Zinc in PDB 5mm9: Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding

The structure of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5mm9 was solved by S.Skagseth, S.Akhter, M.H.Paulsen, O.Samuelsen, Z.Muhammad, H.-K.S.Leiros, A.Bayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.109, 79.070, 67.471, 90.00, 130.26, 90.00
R / Rfree (%)	15.7 / 20.1

The structure of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding (pdb code 5mm9). 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-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5mm9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:10.7 occ:0.89 HAK1 A:8SH404 1.9 23.8 1.0 ND1 A:HIS118 2.0 12.4 1.0 NE2 A:HIS196 2.0 11.8 1.0 NE2 A:HIS116 2.1 11.2 1.0 SAK A:8SH404 2.3 19.8 1.0 CE1 A:HIS118 2.9 14.2 1.0 HB2 A:HIS118 2.9 16.3 1.0 CE1 A:HIS196 2.9 10.9 1.0 HAJ1 A:8SH404 3.0 25.7 1.0 CD2 A:HIS196 3.0 12.4 1.0 CG A:HIS118 3.0 11.2 1.0 CE1 A:HIS116 3.0 10.4 1.0 HE1 A:HIS118 3.1 17.1 1.0 CD2 A:HIS116 3.1 11.5 1.0 HE1 A:HIS196 3.1 13.1 1.0 CAJ A:8SH404 3.2 21.4 1.0 HE1 A:HIS116 3.2 12.5 1.0 HD2 A:HIS196 3.2 14.8 1.0 HD2 A:HIS116 3.3 13.8 1.0 CB A:HIS118 3.4 13.6 1.0 HAJ2 A:8SH404 3.6 25.7 1.0 HB3 A:HIS118 3.7 16.3 1.0 ZN A:ZN402 3.7 13.3 0.8 HB2 A:CYS221 3.7 11.6 1.0 OD1 A:ASP120 3.9 13.9 1.0 HB3 A:CYS221 4.0 11.6 1.0 NE2 A:HIS118 4.0 13.7 1.0 ND1 A:HIS196 4.1 15.0 1.0 CD2 A:HIS118 4.1 13.5 1.0 CG A:HIS196 4.1 14.1 1.0 ND1 A:HIS116 4.1 11.4 1.0 CB A:CYS221 4.2 9.7 1.0 CG A:HIS116 4.2 9.2 1.0 SG A:CYS221 4.3 14.3 1.0 HAI1 A:8SH404 4.5 43.9 1.0 CAI A:8SH404 4.5 36.5 1.0 H A:HIS118 4.5 13.9 1.0 OD2 A:ASP120 4.6 14.2 1.0 HD22 A:ASN233 4.6 38.1 1.0 CG A:ASP120 4.7 11.2 1.0 HG2 A:ARG121 4.7 13.1 1.0 CA A:HIS118 4.8 11.7 1.0 HB3 A:SER197 4.8 13.8 1.0 HAL2 A:8SH404 4.9 24.3 1.0 HD2 A:HIS118 5.0 16.2 1.0 HG3 A:ARG121 5.0 13.1 1.0

Zinc binding site 2 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.3 occ:0.78 HAK1 A:8SH404 1.9 23.8 1.0 OD2 A:ASP120 2.0 14.2 1.0 SAK A:8SH404 2.1 19.8 1.0 NE2 A:HIS263 2.1 12.0 1.0 SG A:CYS221 2.2 14.3 1.0 HAL2 A:8SH404 2.6 24.3 1.0 CD2 A:HIS263 3.0 14.0 1.0 CG A:ASP120 3.0 11.2 1.0 CE1 A:HIS263 3.1 13.6 1.0 HD2 A:HIS263 3.2 16.8 1.0 HB3 A:CYS221 3.2 11.6 1.0 HH21 A:ARG121 3.2 20.8 1.0 CB A:CYS221 3.3 9.7 1.0 HE1 A:HIS263 3.4 16.3 1.0 HE A:ARG121 3.4 14.7 1.0 OD1 A:ASP120 3.5 13.9 1.0 CAJ A:8SH404 3.5 21.4 1.0 HE1 A:HIS116 3.6 12.5 1.0 HAJ2 A:8SH404 3.6 25.7 1.0 CAL A:8SH404 3.6 20.3 1.0 HAN1 A:8SH404 3.6 33.3 1.0 ZN A:ZN401 3.7 10.7 0.9 HB2 A:CYS221 3.7 11.6 1.0 NH2 A:ARG121 3.9 17.3 1.0 NE A:ARG121 3.9 12.2 1.0 CAI A:8SH404 4.0 36.5 1.0 HAI1 A:8SH404 4.1 43.9 1.0 HAL1 A:8SH404 4.2 24.3 1.0 CG A:HIS263 4.2 14.5 1.0 ND1 A:HIS263 4.2 12.5 1.0 CE1 A:HIS116 4.3 10.4 1.0 CZ A:ARG121 4.3 12.4 1.0 HAJ1 A:8SH404 4.3 25.7 1.0 CB A:ASP120 4.3 13.6 1.0 HB2 A:ASP120 4.4 16.3 1.0 NE2 A:HIS116 4.4 11.2 1.0 HA3 A:GLY262 4.4 14.1 1.0 HH22 A:ARG121 4.4 20.8 1.0 CAN A:8SH404 4.5 27.8 1.0 NE2 A:HIS196 4.6 11.8 1.0 HA A:CYS221 4.6 14.9 1.0 CA A:CYS221 4.6 12.4 1.0 CAM A:8SH404 4.6 33.3 1.0 O A:HOH590 4.6 18.2 1.0 HB3 A:ASP120 4.6 16.3 1.0 HE1 A:HIS196 4.6 13.1 1.0 HG2 A:ARG121 4.7 13.1 1.0 CE1 A:HIS196 4.8 10.9 1.0 HAN2 A:8SH404 4.8 33.3 1.0 HAM2 A:8SH404 4.8 39.9 1.0 CD A:ARG121 5.0 13.1 1.0 O A:HOH677 5.0 13.9 1.0

Zinc binding site 3 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.5 occ:0.76 ND1 A:HIS285 2.1 11.8 1.0 O A:HOH703 2.3 11.4 1.0 O A:HOH517 2.4 17.8 1.0 CE1 A:HIS285 3.0 18.1 1.0 HE1 A:HIS285 3.1 21.7 1.0 CG A:HIS285 3.2 13.1 1.0 HA A:HIS285 3.2 13.3 1.0 HB2 A:HIS285 3.3 15.5 1.0 CB A:HIS285 3.6 12.9 1.0 CA A:HIS285 3.9 11.1 1.0 HD22 A:ASN288 4.0 22.2 0.4 NE2 A:HIS285 4.1 13.6 1.0 HD22 A:LEU226 4.2 20.2 1.0 HB2 A:ASN288 4.2 18.9 0.6 CD2 A:HIS285 4.3 12.3 1.0 HB3 A:ASN288 4.3 16.8 0.4 HG23 A:VAL289 4.3 20.4 1.0 O A:HIS285 4.4 12.9 1.0 HG22 A:THR229 4.5 22.2 1.0 OD1 A:ASN288 4.5 21.9 0.6 HB3 A:HIS285 4.6 15.5 1.0 C A:HIS285 4.6 14.9 1.0 HD23 A:LEU226 4.7 20.2 1.0 HA A:LEU226 4.7 18.7 1.0 ND2 A:ASN288 4.8 18.5 0.4 O A:LEU226 4.9 20.6 1.0 CD2 A:LEU226 4.9 16.8 1.0 HB3 A:ASN288 4.9 18.9 0.6 CB A:ASN288 4.9 15.7 0.6

Zinc binding site 4 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:13.2 occ:1.00 ND1 B:HIS118 1.9 13.1 1.0 HAK1 B:8SH405 1.9 19.6 1.0 NE2 B:HIS116 2.1 10.8 1.0 NE2 B:HIS196 2.1 10.0 1.0 SAK B:8SH405 2.3 16.3 1.0 CE1 B:HIS118 2.9 16.4 1.0 HB2 B:HIS118 2.9 16.1 1.0 CG B:HIS118 2.9 15.1 1.0 CE1 B:HIS196 3.0 14.2 1.0 CE1 B:HIS116 3.0 12.1 1.0 CD2 B:HIS116 3.0 9.2 1.0 HE1 B:HIS118 3.0 19.6 1.0 CD2 B:HIS196 3.1 15.0 1.0 HAJ1 B:8SH405 3.1 28.9 1.0 HE1 B:HIS196 3.2 17.1 1.0 HD2 B:HIS116 3.2 11.0 1.0 HE1 B:HIS116 3.2 14.6 1.0 CAJ B:8SH405 3.3 24.1 1.0 HD2 B:HIS196 3.3 18.0 1.0 CB B:HIS118 3.3 13.4 1.0 HB3 B:HIS118 3.6 16.1 1.0 HAJ2 B:8SH405 3.7 28.9 1.0 HB2 B:CYS221 3.7 16.1 1.0 ZN B:ZN402 3.8 14.1 0.9 OD1 B:ASP120 3.9 13.0 1.0 HB3 B:CYS221 4.0 16.1 1.0 NE2 B:HIS118 4.0 16.4 1.0 CD2 B:HIS118 4.0 15.2 1.0 ND1 B:HIS116 4.1 9.4 1.0 ND1 B:HIS196 4.1 13.8 1.0 CB B:CYS221 4.2 13.4 1.0 CG B:HIS116 4.2 8.3 1.0 CG B:HIS196 4.2 16.2 1.0 SG B:CYS221 4.4 12.9 1.0 H B:HIS118 4.5 13.5 1.0 CAI B:8SH405 4.6 23.1 1.0 HAI1 B:8SH405 4.6 27.8 1.0 OD2 B:ASP120 4.6 14.3 1.0 CG B:ASP120 4.7 12.6 1.0 HD22 B:ASN233 4.7 36.6 1.0 HG2 B:ARG121 4.7 15.8 1.0 HB3 B:ASN233 4.8 21.7 1.0 CA B:HIS118 4.8 11.8 1.0 HD2 B:HIS118 4.9 18.2 1.0 HG3 B:ARG121 4.9 15.8 1.0

Zinc binding site 5 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:14.1 occ:0.89 HAK1 B:8SH405 1.9 19.6 1.0 OD2 B:ASP120 2.0 14.3 1.0 NE2 B:HIS263 2.1 17.2 1.0 SG B:CYS221 2.2 12.9 1.0 SAK B:8SH405 2.3 16.3 1.0 HAL2 B:8SH405 2.7 26.2 1.0 CG B:ASP120 3.0 12.6 1.0 CD2 B:HIS263 3.0 12.1 1.0 HH21 B:ARG121 3.1 22.3 1.0 CE1 B:HIS263 3.1 17.1 1.0 HD2 B:HIS263 3.2 14.6 1.0 HB3 B:CYS221 3.3 16.1 1.0 HE1 B:HIS263 3.3 20.5 1.0 HE B:ARG121 3.3 17.8 1.0 CB B:CYS221 3.4 13.4 1.0 HAJ2 B:8SH405 3.4 28.9 1.0 OD1 B:ASP120 3.4 13.0 1.0 CAJ B:8SH405 3.5 24.1 1.0 HE1 B:HIS116 3.5 14.6 1.0 CAL B:8SH405 3.7 21.9 1.0 NH2 B:ARG121 3.7 18.6 1.0 HAN1 B:8SH405 3.7 24.6 1.0 ZN B:ZN401 3.8 13.2 1.0 HB2 B:CYS221 3.8 16.1 1.0 NE B:ARG121 3.9 14.9 1.0 CAI B:8SH405 4.1 23.1 1.0 ND1 B:HIS263 4.2 11.8 1.0 CZ B:ARG121 4.2 17.5 1.0 HAL1 B:8SH405 4.2 26.2 1.0 CG B:HIS263 4.2 12.3 1.0 CE1 B:HIS116 4.2 12.1 1.0 HH22 B:ARG121 4.2 22.3 1.0 HAI1 B:8SH405 4.3 27.8 1.0 CB B:ASP120 4.3 16.6 1.0 HB2 B:ASP120 4.3 19.9 1.0 HAJ1 B:8SH405 4.4 28.9 1.0 HA3 B:GLY262 4.4 14.5 1.0 NE2 B:HIS116 4.4 10.8 1.0 HAN2 B:8SH405 4.5 24.6 1.0 CAN B:8SH405 4.5 20.5 1.0 HB3 B:ASP120 4.5 19.9 1.0 HA B:CYS221 4.6 12.9 1.0 O B:HOH647 4.6 15.5 1.0 HG2 B:ARG121 4.6 15.8 1.0 CA B:CYS221 4.6 10.7 1.0 NE2 B:HIS196 4.7 10.0 1.0 CAM B:8SH405 4.7 27.5 1.0 HE1 B:HIS196 4.8 17.1 1.0 CE1 B:HIS196 4.9 14.2 1.0 CD B:ARG121 5.0 11.6 1.0

Zinc binding site 6 out of 6 in the Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vim-2_2B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn404 b:15.9 occ:1.00 ND1 B:HIS285 2.1 11.0 1.0 O B:HOH708 2.3 10.6 1.0 O B:HOH701 2.3 6.6 1.0 CE1 B:HIS285 2.9 13.5 1.0 HE1 B:HIS285 3.0 16.2 1.0 CG B:HIS285 3.2 13.0 1.0 HB2 B:HIS285 3.3 16.4 1.0 HA B:HIS285 3.3 17.0 1.0 CB B:HIS285 3.6 13.7 1.0 CA B:HIS285 3.9 14.2 1.0 HD22 B:ASN288 3.9 26.6 1.0 HG22 B:THR229 4.1 19.9 1.0 NE2 B:HIS285 4.1 13.2 1.0 HB2 B:ASN288 4.2 16.6 1.0 CD2 B:HIS285 4.2 13.7 1.0 O B:HIS285 4.3 13.2 1.0 HG23 B:VAL289 4.3 19.7 1.0 HD22 B:LEU226 4.4 17.5 1.0 C B:HIS285 4.5 15.7 1.0 HB3 B:HIS285 4.5 16.4 1.0 ND2 B:ASN288 4.8 22.2 1.0 HD23 B:LEU226 4.9 17.5 1.0 HA B:LEU226 4.9 18.1 1.0 HG22 B:VAL289 4.9 19.7 1.0 HB3 B:ASN288 5.0 16.6 1.0 CB B:ASN288 5.0 13.9 1.0 CG2 B:VAL289 5.0 16.4 1.0

S.Skagseth, S.Akhter, M.H.Paulsen, Z.Muhammad, S.Lauksund, H.S.Leiros, A.Bayer. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding. Eur J Med Chem V. 135 159 2017.
ISSN: ISSN 1768-3254
PubMed: 28445786
DOI: 10.1016/J.EJMECH.2017.04.035