Zinc in PDB 5acs: Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1

The structure of Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acs was solved by S.Skagseth, T.J.Carlsen, G.E.K.Bjerga, J.Spencer, O.Samuelsen, H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.91 / 1.46
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.434, 131.222, 40.842, 90.00, 94.83, 90.00
R / Rfree (%)	12.8 / 16.7

The binding sites of Zinc atom in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 (pdb code 5acs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1297 b:21.4 occ:1.00 ND1 A:HIS118 2.0 19.9 1.0 NE2 A:HIS196 2.0 14.9 1.0 NE2 A:HIS116 2.1 14.8 1.0 O A:HOH2103 2.1 21.7 1.0 HB2 A:HIS118 2.9 17.6 1.0 O A:HOH2107 2.9 32.6 1.0 CE1 A:HIS116 3.0 15.1 1.0 CE1 A:HIS118 3.0 20.8 1.0 CD2 A:HIS196 3.0 13.0 1.0 CG A:HIS118 3.0 16.6 1.0 CE1 A:HIS196 3.0 15.6 1.0 CD2 A:HIS116 3.1 12.4 1.0 HE1 A:HIS116 3.1 18.1 1.0 HE1 A:HIS118 3.1 24.9 1.0 HD2 A:HIS196 3.2 15.6 1.0 HE1 A:HIS196 3.2 18.8 1.0 HD2 A:HIS116 3.3 14.9 1.0 CB A:HIS118 3.4 14.7 1.0 O A:HOH2111 3.5 26.9 1.0 HB3 A:HIS118 3.5 17.6 1.0 HG21 A:THR197 3.7 18.1 1.0 HG22 A:THR197 3.9 18.1 1.0 HB2 A:CYS221 3.9 15.8 1.0 OD1 A:ASP120 4.1 19.1 1.0 ZN A:ZN1298 4.1 19.5 1.0 NE2 A:HIS118 4.1 21.9 1.0 ND1 A:HIS116 4.1 12.2 1.0 CD2 A:HIS118 4.1 19.6 1.0 ND1 A:HIS196 4.1 14.6 1.0 CG A:HIS196 4.1 11.8 1.0 CG A:HIS116 4.2 11.0 1.0 CG2 A:THR197 4.3 15.1 1.0 HB3 A:CYS221 4.3 15.8 1.0 HG2 B:GLU62 4.4 56.8 0.7 CB A:CYS221 4.4 13.1 1.0 O A:HOH2064 4.5 28.7 1.0 H A:HIS118 4.6 15.4 1.0 SG A:CYS221 4.6 13.5 1.0 HG23 A:THR197 4.6 18.1 1.0 HB3 B:GLU62 4.6 55.9 0.7 HG2 A:ARG121 4.8 10.5 1.0 CA A:HIS118 4.8 13.6 1.0 HD1 A:HIS116 4.8 14.6 1.0 HE2 A:HIS118 4.9 26.2 1.0 CG A:ASP120 4.9 14.8 1.0 OD2 A:ASP120 4.9 15.1 1.0 HD1 A:HIS196 4.9 17.5 1.0 HD2 A:HIS118 5.0 23.5 1.0

Zinc binding site 2 out of 4 in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1298 b:19.5 occ:1.00 OD2 A:ASP120 2.0 15.1 1.0 NE2 A:HIS263 2.1 13.6 1.0 O A:HOH2111 2.1 26.9 1.0 O A:HOH2103 2.2 21.7 1.0 SG A:CYS221 2.2 13.5 1.0 CG A:ASP120 3.0 14.8 1.0 CE1 A:HIS263 3.0 13.5 1.0 CD2 A:HIS263 3.0 14.9 1.0 HB3 A:CYS221 3.2 15.8 1.0 HD2 A:HIS263 3.2 17.9 1.0 HE1 A:HIS263 3.2 16.2 1.0 HH21 A:ARG121 3.3 15.2 1.0 CB A:CYS221 3.3 13.1 1.0 OD1 A:ASP120 3.4 19.1 1.0 HE A:ARG121 3.4 13.8 1.0 HB3 B:GLU62 3.5 55.9 0.7 HE1 A:HIS116 3.6 18.1 1.0 HB2 A:CYS221 3.8 15.8 1.0 NH2 A:ARG121 3.9 12.7 1.0 NE A:ARG121 4.0 11.5 1.0 ZN A:ZN1297 4.1 21.4 1.0 ND1 A:HIS263 4.1 13.4 1.0 CG A:HIS263 4.2 14.4 1.0 CZ A:ARG121 4.3 11.7 1.0 O A:HOH2107 4.3 32.6 1.0 CB A:ASP120 4.3 14.2 1.0 HA3 A:GLY262 4.3 13.3 1.0 CE1 A:HIS116 4.4 15.1 1.0 HH22 A:ARG121 4.4 15.2 1.0 HB2 A:ASP120 4.4 17.0 1.0 H B:GLY63 4.5 43.3 0.7 CB B:GLU62 4.5 46.5 0.7 HA A:CYS221 4.6 13.5 1.0 CA A:CYS221 4.6 11.2 1.0 NE2 A:HIS196 4.6 14.9 1.0 HA2 B:GLY63 4.6 41.5 1.0 HB3 A:ASP120 4.6 17.0 1.0 N B:GLY63 4.7 36.1 1.0 HB2 B:GLU62 4.7 55.9 0.7 HG2 A:ARG121 4.7 10.5 1.0 NE2 A:HIS116 4.7 14.8 1.0 O A:HOH2207 4.8 26.9 1.0 HE1 A:HIS196 4.8 18.8 1.0 HD1 A:HIS263 4.9 16.1 1.0 HG2 B:GLU62 4.9 56.8 0.7 HD2 A:ARG121 4.9 13.2 1.0 CE1 A:HIS196 4.9 15.6 1.0 CD A:ARG121 5.0 11.0 1.0 O A:HOH2190 5.0 19.2 1.0

Zinc binding site 3 out of 4 in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1296 b:22.5 occ:1.00 NE2 B:HIS196 2.0 18.0 1.0 ND1 B:HIS118 2.0 17.7 1.0 NE2 B:HIS116 2.0 16.8 1.0 O B:HOH2075 2.0 18.8 1.0 CE1 B:HIS116 2.9 16.1 1.0 HB2 B:HIS118 2.9 19.8 1.0 CD2 B:HIS196 2.9 16.9 1.0 CE1 B:HIS118 3.0 19.0 1.0 CG B:HIS118 3.0 18.6 1.0 CE1 B:HIS196 3.0 18.4 1.0 O A:HOH2037 3.0 25.9 1.0 HE1 B:HIS116 3.1 19.3 1.0 CD2 B:HIS116 3.1 13.5 1.0 HD2 B:HIS196 3.1 20.3 1.0 HE1 B:HIS118 3.1 22.8 1.0 HE1 B:HIS196 3.3 22.1 1.0 HD2 B:HIS116 3.3 16.2 1.0 CB B:HIS118 3.4 16.5 1.0 HB3 B:HIS118 3.6 19.8 1.0 HB2 B:CYS221 3.7 17.9 1.0 HG21 B:THR197 3.8 17.9 1.0 ZN B:ZN1297 3.8 23.7 1.0 HG22 B:THR197 3.9 17.9 1.0 OD1 B:ASP120 4.0 19.7 1.0 ND1 B:HIS116 4.0 12.4 1.0 NE2 B:HIS118 4.1 20.2 1.0 HB3 B:CYS221 4.1 17.9 1.0 CG B:HIS196 4.1 16.2 1.0 CD2 B:HIS118 4.1 19.3 1.0 ND1 B:HIS196 4.1 17.5 1.0 CG B:HIS116 4.2 11.9 1.0 CB B:CYS221 4.2 14.9 1.0 CG2 B:THR197 4.3 15.0 1.0 HB3 A:GLU62 4.3 51.1 1.0 SG B:CYS221 4.3 16.7 1.0 H B:HIS118 4.6 16.1 1.0 HG2 B:ARG121 4.6 16.5 1.0 HG23 B:THR197 4.6 17.9 1.0 O A:HOH2036 4.7 28.3 1.0 OD2 B:ASP120 4.7 16.2 1.0 CG B:ASP120 4.8 16.7 1.0 HD1 B:HIS116 4.8 14.8 1.0 CA B:HIS118 4.8 13.7 1.0 HE2 B:HIS118 4.8 24.2 1.0 HD1 B:HIS196 4.9 21.0 1.0 HG3 B:ARG121 4.9 16.5 1.0 HD2 B:HIS118 5.0 23.1 1.0

Zinc binding site 4 out of 4 in the Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Y233A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1297 b:23.7 occ:1.00 OD2 B:ASP120 2.0 16.2 1.0 O B:HOH2075 2.1 18.8 1.0 NE2 B:HIS263 2.1 16.9 1.0 SG B:CYS221 2.2 16.7 1.0 CG B:ASP120 3.0 16.7 1.0 CD2 B:HIS263 3.0 17.9 1.0 CE1 B:HIS263 3.1 15.9 1.0 HB3 B:CYS221 3.2 17.9 1.0 HD2 B:HIS263 3.2 21.4 1.0 CB B:CYS221 3.3 14.9 1.0 HE1 B:HIS263 3.3 19.1 1.0 HE B:ARG121 3.3 15.8 1.0 HH21 B:ARG121 3.3 20.5 1.0 OD1 B:ASP120 3.4 19.7 1.0 HE1 B:HIS116 3.6 19.3 1.0 HB2 B:CYS221 3.7 17.9 1.0 HB3 A:GLU62 3.8 51.1 1.0 ZN B:ZN1296 3.8 22.5 1.0 NE B:ARG121 3.8 13.2 1.0 NH2 B:ARG121 3.8 17.1 1.0 CZ B:ARG121 4.2 14.7 1.0 ND1 B:HIS263 4.2 14.0 1.0 CG B:HIS263 4.2 16.5 1.0 HA2 A:GLY63 4.2 51.9 1.0 O A:HOH2037 4.2 25.9 1.0 H A:GLY63 4.3 52.7 1.0 CE1 B:HIS116 4.3 16.1 1.0 CB B:ASP120 4.3 15.0 1.0 HA3 B:GLY262 4.3 15.6 1.0 HB2 B:ASP120 4.4 18.0 1.0 HH22 B:ARG121 4.4 20.5 1.0 N A:GLY63 4.5 43.9 1.0 NE2 B:HIS196 4.5 18.0 1.0 HG2 B:ARG121 4.5 16.5 1.0 NE2 B:HIS116 4.5 16.8 1.0 HA B:CYS221 4.6 16.5 1.0 CA B:CYS221 4.6 13.8 1.0 CB A:GLU62 4.6 42.6 1.0 HB2 A:GLU62 4.6 51.1 1.0 HD2 B:ARG121 4.7 16.3 1.0 HB3 B:ASP120 4.7 18.0 1.0 HE1 B:HIS196 4.8 22.1 1.0 CD B:ARG121 4.8 13.6 1.0 CA A:GLY63 4.8 43.2 1.0 CE1 B:HIS196 4.9 18.4 1.0 O A:HOH2038 4.9 32.7 1.0 C A:GLU62 4.9 43.8 1.0 O B:HOH2158 4.9 22.4 1.0 HA3 A:GLY63 4.9 51.9 1.0 HD1 B:HIS263 5.0 16.8 1.0

S.Skagseth, T.J.Carlsen, G.E.K.Bjerga, J.Spencer, O.Samuelsen, H.S.Leiros. Role of Residues W228 and Y233 in the Structure and Activity of Metallo-Beta-Lactamase Gim-1. Antimicrob.Agents Chemother. V. 60 990 2015.
ISSN: ISSN 0066-4804
PubMed: 26643332
DOI: 10.1128/AAC.02017-15