Zinc in PDB 6tma: Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases

The structure of Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tma 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)	39.63 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.275, 79.269, 67.688, 90.00, 130.35, 90.00
R / Rfree (%)	15.6 / 19.4

The structure of Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases also contains other interesting chemical elements:

Iodine	(I)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases (pdb code 6tma). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases, PDB code: 6tma:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Vim-1_1DJ- 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_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.5 occ:1.00 HO A:OH404 1.9 34.0 1.0 ND1 A:HIS118 2.0 20.0 1.0 NE2 A:HIS196 2.0 15.1 1.0 NE2 A:HIS116 2.1 17.8 1.0 O A:OH404 2.2 28.4 1.0 HB2 A:HIS118 2.9 21.4 1.0 CE1 A:HIS196 2.9 18.9 1.0 CE1 A:HIS118 3.0 26.6 1.0 CG A:HIS118 3.0 17.1 1.0 CE1 A:HIS116 3.0 18.5 1.0 CD2 A:HIS196 3.0 14.3 1.0 CD2 A:HIS116 3.1 15.1 1.0 HE1 A:HIS196 3.1 22.7 1.0 HE1 A:HIS118 3.2 31.9 1.0 HE1 A:HIS116 3.2 22.2 1.0 HD2 A:HIS196 3.3 17.1 1.0 HD2 A:HIS116 3.3 18.2 1.0 CB A:HIS118 3.3 17.8 1.0 HB3 A:HIS118 3.6 21.4 1.0 HB2 A:CYS221 3.8 19.1 1.0 ZN A:ZN402 3.9 19.6 1.0 OD1 A:ASP120 4.0 21.3 1.0 ND1 A:HIS196 4.1 15.3 1.0 HB3 A:CYS221 4.1 19.1 1.0 NE2 A:HIS118 4.1 24.4 1.0 ND1 A:HIS116 4.1 16.2 1.0 CD2 A:HIS118 4.1 20.4 1.0 CG A:HIS196 4.1 13.1 1.0 N02 A:9O8407 4.1 78.3 0.3 H212 A:9O8407 4.2 94.4 0.3 CG A:HIS116 4.2 14.0 1.0 H212 A:9O8407 4.2 94.3 0.7 CB A:CYS221 4.2 15.9 1.0 H062 A:9O8407 4.3 95.6 0.3 N02 A:9O8407 4.3 78.4 0.7 SG A:CYS221 4.3 17.1 1.0 H061 A:9O8407 4.4 95.5 0.7 C03 A:9O8407 4.5 79.6 0.7 C03 A:9O8407 4.5 79.3 0.3 N01 A:9O8407 4.5 78.4 0.3 H A:HIS118 4.5 20.8 1.0 N01 A:9O8407 4.6 78.4 0.7 OD2 A:ASP120 4.6 23.8 1.0 CG A:ASP120 4.7 22.4 1.0 H211 A:9O8407 4.7 94.4 0.3 HB3 A:SER197 4.8 18.1 1.0 HG2 A:ARG121 4.8 17.5 1.0 CA A:HIS118 4.8 17.5 1.0 C21 A:9O8407 4.8 78.7 0.3 HD1 A:HIS196 4.8 18.4 1.0 C19 A:9O8407 4.8 78.4 0.7 HE2 A:HIS118 4.9 29.3 1.0 C06 A:9O8407 4.9 79.6 0.7 HD1 A:HIS116 4.9 19.4 1.0 C04 A:9O8407 4.9 78.4 0.7 C21 A:9O8407 4.9 78.6 0.7 C06 A:9O8407 4.9 79.7 0.3 HG3 A:ARG121 4.9 17.5 1.0 HE A:ARG121 4.9 19.7 1.0 N05 A:9O8407 4.9 78.4 0.7 O20 A:9O8407 5.0 78.8 0.3 C19 A:9O8407 5.0 79.1 0.3 HD2 A:HIS118 5.0 24.5 1.0

Zinc binding site 2 out of 6 in the Vim-1_1DJ- 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_1DJ- 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:19.6 occ:1.00 NE2 A:HIS263 2.1 17.5 1.0 HO A:OH404 2.1 34.0 1.0 OD2 A:ASP120 2.1 23.8 1.0 N02 A:9O8407 2.2 78.4 0.7 SG A:CYS221 2.2 17.1 1.0 N02 A:9O8407 2.3 78.3 0.3 O A:OH404 2.4 28.4 1.0 N01 A:9O8407 3.0 78.4 0.7 HH21 A:ARG121 3.0 27.4 1.0 CE1 A:HIS263 3.0 17.4 1.0 CD2 A:HIS263 3.1 18.7 1.0 N01 A:9O8407 3.2 78.4 0.3 HE1 A:HIS263 3.2 20.9 1.0 HB3 A:CYS221 3.2 19.1 1.0 C03 A:9O8407 3.2 79.6 0.7 CG A:ASP120 3.2 22.4 1.0 HD2 A:HIS263 3.2 22.5 1.0 C03 A:9O8407 3.3 79.3 0.3 H081 A:9O8407 3.3 94.9 0.3 CB A:CYS221 3.4 15.9 1.0 H062 A:9O8407 3.4 95.5 0.7 HE A:ARG121 3.4 19.7 1.0 H062 A:9O8407 3.5 95.6 0.3 OD1 A:ASP120 3.6 21.3 1.0 C06 A:9O8407 3.7 79.7 0.3 HE1 A:HIS116 3.8 22.2 1.0 C06 A:9O8407 3.8 79.6 0.7 N08 A:9O8407 3.8 79.1 0.3 NH2 A:ARG121 3.8 22.8 1.0 ZN A:ZN401 3.9 20.5 1.0 HB2 A:CYS221 3.9 19.1 1.0 H061 A:9O8407 4.1 95.5 0.7 NE A:ARG121 4.1 16.4 1.0 ND1 A:HIS263 4.1 18.3 1.0 N05 A:9O8407 4.1 78.4 0.7 CG A:HIS263 4.2 17.4 1.0 C04 A:9O8407 4.3 78.4 0.7 N05 A:9O8407 4.4 78.7 0.3 HH22 A:ARG121 4.4 27.4 1.0 O A:HOH521 4.4 20.2 1.0 CZ A:ARG121 4.4 19.0 1.0 HE1 A:HIS196 4.4 22.7 1.0 HA A:CYS221 4.4 17.9 1.0 C04 A:9O8407 4.5 79.0 0.3 CE1 A:HIS116 4.5 18.5 1.0 CB A:ASP120 4.5 21.0 1.0 HA3 A:GLY262 4.5 19.1 1.0 NE2 A:HIS196 4.5 15.1 1.0 CA A:CYS221 4.5 14.9 1.0 HB2 A:ASP120 4.6 25.2 1.0 CE1 A:HIS196 4.6 18.9 1.0 O10 A:9O8407 4.7 79.0 0.7 NE2 A:HIS116 4.7 17.8 1.0 H061 A:9O8407 4.7 95.6 0.3 HB3 A:ASP120 4.7 25.2 1.0 HD1 A:HIS263 4.9 22.0 1.0 HG2 A:ARG121 5.0 17.5 1.0

Zinc binding site 3 out of 6 in the Vim-1_1DJ- 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 3 of Vim-1_1DJ- 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:22.2 occ:1.00 CL A:CL405 2.0 48.5 1.0 NE2 A:HIS170 2.0 22.1 1.0 CL A:CL406 2.3 35.1 1.0 CE1 A:HIS170 2.7 23.1 1.0 HE1 A:HIS170 2.8 27.7 1.0 CD2 A:HIS170 3.2 20.0 1.0 HD2 A:HIS170 3.6 24.0 1.0 O A:HOH745 3.6 46.6 1.0 HB1 A:ALA135 3.6 20.9 1.0 HB2 A:ALA135 3.8 20.9 1.0 ND1 A:HIS170 4.0 24.5 1.0 CB A:ALA135 4.2 17.4 1.0 CG A:HIS170 4.2 21.2 1.0 O A:HOH566 4.4 38.7 1.0 HA A:ALA135 4.5 23.2 1.0 HG21 A:THR169 4.6 30.9 1.0 HD1 A:HIS170 4.7 29.4 1.0 HG22 A:THR169 4.9 30.9 1.0 CA A:ALA135 4.9 19.4 1.0 O A:HOH737 4.9 26.1 1.0 HB3 A:ALA135 4.9 20.9 1.0

Zinc binding site 4 out of 6 in the Vim-1_1DJ- 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 4 of Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:20.8 occ:1.00 O B:OH404 1.9 20.9 1.0 ND1 B:HIS118 2.0 18.0 1.0 NE2 B:HIS196 2.0 15.8 1.0 NE2 B:HIS116 2.1 14.0 1.0 HO B:OH404 2.3 25.1 1.0 HB2 B:HIS118 2.8 20.1 1.0 CG B:HIS118 2.9 16.3 1.0 CE1 B:HIS118 3.0 18.9 1.0 CD2 B:HIS196 3.0 14.0 1.0 CE1 B:HIS196 3.0 16.3 1.0 CE1 B:HIS116 3.0 15.7 1.0 CD2 B:HIS116 3.0 14.3 1.0 HD2 B:HIS196 3.2 16.8 1.0 HE1 B:HIS118 3.2 22.6 1.0 HE1 B:HIS196 3.2 19.5 1.0 HE1 B:HIS116 3.2 18.9 1.0 HD2 B:HIS116 3.2 17.1 1.0 CB B:HIS118 3.3 16.7 1.0 HB3 B:HIS118 3.5 20.1 1.0 HB2 B:CYS221 3.9 17.5 1.0 OD1 B:ASP120 4.0 20.1 1.0 NE2 B:HIS118 4.1 22.1 1.0 CD2 B:HIS118 4.1 16.3 1.0 ND1 B:HIS196 4.1 16.2 1.0 ND1 B:HIS116 4.1 15.1 1.0 ZN B:ZN402 4.1 21.1 1.0 CG B:HIS196 4.1 13.3 1.0 CG B:HIS116 4.2 14.6 1.0 H212 B:9O8407 4.2 79.1 0.5 HB3 B:CYS221 4.2 17.5 1.0 H212 B:9O8407 4.2 79.4 0.4 H213 B:9O8407 4.3 79.4 0.4 H213 B:9O8407 4.3 79.1 0.5 CB B:CYS221 4.4 14.6 1.0 H B:HIS118 4.5 16.8 1.0 SG B:CYS221 4.5 17.5 1.0 N02 B:9O8407 4.6 66.4 0.4 H061 B:9O8407 4.6 80.7 0.4 N02 B:9O8407 4.6 66.4 0.5 C21 B:9O8407 4.6 65.9 0.5 HB3 B:SER197 4.7 17.8 1.0 C21 B:9O8407 4.7 66.1 0.4 CA B:HIS118 4.7 17.2 1.0 O20 B:9O8407 4.7 65.5 0.5 N01 B:9O8407 4.8 67.9 0.5 OD2 B:ASP120 4.8 22.9 1.0 CG B:ASP120 4.8 23.7 1.0 C03 B:9O8407 4.8 67.2 0.4 H061 B:9O8407 4.8 80.7 0.5 HE2 B:HIS118 4.8 26.5 1.0 HD1 B:HIS116 4.9 18.1 1.0 N01 B:9O8407 4.9 68.7 0.4 HD1 B:HIS196 4.9 19.4 1.0 HG2 B:ARG121 4.9 20.2 1.0 C03 B:9O8407 4.9 67.2 0.5 HD2 B:HIS118 4.9 19.6 1.0 O20 B:9O8407 4.9 65.7 0.4 C19 B:9O8407 4.9 66.5 0.5 N B:HIS118 5.0 14.0 1.0

Zinc binding site 5 out of 6 in the Vim-1_1DJ- 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 5 of Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.1 occ:1.00 OD2 B:ASP120 2.1 22.9 1.0 NE2 B:HIS263 2.1 20.0 1.0 SG B:CYS221 2.3 17.5 1.0 N02 B:9O8407 2.6 66.4 0.4 N02 B:9O8407 2.6 66.4 0.5 O B:OH404 2.8 20.9 1.0 HH21 B:ARG121 2.9 33.3 1.0 CE1 B:HIS263 3.0 21.7 1.0 CD2 B:HIS263 3.1 17.5 1.0 CG B:ASP120 3.1 23.7 1.0 H081 B:9O8407 3.2 81.0 0.4 H061 B:9O8407 3.2 80.7 0.4 HE1 B:HIS263 3.2 26.0 1.0 HB3 B:CYS221 3.2 17.5 1.0 HD2 B:HIS263 3.3 21.0 1.0 C03 B:9O8407 3.4 67.2 0.4 HE B:ARG121 3.4 21.8 1.0 CB B:CYS221 3.4 14.6 1.0 H081 B:9O8407 3.5 80.8 0.5 N01 B:9O8407 3.5 67.9 0.5 OD1 B:ASP120 3.5 20.1 1.0 HO B:OH404 3.5 25.1 1.0 C06 B:9O8407 3.6 67.3 0.4 C03 B:9O8407 3.6 67.2 0.5 N01 B:9O8407 3.6 68.7 0.4 N08 B:9O8407 3.7 67.5 0.4 NH2 B:ARG121 3.7 27.7 1.0 HE1 B:HIS116 3.8 18.9 1.0 H061 B:9O8407 3.8 80.7 0.5 HB2 B:CYS221 3.9 17.5 1.0 N08 B:9O8407 4.0 67.3 0.5 C06 B:9O8407 4.0 67.3 0.5 ZN B:ZN401 4.1 20.8 1.0 NE B:ARG121 4.2 18.2 1.0 ND1 B:HIS263 4.2 16.1 1.0 CG B:HIS263 4.2 17.1 1.0 HH22 B:ARG121 4.3 33.3 1.0 CB B:ASP120 4.4 23.3 1.0 O B:HOH563 4.4 20.4 1.0 HA B:CYS221 4.4 17.6 1.0 CZ B:ARG121 4.4 24.8 1.0 HB2 B:ASP120 4.5 27.9 1.0 HE1 B:HIS196 4.5 19.5 1.0 H062 B:9O8407 4.5 80.7 0.4 CE1 B:HIS116 4.5 15.7 1.0 CA B:CYS221 4.6 14.6 1.0 NE2 B:HIS196 4.6 15.8 1.0 N05 B:9O8407 4.6 70.4 0.5 HB3 B:ASP120 4.6 27.9 1.0 HA3 B:GLY262 4.6 18.5 1.0 C04 B:9O8407 4.6 66.4 0.4 CE1 B:HIS196 4.7 16.3 1.0 N05 B:9O8407 4.7 69.8 0.4 C04 B:9O8407 4.7 66.4 0.5 NE2 B:HIS116 4.8 14.0 1.0 HG2 B:ARG121 4.9 20.2 1.0 HD1 B:HIS263 4.9 19.4 1.0 H062 B:9O8407 5.0 80.7 0.5

Zinc binding site 6 out of 6 in the Vim-1_1DJ- 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 6 of Vim-1_1DJ- Triazole Inhibitors with Promising Inhibitor Effects Against Antibiotic Resistance Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:19.5 occ:1.00 NE2 B:HIS170 2.0 18.3 1.0 CL B:CL406 2.0 44.9 1.0 CL B:CL405 2.1 30.0 1.0 CE1 B:HIS170 2.9 21.2 1.0 HE1 B:HIS170 3.1 25.4 1.0 CD2 B:HIS170 3.1 15.1 1.0 HD2 B:HIS170 3.3 18.2 1.0 HB1 B:ALA135 3.6 22.9 1.0 HB2 B:ALA135 3.9 22.9 1.0 ND1 B:HIS170 4.1 17.7 1.0 CB B:ALA135 4.2 19.1 1.0 HG21 B:THR169 4.2 22.6 1.0 CG B:HIS170 4.2 14.9 1.0 HA B:ALA135 4.5 19.5 1.0 HG22 B:THR169 4.7 22.6 1.0 HD1 B:HIS170 4.8 21.3 1.0 CG2 B:THR169 4.9 18.8 1.0 HB3 B:ALA135 4.9 22.9 1.0 CA B:ALA135 5.0 16.2 1.0

H.-K.S.Leiros, H.-K.S.Leiros. N/A N/A.