Zinc 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:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24, PDB code: 6tgi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6tgi

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn501

b:14.1
occ:1.00
 N01 A:N8Z508 1.9 20.6 1.0
ND1 A:HIS116 2.0 14.3 1.0
NE2 A:HIS114 2.0 10.1 1.0
NE2 A:HIS179 2.0 12.5 1.0
C02 A:N8Z508 2.9 20.6 1.0
CE1 A:HIS116 2.9 15.0 1.0
CD2 A:HIS114 3.0 11.3 1.0
CD2 A:HIS179 3.0 11.7 1.0
N16 A:N8Z508 3.0 21.1 1.0
CG A:HIS116 3.0 12.2 1.0
CE1 A:HIS114 3.0 10.5 1.0
CE1 A:HIS179 3.1 14.9 1.0
CB A:HIS116 3.3 13.3 1.0
S03 A:N8Z508 3.4 21.2 1.0
OD1 A:ASP118 4.1 16.5 1.0
NE2 A:HIS116 4.1 15.6 1.0
N04 A:N8Z508 4.1 21.1 1.0
ND1 A:HIS114 4.1 11.1 1.0
CG A:HIS114 4.1 10.6 1.0
CD2 A:HIS116 4.1 13.7 1.0
C07 A:N8Z508 4.1 23.5 1.0
CG A:HIS179 4.1 11.8 1.0
ND1 A:HIS179 4.2 12.3 1.0
ND2 A:ASN210 4.4 35.8 1.0
ZN A:ZN502 4.6 17.7 1.0
CA A:HIS116 4.7 12.0 1.0
CB A:CYS198 4.7 12.8 1.0
O A:HOH695 4.8 33.3 1.0
O A:HOH721 4.8 17.1 1.0
CG A:ASP118 5.0 17.4 1.0
N A:HIS116 5.0 12.3 1.0

Zinc binding site 2 out of 6 in 6tgi

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Zinc binding site 2 out of 6 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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
A:Zn502

b:17.7
occ:1.00
 OD2 A:ASP118 2.0 16.3 1.0
NE2 A:HIS240 2.1 17.3 1.0
SG A:CYS198 2.2 15.3 1.0
S03 A:N8Z508 2.3 21.2 1.0
CD2 A:HIS240 3.0 17.0 1.0
C02 A:N8Z508 3.1 20.6 1.0
CG A:ASP118 3.1 17.4 1.0
CE1 A:HIS240 3.1 16.5 1.0
CB A:CYS198 3.2 12.8 1.0
OD1 A:ASP118 3.5 16.5 1.0
NH2 A:ARG119 3.7 17.7 1.0
N04 A:N8Z508 3.7 21.1 1.0
NE A:ARG119 3.9 14.6 1.0
C05 A:N8Z508 3.9 26.4 1.0
C06 A:N8Z508 3.9 25.2 1.0
N01 A:N8Z508 4.0 20.6 1.0
CZ A:ARG119 4.1 17.1 1.0
CE1 A:HIS114 4.2 10.5 1.0
CG A:HIS240 4.2 14.8 1.0
ND1 A:HIS240 4.2 14.3 1.0
CB A:ASP118 4.4 16.5 1.0
O A:HOH635 4.4 17.1 1.0
CA A:CYS198 4.4 12.0 1.0
ZN A:ZN501 4.6 14.1 1.0
NE2 A:HIS114 4.7 10.1 1.0
C07 A:N8Z508 4.8 23.5 1.0
C A:FMT505 4.8 20.3 1.0
CD A:ARG119 4.9 14.5 1.0
N16 A:N8Z508 4.9 21.1 1.0

Zinc binding site 3 out of 6 in 6tgi

Go back to Zinc Binding Sites List in 6tgi
Zinc binding site 3 out of 6 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 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:Zn507

b:16.0
occ:1.00
 O1 A:FMT504 1.9 17.4 1.0
O2 A:FMT503 1.9 22.0 1.0
NE2 A:HIS153 2.0 14.8 1.0
C A:FMT504 2.7 18.5 1.0
O2 A:FMT504 2.9 18.7 1.0
C A:FMT503 2.9 24.8 1.0
CE1 A:HIS153 3.0 15.8 1.0
CD2 A:HIS153 3.1 15.8 1.0
O1 A:FMT503 3.2 21.8 1.0
ND1 A:HIS153 4.1 15.4 1.0
CB A:ALA132 4.2 13.4 1.0
CG A:HIS153 4.2 14.0 1.0
CA A:ALA132 4.7 14.0 1.0
O A:HOH740 4.7 48.7 1.0
CG2 A:THR152 4.8 17.6 1.0
O A:HOH614 4.9 27.3 1.0

Zinc binding site 4 out of 6 in 6tgi

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Zinc binding site 4 out of 6 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 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:Zn501

b:14.1
occ:1.00
 N01 B:N8Z508 1.9 19.0 1.0
ND1 B:HIS116 2.0 14.3 1.0
NE2 B:HIS179 2.0 12.1 1.0
NE2 B:HIS114 2.1 9.5 1.0
C02 B:N8Z508 2.9 19.5 1.0
CE1 B:HIS116 2.9 14.5 1.0
N16 B:N8Z508 3.0 20.2 1.0
CD2 B:HIS179 3.0 12.4 1.0
CG B:HIS116 3.0 11.9 1.0
CE1 B:HIS179 3.0 15.0 1.0
CD2 B:HIS114 3.0 10.8 1.0
CE1 B:HIS114 3.0 9.4 1.0
CB B:HIS116 3.4 13.0 1.0
S03 B:N8Z508 3.4 20.7 1.0
OD1 B:ASP118 4.0 16.3 1.0
NE2 B:HIS116 4.1 15.7 1.0
CD2 B:HIS116 4.1 12.9 1.0
ND1 B:HIS179 4.1 11.9 1.0
ND1 B:HIS114 4.1 10.7 1.0
C07 B:N8Z508 4.1 24.8 1.0
CG B:HIS179 4.1 12.3 1.0
N04 B:N8Z508 4.1 21.0 1.0
CG B:HIS114 4.2 10.8 1.0
ZN B:ZN502 4.6 17.7 1.0
ND2 B:ASN210 4.6 37.2 1.0
O B:HOH654 4.7 33.0 1.0
CB B:CYS198 4.7 14.7 1.0
O B:HOH733 4.7 16.5 1.0
CA B:HIS116 4.8 12.4 1.0
CG B:ASP118 4.9 16.8 1.0

Zinc binding site 5 out of 6 in 6tgi

Go back to Zinc Binding Sites List in 6tgi
Zinc binding site 5 out of 6 in the Crystal Structure of Vim-2 in Complex with Triazole-Based Inhibitor OP24


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 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:Zn502

b:17.7
occ:1.00
 OD2 B:ASP118 2.0 15.9 1.0
NE2 B:HIS240 2.1 15.4 1.0
S03 B:N8Z508 2.1 20.7 1.0
SG B:CYS198 2.2 16.0 1.0
CD2 B:HIS240 3.0 16.3 1.0
CG B:ASP118 3.1 16.8 1.0
C02 B:N8Z508 3.1 19.5 1.0
CE1 B:HIS240 3.1 15.6 1.0
CB B:CYS198 3.3 14.7 1.0
OD1 B:ASP118 3.5 16.3 1.0
NH2 B:ARG119 3.7 19.2 1.0
N04 B:N8Z508 3.8 21.0 1.0
NE B:ARG119 3.9 15.2 1.0
C05 B:N8Z508 4.0 26.1 1.0
N01 B:N8Z508 4.0 19.0 1.0
C06 B:N8Z508 4.1 25.2 1.0
CZ B:ARG119 4.1 17.1 1.0
CG B:HIS240 4.2 14.4 1.0
ND1 B:HIS240 4.2 13.7 1.0
CE1 B:HIS114 4.2 9.4 1.0
CB B:ASP118 4.4 15.7 1.0
O B:HOH632 4.4 16.7 1.0
CA B:CYS198 4.4 13.2 1.0
ZN B:ZN501 4.6 14.1 1.0
C B:FMT505 4.8 17.3 1.0
NE2 B:HIS114 4.8 9.5 1.0
C07 B:N8Z508 4.9 24.8 1.0
CD B:ARG119 4.9 14.7 1.0
N16 B:N8Z508 5.0 20.2 1.0

Zinc binding site 6 out of 6 in 6tgi

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 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:Zn507

b:16.0
occ:1.00
 O1 B:FMT503 1.9 26.2 1.0
O2 B:FMT504 1.9 15.8 1.0
ND1 B:HIS251 2.1 12.7 1.0
C B:FMT504 2.7 17.6 1.0
C B:FMT503 2.9 28.4 1.0
O1 B:FMT504 2.9 18.2 1.0
CE1 B:HIS251 3.0 14.4 1.0
CG B:HIS251 3.1 14.0 1.0
O2 B:FMT503 3.2 26.4 1.0
CB B:HIS251 3.5 13.6 1.0
CA B:HIS251 3.8 14.4 1.0
NE2 B:HIS251 4.1 13.3 1.0
CD2 B:HIS251 4.2 13.9 1.0
ND2 B:ASN254 4.3 16.7 1.0
O B:HIS251 4.5 15.4 1.0
CD2 B:LEU203 4.5 16.6 1.0
C B:HIS251 4.6 14.7 1.0
N B:HIS251 4.9 13.4 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: Wed Dec 16 12:53:10 2020

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