site 2 out of 2 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl508

b:36.4
occ:1.00
CL1 B:N8Z508 0.0 36.4 1.0
C14 B:N8Z508 1.8 32.4 1.0
C08 B:N8Z508 2.8 28.6 1.0
C12 B:N8Z508 2.8 32.8 1.0
C07 B:N8Z508 3.3 24.8 1.0
C13 B:N8Z508 3.4 34.0 1.0
N B:ASP118 3.5 15.3 1.0
N16 B:N8Z508 3.6 20.2 1.0
NE1 B:TRP87 3.6 19.4 1.0
CB B:ASP117 3.8 19.8 1.0
O B:HOH624 3.9 24.9 1.0
N10 B:N8Z508 3.9 37.8 1.0
N09 B:N8Z508 3.9 29.9 1.0
CE2 B:TRP87 4.0 18.1 1.0
N B:ASP117 4.0 16.3 1.0
O B:HOH654 4.0 33.0 1.0
CB B:ASP118 4.1 15.7 1.0
OD1 B:ASP118 4.1 16.3 1.0
CZ2 B:TRP87 4.1 18.7 1.0
C B:ASP117 4.1 16.2 1.0
CA B:ASP117 4.2 17.0 1.0
N04 B:N8Z508 4.3 21.0 1.0
CA B:ASP118 4.3 14.5 1.0
CG B:ASP118 4.3 16.8 1.0
C06 B:N8Z508 4.4 25.2 1.0
O B:HOH771 4.5 19.5 1.0
CD1 B:TRP87 4.5 17.6 1.0
N01 B:N8Z508 4.6 19.0 1.0
CB B:HIS116 4.7 13.0 1.0
C02 B:N8Z508 4.9 19.5 1.0
C B:HIS116 4.9 13.3 1.0
CG B:ASP117 5.0 26.9 1.0
C05 B:N8Z508 5.0 26.1 1.0
CD2 B:TRP87 5.0 17.0 1.0

Reference:

F.Spyrakis, M.Santucci, L.Maso, S.Cross, E.Gianquinto, F.Sannio, F.Verdirosa, F.De Luca, J.D.Docquier, L.Cendron, D.Tondi, A.Venturelli, G.Cruciani, M.P.Costi. Virtual Screening Identifies Broad-Spectrum Beta-Lactamase Inhibitors with Activity on Clinically Relevant Serine- and Metallo-Carbapenemases. Sci Rep V. 10 12763 2020.
ISSN: ESSN 2045-2322
PubMed: 32728062
DOI: 10.1038/S41598-020-69431-Y
Page generated: Sat Dec 12 13:44:34 2020

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