Zinc in PDB 6tmc: Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases

The structure of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmc was solved by H.-K.S.Leiros, T.Christopeit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.26 / 1.40
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.805, 63.925, 90.748, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 16.8

The structure of Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the Vim-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases (pdb code 6tmc). 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-1_1DH-Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tmc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vim-1_1DH-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-1_1DH-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:18.8 occ:1.00 O A:OH404 1.9 16.0 1.0 NE2 A:HIS196 2.0 16.2 1.0 ND1 A:HIS118 2.0 18.6 1.0 HO A:OH404 2.1 19.1 1.0 NE2 A:HIS116 2.1 15.6 1.0 O A:HOH616 2.6 21.9 1.0 HB2 A:HIS118 2.8 19.2 1.0 CE1 A:HIS196 3.0 15.7 1.0 CG A:HIS118 3.0 18.1 1.0 CE1 A:HIS118 3.0 20.9 1.0 CD2 A:HIS196 3.0 17.3 1.0 CE1 A:HIS116 3.0 14.7 1.0 CD2 A:HIS116 3.1 15.1 1.0 HE1 A:HIS196 3.2 18.9 1.0 HE1 A:HIS118 3.2 25.1 1.0 HD2 A:HIS196 3.2 20.8 1.0 HE1 A:HIS116 3.2 17.6 1.0 CB A:HIS118 3.3 16.0 1.0 HD2 A:HIS116 3.3 18.1 1.0 HB3 A:HIS118 3.6 19.2 1.0 O04 A:NL5401 4.0 15.2 0.8 H013 A:NL5401 4.1 17.8 0.8 ND1 A:HIS196 4.1 17.8 1.0 NE2 A:HIS118 4.1 21.6 1.0 OD1 A:ASP120 4.1 15.2 1.0 CD2 A:HIS118 4.1 17.9 1.0 CG A:HIS196 4.1 16.7 1.0 HB2 A:CYS221 4.1 19.6 1.0 ND1 A:HIS116 4.2 15.5 1.0 CG A:HIS116 4.2 15.4 1.0 O A:HOH551 4.3 23.1 1.0 HB3 A:CYS221 4.4 19.6 1.0 H A:HIS118 4.4 17.5 1.0 HB3 A:SER197 4.4 21.0 1.0 H211 A:NL5401 4.5 18.1 0.8 N21 A:NL5401 4.5 15.1 0.8 H032 A:NL5401 4.6 18.4 0.8 CB A:CYS221 4.6 16.3 1.0 SG A:CYS221 4.6 16.2 1.0 ZN A:ZN403 4.6 17.7 1.0 CA A:HIS118 4.7 15.2 1.0 C06 A:NL5401 4.7 11.7 0.8 C01 A:NL5401 4.7 14.8 0.8 H011 A:NL5401 4.8 17.8 0.8 HD1 A:HIS196 4.9 21.4 1.0 HE2 A:HIS118 4.9 25.9 1.0 C02 A:NL5401 4.9 15.9 0.8 HD1 A:HIS116 4.9 18.6 1.0 O A:HOH611 4.9 31.9 1.0 N20 A:NL5401 5.0 14.6 0.8 OD2 A:ASP120 5.0 14.6 1.0 N A:HIS118 5.0 14.6 1.0 HD2 A:HIS118 5.0 21.5 1.0 CG A:ASP120 5.0 15.1 1.0 C05 A:NL5401 5.0 15.8 0.8

Zinc binding site 2 out of 2 in the Vim-1_1DH-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-1_1DH-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:17.7 occ:1.00 H211 A:NL5401 1.1 18.1 0.8 NE2 A:HIS263 2.0 14.3 1.0 OD2 A:ASP120 2.0 14.6 1.0 N21 A:NL5401 2.1 15.1 0.8 SG A:CYS221 2.3 16.2 1.0 HO A:OH404 2.6 19.1 1.0 N20 A:NL5401 2.9 14.6 0.8 CD2 A:HIS263 2.9 15.6 1.0 CE1 A:HIS263 3.0 15.1 1.0 CG A:ASP120 3.1 15.1 1.0 C06 A:NL5401 3.1 11.7 0.8 HD2 A:HIS263 3.1 18.7 1.0 HE1 A:HIS263 3.2 18.1 1.0 H052 A:NL5401 3.2 18.9 0.8 O A:OH404 3.2 16.0 1.0 HH21 A:ARG121 3.3 20.9 1.0 HB3 A:CYS221 3.3 19.6 1.0 CB A:CYS221 3.5 16.3 1.0 OD1 A:ASP120 3.6 15.2 1.0 C05 A:NL5401 3.6 15.8 0.8 HE A:ARG121 3.8 18.0 1.0 NH2 A:ARG121 3.9 17.4 1.0 HE1 A:HIS116 4.0 17.6 1.0 N19 A:NL5401 4.1 14.2 0.8 HB2 A:CYS221 4.1 19.6 1.0 O04 A:NL5401 4.1 15.2 0.8 ND1 A:HIS263 4.1 15.5 1.0 CG A:HIS263 4.1 17.1 1.0 C07 A:NL5401 4.2 14.3 0.8 HB2 A:ASP120 4.3 15.7 1.0 CB A:ASP120 4.3 13.1 1.0 HA A:CYS221 4.3 18.4 1.0 O A:HOH569 4.3 18.4 1.0 H171 A:NL5401 4.3 32.4 0.8 HH22 A:ARG121 4.3 20.9 1.0 NE A:ARG121 4.4 15.0 1.0 HE1 A:HIS196 4.4 18.9 1.0 HB3 A:ASP120 4.5 15.7 1.0 H051 A:NL5401 4.5 18.9 0.8 CA A:CYS221 4.5 15.3 1.0 CZ A:ARG121 4.5 15.8 1.0 H033 A:NL5401 4.6 18.4 0.8 ZN A:ZN402 4.6 18.8 1.0 CE1 A:HIS196 4.7 15.7 1.0 HA3 A:GLY262 4.7 18.5 1.0 C17 A:NL5401 4.8 26.9 0.8 CE1 A:HIS116 4.8 14.7 1.0 NE2 A:HIS196 4.8 16.2 1.0 H181 A:NL5401 4.9 29.2 0.8 H032 A:NL5401 4.9 18.4 0.8 HD1 A:HIS263 4.9 18.6 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