Zinc in PDB 5nhz: Vim-2_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding

The structure of Vim-2_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5nhz was solved by S.Skagseth, S.Akhter, M.H.Paulsen, O.Samuelsen, Z.Muhammad, K.-K.S.Leiros, A.Bayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.75 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.779, 90.872, 124.075, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.4

The structure of Vim-2_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Vim-2_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding (pdb code 5nhz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Vim-2_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5nhz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Vim-2_10B. 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_10B. 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:30.3 occ:1.00 ND1 A:HIS118 2.0 27.8 1.0 NE2 A:HIS116 2.0 24.1 1.0 NE2 A:HIS196 2.0 26.7 1.0 HAE A:8XZ403 2.8 69.2 0.6 HB2 A:HIS118 2.8 30.9 1.0 CE1 A:HIS118 2.9 29.0 1.0 CE1 A:HIS116 3.0 22.5 1.0 CD2 A:HIS196 3.0 23.8 1.0 CG A:HIS118 3.0 27.6 1.0 CD2 A:HIS116 3.0 22.8 1.0 CE1 A:HIS196 3.1 26.7 1.0 HE1 A:HIS118 3.1 34.8 1.0 HD2 A:HIS196 3.1 28.5 1.0 HE1 A:HIS116 3.2 27.0 1.0 SAD A:8XZ403 3.2 42.8 1.0 HD2 A:HIS116 3.2 27.4 1.0 HE1 A:HIS196 3.3 32.0 1.0 CB A:HIS118 3.3 25.8 1.0 CAE A:8XZ403 3.4 57.7 0.6 HB3 A:HIS118 3.6 30.9 1.0 HAF A:8XZ403 3.8 69.2 0.6 NE2 A:HIS118 4.0 31.4 1.0 ND1 A:HIS116 4.1 22.2 1.0 CD2 A:HIS118 4.1 30.4 1.0 CG A:HIS116 4.1 21.3 1.0 HB2 A:CYS221 4.1 31.5 1.0 CG A:HIS196 4.1 24.3 1.0 ND1 A:HIS196 4.1 27.0 1.0 CAB A:8XZ403 4.2 58.7 1.0 OD1 A:ASP120 4.2 28.4 1.0 HD21 A:ASN233 4.3 57.0 0.5 H A:HIS118 4.4 29.1 1.0 OAC A:8XZ403 4.4 55.8 1.0 HB3 A:CYS221 4.5 31.5 1.0 ZN A:ZN402 4.5 25.1 0.6 O A:HOH505 4.5 71.1 1.0 CB A:CYS221 4.6 26.3 1.0 HB3 A:SER197 4.6 30.1 1.0 CAF A:8XZ403 4.6 54.3 1.0 HAG A:8XZ403 4.7 65.2 1.0 SG A:CYS221 4.7 29.9 1.0 CA A:HIS118 4.7 26.0 1.0 ND2 A:ASN233 4.8 47.5 1.0 O A:HOH555 4.9 36.7 1.0 HD22 A:ASN233 4.9 57.0 0.5 OD2 A:ASP120 4.9 30.6 1.0 HD2 A:HIS118 4.9 36.4 1.0 N A:HIS118 5.0 24.2 1.0

Zinc binding site 2 out of 5 in the Vim-2_10B. 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_10B. 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:25.1 occ:0.56 OAC A:8XZ403 1.7 55.8 1.0 OD2 A:ASP120 1.9 30.6 1.0 NE2 A:HIS263 2.1 32.5 1.0 SG A:CYS221 2.2 29.9 1.0 HAF A:8XZ403 2.6 69.2 0.6 CAB A:8XZ403 2.7 58.7 1.0 HH21 A:ARG121 2.7 42.8 1.0 CE1 A:HIS263 2.9 30.8 1.0 HE1 A:HIS263 3.0 36.9 1.0 CG A:ASP120 3.1 29.4 1.0 CD2 A:HIS263 3.3 31.7 1.0 HE A:ARG121 3.4 35.3 1.0 CAE A:8XZ403 3.4 57.7 0.6 SAD A:8XZ403 3.4 42.8 1.0 HB3 A:CYS221 3.4 31.5 1.0 HAI A:8XZ403 3.4 56.8 0.6 CB A:CYS221 3.5 26.3 1.0 HD2 A:HIS263 3.5 38.0 1.0 NH2 A:ARG121 3.6 35.7 1.0 HE1 A:HIS116 3.6 27.0 1.0 OD1 A:ASP120 3.6 28.4 1.0 HAE A:8XZ403 3.9 69.2 0.6 HAM A:8XZ403 3.9 42.9 0.5 HB2 A:CYS221 4.0 31.5 1.0 CAA A:8XZ403 4.0 59.5 1.0 NE A:ARG121 4.1 29.4 1.0 HH22 A:ARG121 4.1 42.8 1.0 ND1 A:HIS263 4.1 27.4 1.0 HAB A:8XZ403 4.1 71.4 1.0 CAG A:8XZ403 4.3 47.3 0.6 CZ A:ARG121 4.3 32.7 1.0 CG A:HIS263 4.3 29.1 1.0 CB A:ASP120 4.3 29.0 1.0 HB2 A:ASP120 4.4 34.8 1.0 HAC A:8XZ403 4.4 71.4 1.0 O A:HOH614 4.4 38.0 1.0 HAJ A:8XZ403 4.4 47.6 0.8 HA A:CYS221 4.5 30.4 1.0 CE1 A:HIS116 4.5 22.5 1.0 CAF A:8XZ403 4.5 54.3 1.0 HA3 A:GLY262 4.5 29.9 1.0 ZN A:ZN401 4.5 30.3 1.0 HB3 A:ASP120 4.5 34.8 1.0 CA A:CYS221 4.6 25.3 1.0 HAA A:8XZ403 4.7 71.4 1.0 CAH A:8XZ403 4.7 39.7 0.8 CAI A:8XZ403 4.8 35.8 0.5 HG2 A:ARG121 4.8 32.1 1.0 HG A:SER69 4.9 28.4 1.0 NE2 A:HIS116 4.9 24.1 1.0 NE2 A:HIS196 4.9 26.7 1.0

Zinc binding site 3 out of 5 in the Vim-2_10B. 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_10B. 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:58.6 occ:0.57 HG1 B:THR136 2.1 30.7 1.0 H B:THR136 2.2 30.1 1.0 O B:HOH600 2.6 45.7 1.0 HG1 B:THR169 2.7 40.7 1.0 HA B:ALA135 2.8 32.0 1.0 OG1 B:THR136 2.9 25.6 1.0 N B:THR136 3.0 25.1 1.0 O B:VAL134 3.0 26.9 1.0 HG23 B:THR136 3.1 29.4 1.0 OG1 B:THR169 3.2 33.9 1.0 HE B:ARG129 3.2 52.5 1.0 HB2 B:ARG129 3.2 35.0 1.0 HB B:THR169 3.4 41.2 1.0 HG3 B:ARG129 3.5 43.1 1.0 CA B:ALA135 3.6 26.7 1.0 HA B:ARG129 3.7 30.9 1.0 CB B:THR136 3.7 22.7 1.0 O B:HOH519 3.7 49.7 1.0 C B:ALA135 3.7 26.3 1.0 CG2 B:THR136 3.8 24.5 1.0 CB B:THR169 3.8 34.3 1.0 CA B:THR136 3.9 23.6 1.0 HH21 B:ARG129 3.9 48.2 1.0 NE B:ARG129 4.0 43.8 1.0 CB B:ARG129 4.0 29.1 1.0 C B:VAL134 4.0 25.7 1.0 O B:HOH631 4.0 56.1 1.0 H B:THR169 4.1 34.7 1.0 HG21 B:THR136 4.1 29.4 1.0 CG B:ARG129 4.2 35.9 1.0 N B:ALA135 4.3 23.9 1.0 CA B:ARG129 4.3 25.7 1.0 HD2 B:HIS170 4.3 40.4 1.0 HG21 B:THR169 4.4 45.1 1.0 O B:THR136 4.5 27.2 1.0 NH2 B:ARG129 4.6 40.2 1.0 HB B:THR136 4.6 27.2 1.0 HG22 B:THR136 4.6 29.4 1.0 HA B:THR136 4.6 28.3 1.0 HB1 B:ALA135 4.6 32.2 1.0 CD B:ARG129 4.7 45.2 1.0 CB B:ALA135 4.7 26.9 1.0 O B:HOH563 4.7 48.9 1.0 CZ B:ARG129 4.7 41.8 1.0 CG2 B:THR169 4.7 37.6 1.0 C B:THR136 4.7 23.8 1.0 N B:THR169 4.8 28.9 1.0 HB3 B:ARG129 4.8 35.0 1.0 CD2 B:HIS170 4.9 33.7 1.0 O B:ALA135 4.9 27.1 1.0 CA B:THR169 4.9 32.7 1.0 HB2 B:ALA135 5.0 32.2 1.0 NE2 B:HIS170 5.0 34.3 1.0

Zinc binding site 4 out of 5 in the Vim-2_10B. 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_10B. 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:33.3 occ:1.00 ND1 B:HIS118 1.9 31.7 1.0 NE2 B:HIS116 2.1 30.0 1.0 NE2 B:HIS196 2.1 35.8 1.0 CE1 B:HIS118 2.8 34.2 1.0 HB2 B:HIS118 2.9 34.5 1.0 CG B:HIS118 2.9 31.6 1.0 CD2 B:HIS196 2.9 32.9 1.0 SAD B:8XZ407 3.0 45.4 1.0 HE1 B:HIS118 3.0 41.0 1.0 HD2 B:HIS196 3.0 39.4 1.0 CE1 B:HIS116 3.0 27.4 1.0 CD2 B:HIS116 3.1 29.6 1.0 HAE B:8XZ407 3.1 76.9 0.8 HE1 B:HIS116 3.2 32.8 1.0 CE1 B:HIS196 3.2 36.3 1.0 HD2 B:HIS116 3.3 35.5 1.0 CB B:HIS118 3.3 28.8 1.0 HE1 B:HIS196 3.5 43.6 1.0 CAE B:8XZ407 3.6 64.1 0.8 HB3 B:HIS118 3.7 34.5 1.0 NE2 B:HIS118 3.9 35.3 1.0 CD2 B:HIS118 4.0 35.1 1.0 CAB B:8XZ407 4.1 44.0 0.4 ND1 B:HIS116 4.1 26.4 1.0 HB2 B:CYS221 4.1 41.2 1.0 HD22 B:ASN233 4.1 85.2 0.7 CG B:HIS196 4.2 34.5 1.0 HAF B:8XZ407 4.2 76.9 0.8 OD1 B:ASP120 4.2 32.9 1.0 CG B:HIS116 4.2 27.4 1.0 ND1 B:HIS196 4.3 35.0 1.0 ZN B:ZN403 4.4 31.8 0.7 HB3 B:CYS221 4.4 41.2 1.0 H B:HIS118 4.4 34.6 1.0 OAC B:8XZ407 4.4 41.1 1.0 HB3 B:ASN233 4.5 86.4 1.0 HAG B:8XZ407 4.5 71.9 1.0 CB B:CYS221 4.5 34.3 1.0 CAF B:8XZ407 4.6 59.9 1.0 SG B:CYS221 4.6 34.8 1.0 CA B:HIS118 4.7 28.3 1.0 ND2 B:ASN233 4.7 71.0 1.0 HB3 B:SER197 4.7 42.9 1.0 O B:HOH565 4.9 0.6 1.0 HD2 B:HIS118 4.9 42.1 1.0 OD2 B:ASP120 4.9 36.0 1.0 N B:HIS118 4.9 28.9 1.0 CG B:ASP120 5.0 33.4 1.0 O B:ASN233 5.0 71.7 1.0

Zinc binding site 5 out of 5 in the Vim-2_10B. 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_10B. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:31.8 occ:0.70 OAC B:8XZ407 1.8 41.1 1.0 OD2 B:ASP120 2.0 36.0 1.0 SG B:CYS221 2.2 34.8 1.0 NE2 B:HIS263 2.3 36.2 1.0 HH21 B:ARG121 2.6 45.9 1.0 HAF B:8XZ407 2.6 76.9 0.8 CAB B:8XZ407 2.7 44.0 0.4 CE1 B:HIS263 3.2 37.2 1.0 CG B:ASP120 3.2 33.4 1.0 CAE B:8XZ407 3.2 64.1 0.8 SAD B:8XZ407 3.2 45.4 1.0 HE1 B:HIS263 3.3 44.6 1.0 HE B:ARG121 3.3 35.9 1.0 CD2 B:HIS263 3.3 35.5 1.0 HB3 B:CYS221 3.4 41.2 1.0 NH2 B:ARG121 3.4 38.3 1.0 CB B:CYS221 3.5 34.3 1.0 HAE B:8XZ407 3.5 76.9 0.8 HD2 B:HIS263 3.5 42.6 1.0 HE1 B:HIS116 3.5 32.8 1.0 OD1 B:ASP120 3.7 32.9 1.0 NE B:ARG121 4.0 29.9 1.0 HH22 B:ARG121 4.0 45.9 1.0 HB2 B:CYS221 4.0 41.2 1.0 HAM B:8XZ407 4.0 66.5 0.7 CAA B:8XZ407 4.1 44.6 1.0 HAI B:8XZ407 4.1 68.2 1.0 CZ B:ARG121 4.1 35.1 1.0 ND1 B:HIS263 4.3 37.3 1.0 HAA B:8XZ407 4.3 53.5 1.0 CB B:ASP120 4.3 29.2 1.0 CE1 B:HIS116 4.4 27.4 1.0 ZN B:ZN402 4.4 33.3 1.0 HB2 B:ASP120 4.4 35.0 1.0 CG B:HIS263 4.4 35.2 1.0 O B:HOH588 4.4 35.9 1.0 HA B:CYS221 4.4 39.2 1.0 HAB B:8XZ407 4.5 53.5 1.0 CAF B:8XZ407 4.6 59.9 1.0 HAJ B:8XZ407 4.6 66.2 1.0 HB3 B:ASP120 4.6 35.0 1.0 HA3 B:GLY262 4.6 30.3 1.0 CA B:CYS221 4.6 32.7 1.0 CAG B:8XZ407 4.7 56.9 1.0 HAC B:8XZ407 4.8 53.5 1.0 NE2 B:HIS116 4.8 30.0 1.0 HG2 B:ARG121 4.8 34.5 1.0 NE2 B:HIS196 4.8 35.8 1.0 CAI B:8XZ407 4.9 55.4 0.7 CAH B:8XZ407 5.0 55.2 1.0 HG B:SER69 5.0 30.1 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