Zinc in PDB 5acp: W228R-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1

The structure of W228R-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acp 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)	24.83 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.757, 133.619, 40.702, 90.00, 95.26, 90.00
R / Rfree (%)	20.2 / 23.4

The structure of W228R-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the W228R-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1 (pdb code 5acp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the W228R-Investigation of the Impact From Residues W228 and Y233 in the Metallo-Beta-Lactamase Gim-1, PDB code: 5acp:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the W228R-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 W228R-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:36.3 occ:1.00 O A:HOH2039 1.9 31.4 1.0 NE2 A:HIS196 2.0 33.7 1.0 ND1 A:HIS118 2.1 35.0 1.0 NE2 A:HIS116 2.3 33.0 1.0 HB2 A:HIS118 2.9 39.5 1.0 CD2 A:HIS196 2.9 34.0 1.0 CE1 A:HIS118 3.0 35.6 1.0 CG A:HIS118 3.0 35.2 1.0 HD2 A:HIS196 3.1 40.9 1.0 CE1 A:HIS196 3.1 33.5 1.0 CE1 A:HIS116 3.2 31.8 1.0 HE1 A:HIS118 3.2 42.8 1.0 CD2 A:HIS116 3.3 33.8 1.0 HE1 A:HIS116 3.3 38.2 1.0 HE1 A:HIS196 3.3 40.2 1.0 CB A:HIS118 3.4 32.9 1.0 HD2 A:HIS116 3.5 40.6 1.0 OD2 A:OCS221 3.5 38.5 1.0 HB3 A:HIS118 3.5 39.5 1.0 HB2 A:OCS221 3.8 41.1 1.0 HG21 A:THR197 3.9 48.9 1.0 OD1 A:ASP120 4.0 40.3 1.0 HG22 A:THR197 4.1 48.9 1.0 NE2 A:HIS118 4.1 36.9 1.0 CG A:HIS196 4.1 33.7 1.0 CD2 A:HIS118 4.1 37.0 1.0 ND1 A:HIS196 4.1 33.2 1.0 HB3 A:OCS221 4.2 41.1 1.0 ZN A:ZN1297 4.2 59.3 0.2 ND1 A:HIS116 4.3 30.1 1.0 SG A:OCS221 4.3 44.8 1.0 CB A:OCS221 4.3 34.3 1.0 HA2 B:GLY63 4.3 74.2 1.0 CG A:HIS116 4.4 32.8 1.0 O A:HOH2073 4.4 69.2 1.0 CG2 A:THR197 4.5 40.8 1.0 OD3 A:OCS221 4.5 40.2 1.0 H A:HIS118 4.6 41.1 1.0 H B:GLY63 4.8 84.7 1.0 HG2 A:ARG121 4.8 37.9 1.0 OD2 A:ASP120 4.8 44.5 1.0 CA A:HIS118 4.8 33.2 1.0 HD2 A:TYR233 4.8 74.4 1.0 CG A:ASP120 4.9 41.0 1.0 HG23 A:THR197 4.9 48.9 1.0 HD2 A:HIS118 5.0 44.4 1.0

Zinc binding site 2 out of 3 in the W228R-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 W228R-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:59.3 occ:0.23 OD2 A:OCS221 1.8 38.5 1.0 OD2 A:ASP120 1.8 44.5 1.0 NE2 A:HIS263 2.1 37.5 1.0 O A:HOH2039 2.5 31.4 1.0 HA2 B:GLY63 2.5 74.2 1.0 CG A:ASP120 2.6 41.0 1.0 SG A:OCS221 2.7 44.8 1.0 HH21 A:ARG121 2.8 42.4 1.0 CE1 A:HIS263 2.9 37.9 1.0 HE1 A:HIS263 3.0 45.5 1.0 OD1 A:ASP120 3.0 40.3 1.0 OD3 A:OCS221 3.0 40.2 1.0 HE A:ARG121 3.1 39.9 1.0 CD2 A:HIS263 3.2 39.2 1.0 OD1 A:OCS221 3.2 53.3 1.0 CA B:GLY63 3.3 61.8 1.0 HA3 B:GLY63 3.4 74.2 1.0 HD2 A:HIS263 3.4 47.1 1.0 NH2 A:ARG121 3.6 35.3 1.0 CB A:ASP120 3.7 37.6 1.0 O A:HOH2073 3.7 69.2 1.0 HB2 A:ASP120 3.8 45.1 1.0 O B:GLY63 3.8 63.4 1.0 NE A:ARG121 3.8 33.3 1.0 C B:GLY63 3.9 71.0 1.0 HB3 A:ASP120 4.0 45.1 1.0 ND1 A:HIS263 4.0 38.9 1.0 CZ A:ARG121 4.1 34.8 1.0 HH22 A:ARG121 4.2 42.4 1.0 CG A:HIS263 4.2 38.5 1.0 ZN A:ZN1296 4.2 36.3 1.0 HE1 A:HIS116 4.2 38.2 1.0 CB A:OCS221 4.3 34.3 1.0 HB3 A:OCS221 4.5 41.1 1.0 N B:GLY63 4.5 70.6 1.0 HG A:SER69 4.6 41.9 0.7 HG2 A:ARG121 4.6 37.9 1.0 HA3 A:GLY262 4.6 40.7 1.0 HB2 A:OCS221 4.6 41.1 1.0 H B:GLY63 4.7 84.7 1.0 OG A:SER69 4.7 34.9 0.7 HB2 A:SER69 4.8 42.6 0.3 CE1 A:HIS116 4.9 31.8 1.0 O A:GLY262 5.0 32.0 1.0 CD A:ARG121 5.0 34.0 1.0 H A:ASP120 5.0 44.9 1.0

Zinc binding site 3 out of 3 in the W228R-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 W228R-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:52.0 occ:1.00 ND1 B:HIS118 1.9 47.6 1.0 NE2 B:HIS196 2.0 49.7 1.0 O B:HOH2009 2.0 85.1 1.0 NE2 B:HIS116 2.2 45.7 1.0 O B:HOH2011 2.7 61.7 1.0 CE1 B:HIS118 2.9 47.9 1.0 HB2 B:HIS118 2.9 62.8 1.0 CG B:HIS118 2.9 48.6 1.0 CD2 B:HIS196 2.9 49.8 1.0 HD2 B:HIS196 3.1 59.8 1.0 HE1 B:HIS118 3.1 57.5 1.0 CE1 B:HIS196 3.1 50.5 1.0 CE1 B:HIS116 3.1 46.6 1.0 CD2 B:HIS116 3.1 45.8 1.0 HD2 B:HIS116 3.3 55.0 1.0 HE1 B:HIS116 3.3 55.9 1.0 HE1 B:HIS196 3.3 60.5 1.0 CB B:HIS118 3.3 52.3 1.0 HB3 B:HIS118 3.5 62.8 1.0 HG21 B:THR197 3.9 59.1 1.0 OD3 B:OCS221 3.9 63.3 0.6 NE2 B:HIS118 4.0 48.5 1.0 CD2 B:HIS118 4.0 48.4 1.0 HB2 B:OCS221 4.0 60.6 0.9 HG22 B:THR197 4.0 59.1 1.0 OD2 B:OCS221 4.1 62.1 0.8 HB3 B:ASP120 4.1 80.8 1.0 CG B:HIS196 4.1 50.1 1.0 ND1 B:HIS196 4.1 51.0 1.0 ND1 B:HIS116 4.2 48.0 1.0 CG B:HIS116 4.2 46.0 1.0 SG B:OCS221 4.4 64.5 0.8 CG2 B:THR197 4.4 49.2 1.0 HG3 B:ARG121 4.5 68.3 0.9 OD2 B:ASP120 4.5 70.1 1.0 HB2 B:ASP120 4.5 80.8 1.0 CB B:OCS221 4.6 50.5 0.9 H B:HIS118 4.6 64.7 1.0 HB3 B:OCS221 4.6 60.6 0.9 HB3 A:GLU62 4.7 84.4 1.0 HD2 B:TYR233 4.7 82.2 1.0 CB B:ASP120 4.7 67.3 1.0 HG23 B:THR197 4.7 59.1 1.0 CA B:HIS118 4.8 58.2 1.0 HD2 B:HIS118 4.9 58.1 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