Zinc in PDB 6zgm: Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681, PDB code: 6zgm was solved by J.D.Docquier, C.Pozzi, F.Marcoccia, F.De Luca, M.Benvenuti, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.75 / 1.65
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.960, 78.178, 79.659, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.5

The structure of Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681 (pdb code 6zgm). 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 the Thiazolecarboxylate Inhibitor ANT2681, PDB code: 6zgm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681


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 the Thiazolecarboxylate Inhibitor ANT2681 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:7.6 occ:1.00 O A:HOH535 1.9 23.2 1.0 ND1 A:HIS118 1.9 22.3 1.0 NE2 A:HIS196 2.0 17.7 1.0 NE2 A:HIS116 2.1 18.9 1.0 CE1 A:HIS118 2.9 21.9 1.0 CD2 A:HIS196 3.0 16.8 1.0 CG A:HIS118 3.0 20.7 1.0 CE1 A:HIS116 3.0 18.1 1.0 CD2 A:HIS116 3.1 18.1 1.0 CE1 A:HIS196 3.1 19.7 1.0 CB A:HIS118 3.3 20.1 1.0 OD1 A:ASP120 4.0 28.8 1.0 NE2 A:HIS118 4.1 24.9 1.0 CD2 A:HIS118 4.1 23.3 1.0 CG A:HIS196 4.1 16.9 1.0 ZN A:ZN402 4.2 7.5 0.7 ND1 A:HIS116 4.2 18.8 1.0 ND1 A:HIS196 4.2 16.6 1.0 CG A:HIS116 4.2 17.7 1.0 SG A:CYS221 4.2 25.5 1.0 CB A:CYS221 4.3 20.5 1.0 O4 A:QKK406 4.4 22.0 0.7 ND2 A:ASN233 4.7 45.3 1.0 N5 A:QKK406 4.7 23.6 0.7 CA A:HIS118 4.7 21.3 1.0 OD2 A:ASP120 4.8 26.7 1.0 CG A:ASP120 4.8 25.5 1.0 C11 A:QKK406 4.9 26.8 0.7

Zinc binding site 2 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681


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 the Thiazolecarboxylate Inhibitor ANT2681 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:7.5 occ:0.70 N5 A:QKK406 2.1 23.6 0.7 OD2 A:ASP120 2.1 26.7 1.0 O4 A:QKK406 2.2 22.0 0.7 NE2 A:HIS263 2.2 27.4 1.0 SG A:CYS221 2.3 25.5 1.0 O A:HOH535 2.7 23.2 1.0 C9 A:QKK406 2.8 25.6 0.7 C11 A:QKK406 2.9 26.8 0.7 CE1 A:HIS263 3.1 26.1 1.0 C10 A:QKK406 3.2 29.1 0.7 CD2 A:HIS263 3.2 29.4 1.0 CG A:ASP120 3.3 25.5 1.0 CB A:CYS221 3.5 20.5 1.0 OD1 A:ASP120 3.7 28.8 1.0 NH2 A:ARG121 4.0 27.5 1.0 ZN A:ZN401 4.2 7.6 1.0 O3 A:QKK406 4.2 24.0 0.7 C8 A:QKK406 4.2 30.8 0.7 ND1 A:HIS263 4.3 25.3 1.0 CG A:HIS263 4.3 24.2 1.0 O A:HOH578 4.4 29.9 1.0 NE A:ARG121 4.5 26.0 1.0 CB A:ASP120 4.5 27.5 1.0 NE2 A:HIS196 4.6 17.7 1.0 CE1 A:HIS196 4.6 19.7 1.0 S1 A:QKK406 4.6 31.9 0.7 CA A:CYS221 4.6 18.6 1.0 CZ A:ARG121 4.7 26.9 1.0 CE1 A:HIS116 4.8 18.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Vim-2 Acquired Metallo-Beta-Lactamase in Complex with the Thiazolecarboxylate Inhibitor ANT2681


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 the Thiazolecarboxylate Inhibitor ANT2681 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:7.2 occ:1.00 NE2 A:HIS170 2.0 20.8 1.0 OXT A:ACT405 2.2 23.4 1.0 OXT A:ACT404 2.2 22.1 1.0 O A:ACT404 2.7 23.8 1.0 C A:ACT404 2.8 22.9 1.0 CE1 A:HIS170 2.9 23.1 1.0 C A:ACT405 3.0 24.9 1.0 O A:ACT405 3.1 21.3 1.0 CD2 A:HIS170 3.1 20.0 1.0 ND1 A:HIS170 4.1 21.4 1.0 CG A:HIS170 4.2 18.3 1.0 CH3 A:ACT404 4.2 28.9 1.0 CB A:ALA135 4.3 20.0 1.0 CH3 A:ACT405 4.4 22.8 1.0 CA A:ALA135 4.7 20.6 1.0 CG2 A:THR169 4.8 20.8 1.0 O A:HOH508 4.9 35.5 1.0

D.T.Davies, S.Leiris, N.Sprynski, J.Castandet, C.Lozano, J.Bousquet, M.Zalacain, S.Vasa, P.K.Dasari, R.Pattipati, N.Vempala, S.Gujjewar, S.Godi, R.Jallala, R.R.Sathyap, N.A.Darshanoju, V.R.Ravu, R.R.Juventhala, N.Pottabathini, S.Sharma, S.Pothukanuri, K.Holden, P.Warn, F.Marcoccia, M.Benvenuti, C.Pozzi, S.Mangani, J.D.Docquier, M.Lemonnier, M.Everett. ANT2681: Sar Studies Leading to the Identification of A Metallo-Beta-Lactamase Inhibitor with Potential For Clinical Use in Combination with Meropenem For the Treatment of Infections Caused By Ndm-Producingenterobacteriaceae. Acs Infect Dis. V. 6 2419 2020.
ISSN: ESSN 2373-8227
PubMed: 32786279
DOI: 10.1021/ACSINFECDIS.0C00207