Zinc in PDB 5acq: W228A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1

The structure of W228A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acq 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)	25.00 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.549, 131.796, 40.581, 90.00, 95.51, 90.00
R / Rfree (%)	18.8 / 22.7

The binding sites of Zinc atom in the W228A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 (pdb code 5acq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the W228A-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the W228A-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 W228A-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:Zn1296 b:35.9 occ:0.30 OD2 A:OCS221 1.6 54.7 0.5 HE2 A:HIS263 1.6 35.8 0.5 SG A:OCS221 2.0 47.6 1.0 OD3 A:OCS221 2.0 42.2 0.5 OD2 A:ASP120 2.1 36.9 1.0 O A:HOH2077 2.3 29.4 1.0 NE2 A:HIS263 2.5 29.8 0.5 OD1 A:OCS221 2.6 37.2 1.0 O B:GLU62 2.9 76.8 1.0 CG A:ASP120 3.0 37.1 1.0 OD1 A:ASP120 3.3 38.5 1.0 CD2 A:HIS263 3.3 26.8 0.5 HD2 A:HIS263 3.4 32.1 0.5 HE A:ARG121 3.4 29.5 0.8 CE1 A:HIS263 3.5 33.0 0.5 CB A:OCS221 3.6 31.3 1.0 HE1 A:HIS116 3.6 34.7 1.0 HH21 A:ARG121 3.6 29.2 0.7 ZN A:ZN1297 3.7 17.2 0.5 HE1 A:HIS263 3.8 39.7 0.5 O A:HOH2081 3.8 39.3 1.0 HB3 A:OCS221 3.8 37.6 1.0 HA2 B:GLY63 3.8 73.6 1.0 HB2 A:OCS221 3.9 37.6 1.0 C B:GLU62 4.0 68.1 1.0 NE A:ARG121 4.0 24.6 0.8 NH2 A:ARG121 4.1 24.3 0.7 HB3 B:GLU62 4.1 68.4 0.3 NE2 A:HIS196 4.2 24.1 1.0 CE1 A:HIS116 4.3 28.9 1.0 HA3 B:GLY63 4.3 73.6 1.0 O A:HOH2144 4.4 35.5 1.0 CZ A:ARG121 4.4 23.7 0.4 CB A:ASP120 4.4 36.2 1.0 CA B:GLY63 4.4 61.3 1.0 HE1 A:HIS196 4.5 29.6 1.0 NE2 A:HIS116 4.5 29.0 1.0 CG A:HIS263 4.5 28.4 0.5 HB2 A:ASP120 4.5 43.5 1.0 HA3 A:GLY262 4.5 27.0 1.0 CE1 A:HIS196 4.6 24.7 1.0 ND1 A:HIS263 4.6 31.6 0.5 CA A:OCS221 4.6 27.3 1.0 HA A:OCS221 4.6 32.8 1.0 N B:GLY63 4.7 64.2 1.0 HB3 A:ASP120 4.7 43.5 1.0 HG2 A:ARG121 4.7 29.9 0.6 HH22 A:ARG121 4.7 29.2 0.7 HD2 A:ARG121 4.8 28.8 0.6 CD A:ARG121 4.9 24.0 0.6 N A:OCS221 4.9 27.0 1.0 CB B:GLU62 5.0 57.0 0.3

Zinc binding site 2 out of 3 in the W228A-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 W228A-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:17.2 occ:0.50 O A:HOH2077 2.0 29.4 1.0 NE2 A:HIS196 2.0 24.1 1.0 ND1 A:HIS118 2.0 28.1 1.0 NE2 A:HIS116 2.0 29.0 1.0 OD2 A:OCS221 2.7 54.7 0.5 HB2 A:HIS118 2.8 37.0 1.0 CE1 A:HIS116 3.0 28.9 1.0 CG A:HIS118 3.0 29.2 1.0 CE1 A:HIS196 3.0 24.7 1.0 CD2 A:HIS196 3.0 24.2 1.0 CE1 A:HIS118 3.0 29.8 1.0 O A:HOH2081 3.0 39.3 1.0 CD2 A:HIS116 3.0 29.0 1.0 HE1 A:HIS116 3.2 34.7 1.0 HE1 A:HIS196 3.2 29.6 1.0 HD2 A:HIS196 3.2 29.1 1.0 HE1 A:HIS118 3.2 35.7 1.0 HD2 A:HIS116 3.2 34.8 1.0 CB A:HIS118 3.3 30.9 1.0 HB3 A:HIS118 3.4 37.0 1.0 ZN A:ZN1296 3.7 35.9 0.3 HG21 A:THR197 3.9 32.8 1.0 OD1 A:ASP120 3.9 38.5 1.0 HG22 A:THR197 4.0 32.8 1.0 HB2 A:OCS221 4.0 37.6 1.0 ND1 A:HIS116 4.1 29.4 1.0 NE2 A:HIS118 4.1 30.7 1.0 ND1 A:HIS196 4.1 25.2 1.0 SG A:OCS221 4.1 47.6 1.0 CD2 A:HIS118 4.1 30.0 1.0 CG A:HIS196 4.1 24.0 1.0 CG A:HIS116 4.1 28.6 1.0 CG2 A:THR197 4.4 27.3 1.0 CB A:OCS221 4.5 31.3 1.0 HB3 B:GLU62 4.5 68.4 0.3 HG2 B:GLU62 4.5 69.7 0.0 HB3 A:OCS221 4.6 37.6 1.0 HG2 A:ARG121 4.6 29.9 0.6 H A:HIS118 4.6 42.5 1.0 HD2 A:TYR233 4.7 53.6 1.0 CA A:HIS118 4.7 35.0 1.0 HG23 A:THR197 4.8 32.8 1.0 CG A:ASP120 4.8 37.1 1.0 OD2 A:ASP120 4.8 36.9 1.0 OD1 A:OCS221 4.8 37.2 1.0 HD1 A:HIS116 4.8 35.3 1.0 OD3 A:OCS221 4.9 42.2 0.5 HE2 A:HIS118 4.9 36.9 1.0 HD1 A:HIS196 4.9 30.2 1.0 HD2 A:HIS118 5.0 36.0 1.0 HG3 A:ARG121 5.0 29.9 0.6

Zinc binding site 3 out of 3 in the W228A-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 W228A-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:43.0 occ:0.70 NE2 B:HIS196 1.9 39.6 1.0 ND1 B:HIS118 2.0 53.7 1.0 NE2 B:HIS116 2.2 34.6 1.0 O A:HOH2022 2.7 34.3 1.0 CE1 B:HIS118 2.8 55.2 1.0 CE1 B:HIS196 2.8 42.1 1.0 CD2 B:HIS116 2.9 36.3 1.0 HE1 B:HIS118 3.0 66.3 1.0 HE1 B:HIS196 3.0 50.5 1.0 HD2 B:HIS116 3.0 43.6 1.0 CD2 B:HIS196 3.0 42.5 1.0 CG B:HIS118 3.1 51.7 1.0 HB2 B:HIS118 3.1 59.1 1.0 CE1 B:HIS116 3.2 39.2 1.0 HD2 B:HIS196 3.3 51.0 1.0 CB B:HIS118 3.5 49.2 1.0 HE1 B:HIS116 3.5 47.1 1.0 HB3 B:HIS118 3.7 59.1 1.0 HG21 B:THR197 3.9 54.4 1.0 HB2 B:OCS221 3.9 51.0 1.0 HG22 B:THR197 4.0 54.4 1.0 ND1 B:HIS196 4.0 44.5 1.0 NE2 B:HIS118 4.0 54.6 1.0 CG B:HIS196 4.1 44.0 1.0 CD2 B:HIS118 4.1 52.4 1.0 CG B:HIS116 4.2 36.2 1.0 OD2 B:OCS221 4.2 49.5 1.0 ND1 B:HIS116 4.2 37.8 1.0 CG2 B:THR197 4.4 45.3 1.0 HD2 B:TYR233 4.4 59.2 1.0 HB3 B:OCS221 4.4 51.0 1.0 HG3 A:GLU62 4.5 73.9 0.0 HB3 A:GLU62 4.5 74.0 1.0 CB B:OCS221 4.5 42.5 1.0 HG23 B:THR197 4.7 54.4 1.0 HG2 A:GLU62 4.7 73.9 0.0 HD1 B:HIS196 4.7 53.4 1.0 HE2 B:HIS118 4.8 65.6 1.0 H B:HIS118 4.8 55.5 1.0 CA B:HIS118 5.0 48.8 1.0 SG B:OCS221 5.0 46.5 1.0 HD2 B:HIS118 5.0 62.8 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