Zinc in PDB 5lsc: The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor

The structure of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor, PDB code: 5lsc was solved by T.Christopeit, K.-W.Yang, S.-K.Yang, H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.26 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.624, 79.255, 67.200, 90.00, 130.50, 90.00
R / Rfree (%)	13.6 / 16.6

The structure of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Zinc atom in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor (pdb code 5lsc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor, PDB code: 5lsc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn405 b:9.2 occ:1.00 NE2 A:HIS116 2.0 9.1 1.0 ND1 A:HIS118 2.0 10.2 1.0 N03 A:752404 2.0 11.0 1.0 NE2 A:HIS196 2.1 9.3 1.0 HB2 A:HIS118 2.9 12.9 1.0 CE1 A:HIS116 3.0 8.9 1.0 N04 A:752404 3.0 10.1 1.0 CG A:HIS118 3.0 8.9 1.0 C02 A:752404 3.0 11.2 1.0 CD2 A:HIS116 3.0 7.0 1.0 CE1 A:HIS118 3.0 10.4 1.0 CE1 A:HIS196 3.1 10.2 1.0 CD2 A:HIS196 3.1 7.8 1.0 HE1 A:HIS116 3.1 10.7 1.0 HD2 A:HIS196 3.2 9.4 1.0 HD2 A:HIS116 3.2 8.4 1.0 HE1 A:HIS118 3.2 12.5 1.0 HE1 A:HIS196 3.2 12.3 1.0 CB A:HIS118 3.3 10.8 1.0 HB3 A:HIS118 3.4 12.9 1.0 OD1 A:ASP120 3.5 10.3 1.0 S15 A:752404 3.6 14.0 1.0 ZN A:ZN406 3.9 10.4 1.0 HB2 A:CYS221 4.0 8.6 1.0 ND1 A:HIS116 4.1 8.7 1.0 C05 A:752404 4.1 10.9 1.0 N01 A:752404 4.1 14.9 1.0 NE2 A:HIS118 4.1 11.3 1.0 CG A:HIS116 4.1 7.3 1.0 CD2 A:HIS118 4.1 10.3 1.0 ND1 A:HIS196 4.2 9.0 1.0 CG A:HIS196 4.2 8.1 1.0 HB3 A:CYS221 4.3 8.6 1.0 CG A:ASP120 4.3 11.2 1.0 OD2 A:ASP120 4.3 10.6 1.0 CB A:CYS221 4.4 7.2 1.0 SG A:CYS221 4.4 8.4 1.0 H A:HIS118 4.5 12.2 1.0 HG2 A:ARG121 4.6 12.2 1.0 O13 A:752404 4.7 9.9 1.0 CA A:HIS118 4.7 9.9 1.0 HB3 A:ASN233 4.8 25.2 1.0 HB3 A:SER197 4.8 12.6 1.0 HE A:ARG121 4.8 9.6 1.0 HD1 A:HIS116 4.8 10.4 1.0 HE2 A:HIS118 4.9 13.6 1.0 HD1 A:HIS196 4.9 10.8 1.0 HD2 A:HIS118 5.0 12.3 1.0

Zinc binding site 2 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn406 b:10.4 occ:1.00 N04 A:752404 2.0 10.1 1.0 NE2 A:HIS263 2.1 9.9 1.0 OD2 A:ASP120 2.2 10.6 1.0 SG A:CYS221 2.2 8.4 1.0 O13 A:752404 2.4 9.9 1.0 C05 A:752404 2.9 10.9 1.0 N03 A:752404 3.0 11.0 1.0 CD2 A:HIS263 3.1 8.5 1.0 CE1 A:HIS263 3.1 7.7 1.0 HH21 A:ARG121 3.1 16.4 1.0 HB3 A:CYS221 3.2 8.6 1.0 HD2 A:HIS263 3.2 10.2 1.0 C12 A:752404 3.2 12.0 1.0 CG A:ASP120 3.3 11.2 1.0 HE1 A:HIS263 3.3 9.2 1.0 CB A:CYS221 3.3 7.2 1.0 C06 A:752404 3.3 10.8 1.0 C11 A:752404 3.5 11.0 1.0 HE1 A:HIS116 3.6 10.7 1.0 HE A:ARG121 3.6 9.6 1.0 OD1 A:ASP120 3.7 10.3 1.0 HB2 A:CYS221 3.8 8.6 1.0 NH2 A:ARG121 3.9 13.7 1.0 ZN A:ZN405 3.9 9.2 1.0 HE1 A:HIS196 4.0 12.3 1.0 N01 A:752404 4.0 14.9 1.0 C02 A:752404 4.1 11.2 1.0 ND1 A:HIS263 4.2 8.0 1.0 CE1 A:HIS196 4.2 10.2 1.0 CG A:HIS263 4.2 9.3 1.0 NE2 A:HIS196 4.2 9.3 1.0 NE A:ARG121 4.3 8.0 1.0 C10 A:752404 4.3 12.2 1.0 HH22 A:ARG121 4.4 16.4 1.0 CE1 A:HIS116 4.4 8.9 1.0 HA A:CYS221 4.4 10.2 1.0 O14 A:752404 4.4 14.1 1.0 O A:HOH584 4.4 9.2 1.0 CB A:ASP120 4.5 12.1 1.0 HB2 A:ASP120 4.5 14.5 1.0 CA A:CYS221 4.5 8.5 1.0 CZ A:ARG121 4.6 11.8 1.0 C07 A:752404 4.6 12.5 1.0 HA3 A:GLY262 4.6 11.5 1.0 NE2 A:HIS116 4.6 9.1 1.0 HB3 A:ASP120 4.7 14.5 1.0 H101 A:752404 4.7 14.7 1.0 HD1 A:HIS263 5.0 9.6 1.0

Zinc binding site 3 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:13.4 occ:1.00 NE2 A:HIS170 2.1 13.8 1.0 CL A:CL402 2.2 24.1 1.0 CL A:CL401 2.2 21.6 1.0 CE1 A:HIS170 2.9 14.3 1.0 HE1 A:HIS170 2.9 17.2 1.0 CD2 A:HIS170 3.2 14.4 1.0 O A:HOH665 3.3 61.0 1.0 HD2 A:HIS170 3.5 17.3 1.0 HB1 A:ALA135 3.6 15.7 1.0 HB2 A:ALA135 3.7 15.7 1.0 ND1 A:HIS170 4.1 15.2 1.0 CB A:ALA135 4.1 13.1 1.0 CG A:HIS170 4.3 14.7 1.0 HA A:ALA135 4.5 13.0 1.0 O A:HOH543 4.5 20.5 1.0 HG21 A:THR169 4.5 17.6 1.0 HD1 A:HIS170 4.8 18.3 1.0 HG22 A:THR169 4.9 17.6 1.0 HB3 A:ALA135 4.9 15.7 1.0 CA A:ALA135 4.9 10.8 1.0 HH A:TYR137 5.0 20.7 1.0

Zinc binding site 4 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn405 b:10.3 occ:1.00 ND1 B:HIS118 2.0 10.1 1.0 N03 B:752404 2.0 13.4 1.0 NE2 B:HIS116 2.1 9.2 1.0 NE2 B:HIS196 2.1 10.2 1.0 HB2 B:HIS118 2.9 10.1 1.0 N04 B:752404 3.0 12.3 1.0 CG B:HIS118 3.0 8.9 1.0 CE1 B:HIS118 3.0 11.0 1.0 CE1 B:HIS116 3.0 10.2 1.0 CD2 B:HIS196 3.0 8.2 1.0 C02 B:752404 3.0 14.1 1.0 CD2 B:HIS116 3.0 9.3 1.0 CE1 B:HIS196 3.1 10.7 1.0 HD2 B:HIS196 3.2 9.8 1.0 HE1 B:HIS118 3.2 13.2 1.0 HE1 B:HIS116 3.2 12.2 1.0 HD2 B:HIS116 3.2 11.2 1.0 HE1 B:HIS196 3.3 12.8 1.0 CB B:HIS118 3.3 8.4 1.0 OD1 B:ASP120 3.5 11.7 1.0 HB3 B:HIS118 3.5 10.1 1.0 HD22 B:ASN233 3.6 27.6 0.2 S15 B:752404 3.7 16.0 1.0 ZN B:ZN406 3.9 10.6 1.0 HB2 B:CYS221 4.0 9.7 1.0 C05 B:752404 4.1 12.6 1.0 NE2 B:HIS118 4.1 11.4 1.0 ND1 B:HIS116 4.1 10.4 1.0 CD2 B:HIS118 4.1 11.0 1.0 CG B:HIS116 4.2 9.2 1.0 ND1 B:HIS196 4.2 9.4 1.0 N01 B:752404 4.2 14.4 1.0 CG B:HIS196 4.2 7.8 1.0 CG B:ASP120 4.3 10.8 1.0 HB3 B:CYS221 4.3 9.7 1.0 OD2 B:ASP120 4.3 10.9 1.0 ND2 B:ASN233 4.4 23.0 0.2 CB B:CYS221 4.5 8.1 1.0 SG B:CYS221 4.5 9.3 1.0 H B:HIS118 4.5 11.4 1.0 HD21 B:ASN233 4.5 27.6 0.2 HG2 B:ARG121 4.6 15.0 1.0 O14 B:752404 4.7 11.2 1.0 CA B:HIS118 4.7 10.4 1.0 HB3 B:ASN233 4.8 27.0 0.8 HE B:ARG121 4.8 13.2 1.0 HD1 B:HIS116 4.9 12.5 1.0 HE2 B:HIS118 4.9 13.6 1.0 HB3 B:SER197 4.9 9.8 1.0 HB3 B:ASN233 4.9 25.5 0.2 HD1 B:HIS196 5.0 11.2 1.0 HD2 B:HIS118 5.0 13.2 1.0

Zinc binding site 5 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn406 b:10.6 occ:1.00 NE2 B:HIS263 2.1 8.8 1.0 N04 B:752404 2.1 12.3 1.0 OD2 B:ASP120 2.1 10.9 1.0 SG B:CYS221 2.3 9.3 1.0 O14 B:752404 2.3 11.2 1.0 C05 B:752404 2.9 12.6 1.0 CD2 B:HIS263 3.0 8.2 1.0 HH21 B:ARG121 3.0 17.2 1.0 N03 B:752404 3.1 13.4 1.0 CE1 B:HIS263 3.1 7.5 1.0 HD2 B:HIS263 3.1 9.8 1.0 CG B:ASP120 3.2 10.8 1.0 HB3 B:CYS221 3.2 9.7 1.0 C12 B:752404 3.2 10.5 1.0 HE1 B:HIS263 3.3 9.0 1.0 C06 B:752404 3.3 12.7 1.0 CB B:CYS221 3.4 8.1 1.0 C11 B:752404 3.5 12.1 1.0 HE B:ARG121 3.6 13.2 1.0 OD1 B:ASP120 3.7 11.7 1.0 HE1 B:HIS116 3.7 12.2 1.0 NH2 B:ARG121 3.8 14.3 1.0 HB2 B:CYS221 3.9 9.7 1.0 ZN B:ZN405 3.9 10.3 1.0 HE1 B:HIS196 4.0 12.8 1.0 N01 B:752404 4.1 14.4 1.0 C02 B:752404 4.1 14.1 1.0 CG B:HIS263 4.2 9.3 1.0 ND1 B:HIS263 4.2 8.2 1.0 CE1 B:HIS196 4.2 10.7 1.0 NE2 B:HIS196 4.3 10.2 1.0 NE B:ARG121 4.3 11.0 1.0 HH22 B:ARG121 4.3 17.2 1.0 C10 B:752404 4.3 13.8 1.0 O13 B:752404 4.4 11.5 1.0 CB B:ASP120 4.4 11.9 1.0 O B:HOH596 4.4 9.9 1.0 CE1 B:HIS116 4.4 10.2 1.0 HA B:CYS221 4.4 8.8 1.0 HB2 B:ASP120 4.5 14.3 1.0 CZ B:ARG121 4.5 12.3 1.0 C07 B:752404 4.5 13.0 1.0 CA B:CYS221 4.6 7.3 1.0 HB3 B:ASP120 4.6 14.3 1.0 HA3 B:GLY262 4.6 13.2 1.0 NE2 B:HIS116 4.7 9.2 1.0 H101 B:752404 4.7 16.6 1.0 H071 B:752404 5.0 15.6 1.0 HD1 B:HIS263 5.0 9.8 1.0

Zinc binding site 6 out of 6 in the The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn407 b:10.3 occ:0.92 NE2 B:HIS170 2.0 12.6 1.0 CL B:CL402 2.1 27.1 1.0 CL B:CL401 2.2 16.3 1.0 O B:HOH527 2.8 60.4 1.0 CE1 B:HIS170 2.9 14.6 1.0 CD2 B:HIS170 3.1 11.5 1.0 HE1 B:HIS170 3.1 17.5 1.0 HD2 B:HIS170 3.3 13.8 1.0 HB1 B:ALA135 3.6 14.4 1.0 HB2 B:ALA135 3.9 14.4 1.0 ND1 B:HIS170 4.1 12.2 1.0 HG21 B:THR169 4.1 17.1 1.0 CG B:HIS170 4.2 11.3 1.0 CB B:ALA135 4.2 12.0 1.0 O B:HOH536 4.5 25.2 1.0 HG22 B:THR169 4.6 17.1 1.0 HA B:ALA135 4.6 13.7 1.0 CG2 B:THR169 4.8 14.2 1.0 HD1 B:HIS170 4.9 14.7 1.0 HH B:TYR137 4.9 25.6 1.0 HB3 B:ALA135 5.0 14.4 1.0

T.Christopeit, K.W.Yang, S.K.Yang, H.K.Leiros. The Structure of the Metallo-Beta-Lactamase Vim-2 in Complex with A Triazolylthioacetamide Inhibitor. Acta Crystallogr F Struct V. 72 813 2016BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 27834790
DOI: 10.1107/S2053230X16016113