Zinc in PDB 7ovh: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931)

Protein crystallography data

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931), PDB code: 7ovh was solved by G.Tassone, M.Benvenuti, F.Verdirosa, F.Sannio, F.Marcoccia, J.D.Docquier, C.Pozzi, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.74 / 1.80
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.119, 78.355, 79.324, 90, 90, 90
R / Rfree (%) 18.2 / 23.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931) (pdb code 7ovh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931), PDB code: 7ovh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 7ovh

Go back to Zinc Binding Sites List in 7ovh
Zinc binding site 1 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.2
occ:1.00
ND1 A:HIS116 1.9 26.5 1.0
NAI A:UNL306 2.0 39.6 1.0
NE2 A:HIS179 2.0 24.9 1.0
NE2 A:HIS114 2.1 20.7 1.0
CE1 A:HIS116 2.9 29.5 1.0
CG A:HIS116 2.9 24.7 1.0
NAH A:UNL306 3.0 33.9 1.0
CD2 A:HIS179 3.0 19.9 1.0
CD2 A:HIS114 3.0 19.7 1.0
CAJ A:UNL306 3.0 40.7 1.0
CE1 A:HIS179 3.0 22.6 1.0
CE1 A:HIS114 3.2 19.8 1.0
CB A:HIS116 3.3 24.0 1.0
SAL A:UNL306 3.6 36.3 1.0
NE2 A:HIS116 4.1 25.5 1.0
CD2 A:HIS116 4.1 26.6 1.0
OD1 A:ASP118 4.1 28.5 1.0
CAG A:UNL306 4.1 41.0 1.0
CG A:HIS179 4.1 21.3 1.0
ND1 A:HIS179 4.1 20.4 1.0
NAK A:UNL306 4.2 43.0 1.0
CG A:HIS114 4.2 20.4 1.0
ND1 A:HIS114 4.2 21.2 1.0
ZN A:ZN302 4.6 30.2 1.0
ND2 A:ASN210 4.6 68.2 1.0
CA A:HIS116 4.7 25.4 1.0
CB A:CYS198 4.7 27.1 1.0
O A:HOH469 5.0 32.3 1.0
CG A:ASP118 5.0 28.1 1.0
SG A:CYS198 5.0 28.9 1.0

Zinc binding site 2 out of 3 in 7ovh

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Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.2
occ:1.00
OD2 A:ASP118 2.1 29.7 1.0
NE2 A:HIS240 2.1 28.0 1.0
SG A:CYS198 2.2 28.9 1.0
SAL A:UNL306 2.2 36.3 1.0
CAJ A:UNL306 3.1 40.7 1.0
CG A:ASP118 3.1 28.1 1.0
CE1 A:HIS240 3.1 30.1 1.0
CD2 A:HIS240 3.1 28.5 1.0
CB A:CYS198 3.3 27.1 1.0
OD1 A:ASP118 3.5 28.5 1.0
NH2 A:ARG119 3.7 36.5 1.0
NAK A:UNL306 3.7 43.0 1.0
CAM A:UNL306 3.8 46.2 1.0
NE A:ARG119 3.9 29.1 1.0
NAI A:UNL306 4.0 39.6 1.0
CZ A:ARG119 4.2 31.8 1.0
ND1 A:HIS240 4.2 25.8 1.0
CG A:HIS240 4.3 25.5 1.0
CE1 A:HIS114 4.4 19.8 1.0
CB A:ASP118 4.4 29.0 1.0
O A:HOH484 4.5 31.1 1.0
CA A:CYS198 4.5 24.5 1.0
CAN A:UNL306 4.6 51.4 1.0
ZN A:ZN301 4.6 24.2 1.0
CAG A:UNL306 4.8 41.0 1.0
NE2 A:HIS114 4.8 20.7 1.0
NAH A:UNL306 4.9 33.9 1.0
CD A:ARG119 5.0 26.0 1.0

Zinc binding site 3 out of 3 in 7ovh

Go back to Zinc Binding Sites List in 7ovh
Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931)


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 the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 14 (Jmv-6931) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:25.6
occ:1.00
O A:ACT304 1.8 29.1 1.0
OXT A:ACT305 2.0 25.1 1.0
NE2 A:HIS153 2.0 23.4 1.0
C A:ACT305 2.7 28.1 1.0
O A:ACT305 2.7 27.8 1.0
CE1 A:HIS153 2.9 28.8 1.0
C A:ACT304 2.9 29.7 1.0
CD2 A:HIS153 3.1 24.5 1.0
OXT A:ACT304 3.2 23.8 1.0
ND1 A:HIS153 4.1 24.4 1.0
CB A:ALA132 4.1 25.7 1.0
CH3 A:ACT305 4.2 27.6 1.0
CG A:HIS153 4.2 24.4 1.0
CH3 A:ACT304 4.3 26.5 1.0
CA A:ALA132 4.7 25.8 1.0
O A:HOH432 4.8 34.1 1.0

Reference:

A.Legru, F.Verdirosa, J.F.Hernandez, G.Tassone, F.Sannio, M.Benvenuti, P.A.Conde, G.Bossis, C.A.Thomas, M.W.Crowder, M.Dillenberger, K.Becker, C.Pozzi, S.Mangani, J.D.Docquier, L.Gavara. 1,2,4-Triazole-3-Thione Compounds with A 4-Ethyl Alkyl/Aryl Sulfide Substituent Are Broad-Spectrum Metallo-Beta-Lactamase Inhibitors with Re-Sensitization Activity. Eur.J.Med.Chem. V. 226 13873 2021.
ISSN: ISSN 0223-5234
PubMed: 34626878
DOI: 10.1016/J.EJMECH.2021.113873
Page generated: Fri Nov 5 16:56:04 2021

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