Zinc in PDB 8a4m: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7061)

Protein crystallography data

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7061), PDB code: 8a4m was solved by G.Tassone, M.Benvenuti, F.Verdirosa, G.Corsica, F.Sannio, 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) 51.82 / 1.98
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.883, 78.429, 80.036, 90, 90, 90
R / Rfree (%) 19.9 / 25.8

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 8 (Jmv-7061) (pdb code 8a4m). 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 8 (Jmv-7061), PDB code: 8a4m:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8a4m

Go back to Zinc Binding Sites List in 8a4m
Zinc binding site 1 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7061)


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 8 (Jmv-7061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:39.2
occ:0.80
NAI A:L2R306 2.0 40.6 0.8
ND1 A:HIS116 2.1 39.0 1.0
NE2 A:HIS114 2.2 40.2 1.0
NE2 A:HIS179 2.2 29.2 1.0
NAH A:L2R306 3.0 35.0 0.8
CE1 A:HIS116 3.0 40.7 1.0
CAJ A:L2R306 3.0 42.8 0.8
CG A:HIS116 3.1 37.8 1.0
CD2 A:HIS179 3.1 28.4 1.0
CD2 A:HIS114 3.1 40.5 1.0
CE1 A:HIS114 3.1 35.7 1.0
CE1 A:HIS179 3.3 29.7 1.0
CB A:HIS116 3.4 33.2 1.0
SAL A:L2R306 3.6 45.4 0.8
OD1 A:ASP118 4.0 42.1 1.0
CAG A:L2R306 4.1 42.5 0.8
NE2 A:HIS116 4.1 42.0 1.0
NAK A:L2R306 4.2 44.0 0.8
CD2 A:HIS116 4.2 39.7 1.0
ND1 A:HIS114 4.2 37.2 1.0
CG A:HIS114 4.2 36.4 1.0
CG A:HIS179 4.3 28.2 1.0
ND1 A:HIS179 4.4 32.6 1.0
ZN A:ZN302 4.5 37.9 0.8
CB A:CYS198 4.6 26.4 1.0
SG A:CYS198 4.8 35.8 1.0
CA A:HIS116 4.8 37.3 1.0
CG A:ASP118 4.8 40.5 1.0
OD2 A:ASP118 4.8 39.7 1.0

Zinc binding site 2 out of 3 in 8a4m

Go back to Zinc Binding Sites List in 8a4m
Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7061)


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 8 (Jmv-7061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:37.9
occ:0.80
SG A:CYS198 2.1 35.8 1.0
OD2 A:ASP118 2.2 39.7 1.0
SAL A:L2R306 2.4 45.4 0.8
NE2 A:HIS240 2.4 36.3 1.0
CAJ A:L2R306 3.2 42.8 0.8
CE1 A:HIS240 3.2 32.6 1.0
CG A:ASP118 3.4 40.5 1.0
CD2 A:HIS240 3.4 35.5 1.0
CB A:CYS198 3.4 26.4 1.0
NH2 A:ARG119 3.5 53.7 1.0
NE A:ARG119 3.8 49.5 1.0
NAK A:L2R306 3.8 44.0 0.8
CAM A:L2R306 3.9 43.7 0.8
OD1 A:ASP118 3.9 42.1 1.0
NAI A:L2R306 4.0 40.6 0.8
CZ A:ARG119 4.1 50.8 1.0
CE1 A:HIS114 4.2 35.7 1.0
ND1 A:HIS240 4.4 31.5 1.0
O A:HOH461 4.5 34.6 1.0
CG A:HIS240 4.5 30.2 1.0
CA A:CYS198 4.5 26.2 1.0
ZN A:ZN301 4.5 39.2 0.8
CB A:ASP118 4.6 38.9 1.0
NE2 A:HIS114 4.7 40.2 1.0
CAG A:L2R306 4.8 42.5 0.8
O A:HOH402 4.8 53.0 1.0
NAH A:L2R306 4.9 35.0 0.8
CD A:ARG119 4.9 41.6 1.0

Zinc binding site 3 out of 3 in 8a4m

Go back to Zinc Binding Sites List in 8a4m
Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with Compound 8 (Jmv-7061)


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 8 (Jmv-7061) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:50.0
occ:1.00
OXT A:ACT304 1.9 47.6 1.0
NE2 A:HIS153 2.2 28.1 1.0
OXT A:ACT305 2.2 39.0 0.8
CE1 A:HIS153 2.8 31.7 1.0
O A:ACT305 2.8 41.3 0.8
C A:ACT305 2.9 45.2 0.8
C A:ACT304 3.0 50.1 1.0
CD2 A:HIS153 3.4 31.6 1.0
O A:ACT304 3.5 49.4 1.0
ND1 A:HIS153 4.0 29.2 1.0
CB A:ALA132 4.2 29.1 1.0
CH3 A:ACT304 4.2 40.8 1.0
CG A:HIS153 4.3 29.4 1.0
CH3 A:ACT305 4.3 35.0 0.8
CA A:ALA132 4.7 28.7 1.0
CG2 A:THR152 4.9 32.0 1.0

Reference:

A.Legru, F.Verdirosa, Y.Vo-Hoang, G.Tassone, F.Vascon, C.A.Thomas, F.Sannio, G.Corsica, M.Benvenuti, G.Feller, R.Coulon, F.Marcoccia, S.R.Devente, E.Bouajila, C.Piveteau, F.Leroux, R.Deprez-Poulain, B.Deprez, P.Licznar-Fajardo, M.W.Crowder, L.Cendron, C.Pozzi, S.Mangani, J.D.Docquier, J.F.Hernandez, L.Gavara. Optimization of 1,2,4-Triazole-3-Thiones Toward Broad-Spectrum Metallo-Beta-Lactamase Inhibitors Showing Potent Synergistic Activity on Vim- and Ndm-1-Producing Clinical Isolates. J.Med.Chem. V. 65 16392 2022.
ISSN: ISSN 0022-2623
PubMed: 36450011
DOI: 10.1021/ACS.JMEDCHEM.2C01257
Page generated: Fri Jul 28 06:18:31 2023

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