Zinc in PDB 6tm9: Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases

The structure of Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tm9 was solved by H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.24 / 1.07
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.347, 44.343, 60.837, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 15.8

The structure of Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases (pdb code 6tm9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tm9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.8 occ:1.00 HO A:OH404 1.8 11.0 0.9 O A:OH404 1.9 9.2 0.9 NE2 A:HIS196 2.0 9.7 1.0 ND1 A:HIS118 2.0 10.8 1.0 NE2 A:HIS116 2.0 8.9 1.0 HB2 A:HIS118 2.9 11.3 1.0 CE1 A:HIS118 3.0 11.3 1.0 CD2 A:HIS196 3.0 10.5 1.0 CE1 A:HIS196 3.0 10.0 1.0 CE1 A:HIS116 3.0 9.1 1.0 H4 A:9NW401 3.0 13.8 1.0 CD2 A:HIS116 3.0 9.1 1.0 CG A:HIS118 3.1 9.5 1.0 HE1 A:HIS118 3.1 13.5 1.0 HD2 A:HIS196 3.2 12.6 1.0 HE1 A:HIS116 3.2 10.9 1.0 HE1 A:HIS196 3.2 12.0 1.0 HD2 A:HIS116 3.2 10.9 1.0 CB A:HIS118 3.4 9.4 1.0 ZN A:ZN403 3.6 10.4 1.0 HB3 A:HIS118 3.7 11.3 1.0 HB2 A:CYS221 3.7 12.3 1.0 N07 A:9NW401 3.8 11.5 1.0 OD1 A:ASP120 3.9 9.8 1.0 N11 A:9NW401 4.1 11.1 1.0 HB3 A:CYS221 4.1 12.3 1.0 ND1 A:HIS196 4.1 10.8 1.0 NE2 A:HIS118 4.1 12.1 1.0 ND1 A:HIS116 4.1 8.6 1.0 CG A:HIS196 4.1 10.3 1.0 SG A:CYS221 4.1 10.2 1.0 CD2 A:HIS118 4.2 11.1 1.0 CG A:HIS116 4.2 8.9 1.0 CB A:CYS221 4.2 10.3 1.0 O A:HOH726 4.2 15.7 1.0 H A:HIS118 4.5 10.5 1.0 OD2 A:ASP120 4.5 10.6 1.0 C09 A:9NW401 4.5 11.1 1.0 C05 A:9NW401 4.6 12.9 1.0 HE A:ARG121 4.6 11.7 1.0 CG A:ASP120 4.6 9.0 1.0 C08 A:9NW401 4.7 11.2 1.0 HB3 A:SER197 4.7 13.1 1.0 HG2 A:ARG121 4.7 10.6 1.0 N12 A:9NW401 4.7 10.9 1.0 H041 A:9NW401 4.8 19.2 1.0 HG3 A:ARG121 4.8 10.6 1.0 O A:HOH590 4.8 17.0 1.0 CA A:HIS118 4.8 9.3 1.0 C04 A:9NW401 4.8 16.0 1.0 HE2 A:HIS118 4.9 14.5 1.0 HD1 A:HIS196 4.9 12.9 1.0 HD1 A:HIS116 4.9 10.2 1.0

Zinc binding site 2 out of 2 in the Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2_1DD-. Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:10.4 occ:1.00 HO A:OH404 2.0 11.0 0.9 NE2 A:HIS263 2.1 9.9 1.0 O A:OH404 2.1 9.2 0.9 N11 A:9NW401 2.1 11.1 1.0 OD2 A:ASP120 2.3 10.6 1.0 SG A:CYS221 2.4 10.2 1.0 N12 A:9NW401 3.0 10.9 1.0 CD2 A:HIS263 3.1 9.8 1.0 HH21 A:ARG121 3.1 13.8 1.0 CE1 A:HIS263 3.1 9.5 1.0 C09 A:9NW401 3.2 11.1 1.0 HD2 A:HIS263 3.2 11.8 1.0 CG A:ASP120 3.3 9.0 1.0 HB3 A:CYS221 3.3 12.3 1.0 HE1 A:HIS263 3.3 11.4 1.0 H6 A:9NW401 3.4 13.5 1.0 CB A:CYS221 3.5 10.3 1.0 ZN A:ZN402 3.6 9.8 1.0 HE A:ARG121 3.6 11.7 1.0 OD1 A:ASP120 3.6 9.8 1.0 C08 A:9NW401 3.7 11.2 1.0 H4 A:9NW401 3.8 13.8 1.0 N07 A:9NW401 3.9 11.5 1.0 HB2 A:CYS221 3.9 12.3 1.0 NH2 A:ARG121 3.9 11.5 1.0 HE1 A:HIS116 3.9 10.9 1.0 HE1 A:HIS196 4.0 12.0 1.0 H061 A:9NW401 4.1 14.8 1.0 NE2 A:HIS196 4.2 9.7 1.0 N13 A:9NW401 4.2 12.2 1.0 CE1 A:HIS196 4.2 10.0 1.0 CG A:HIS263 4.2 9.7 1.0 ND1 A:HIS263 4.2 9.2 1.0 C10 A:9NW401 4.3 12.0 1.0 NE A:ARG121 4.3 9.8 1.0 HH22 A:ARG121 4.4 13.8 1.0 CE1 A:HIS116 4.6 9.1 1.0 CB A:ASP120 4.6 9.1 1.0 NE2 A:HIS116 4.6 8.9 1.0 CZ A:ARG121 4.6 9.4 1.0 HB2 A:ASP120 4.6 10.9 1.0 H7 A:9NW401 4.6 13.5 1.0 O A:HOH584 4.7 11.4 1.0 C06 A:9NW401 4.7 12.3 1.0 HA A:CYS221 4.7 12.1 1.0 CA A:CYS221 4.8 10.1 1.0 H3 A:9NW401 4.8 23.6 1.0 C05 A:9NW401 4.8 12.9 1.0 HB3 A:ASP120 4.8 10.9 1.0 HA3 A:GLY262 4.8 13.1 1.0 C24 A:9NW401 4.9 19.6 1.0

Z.Muhammad, S.Skagseth, M.Boomgaren, S.Akhter, C.Frohlich, A.Ismael, T.Christopeit, A.Bayer, H.S.Leiros. Structural Studies of Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases. Bioorg.Med.Chem. V. 28 15598 2020.
ISSN: ESSN 1464-3391
PubMed: 32631568
DOI: 10.1016/J.BMC.2020.115598