Zinc in PDB 2ynw: Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases

The structure of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynw was solved by P.S.Borra, O.Samuelsen, J.Spencer, M.S.Lorentzen, H.-K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.861 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.160, 135.534, 38.541, 90.00, 90.83, 90.00
R / Rfree (%)	16.69 / 19.86

The binding sites of Zinc atom in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases (pdb code 2ynw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1296 b:6.8 occ:1.00 O A:HOH2053 2.0 9.0 1.0 ND1 A:HIS118 2.0 7.2 1.0 NE2 A:HIS196 2.1 6.2 1.0 NE2 A:HIS116 2.1 3.6 1.0 CE1 A:HIS118 2.9 10.0 1.0 CD2 A:HIS196 3.0 6.5 1.0 CE1 A:HIS116 3.0 3.7 1.0 HB2 A:HIS118 3.0 7.1 1.0 CG A:HIS118 3.1 7.2 1.0 HE1 A:HIS118 3.1 12.0 1.0 CD2 A:HIS116 3.1 2.9 1.0 HD2 A:HIS196 3.1 7.8 1.0 CE1 A:HIS196 3.1 15.7 1.0 HE1 A:HIS116 3.2 4.4 1.0 HD2 A:HIS116 3.3 3.4 1.0 HE1 A:HIS196 3.3 18.8 1.0 CB A:HIS118 3.5 5.9 1.0 ZN A:ZN1297 3.5 9.8 1.0 HB2 A:CYS221 3.6 8.1 1.0 HB3 A:HIS118 3.7 7.1 1.0 O B:HOH2011 3.8 17.6 1.0 HG21 A:THR197 3.9 12.6 1.0 OD1 A:ASP120 4.0 8.0 1.0 HB3 A:CYS221 4.0 8.1 1.0 HG22 A:THR197 4.0 12.6 1.0 NE2 A:HIS118 4.1 13.1 1.0 CB A:CYS221 4.1 6.8 1.0 ND1 A:HIS116 4.1 1.9 1.0 CD2 A:HIS118 4.1 10.6 1.0 CG A:HIS196 4.2 5.7 1.0 ND1 A:HIS196 4.2 6.8 1.0 CG A:HIS116 4.2 0.4 1.0 SG A:CYS221 4.2 6.7 1.0 CG2 A:THR197 4.4 10.5 1.0 OD2 A:ASP120 4.5 4.7 1.0 HG2 A:ARG121 4.6 3.6 1.0 H A:HIS118 4.6 2.7 1.0 CG A:ASP120 4.7 10.6 1.0 O2 B:SO41298 4.7 37.7 1.0 HG23 A:THR197 4.8 12.6 1.0 HE2 A:HIS118 4.8 15.7 1.0 CA A:HIS118 4.9 6.1 1.0 HD1 A:HIS116 4.9 2.3 1.0 HA2 B:GLY63 5.0 21.7 1.0 HG3 A:ARG121 5.0 3.6 1.0 HD1 A:HIS196 5.0 8.2 1.0

Zinc binding site 2 out of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1297 b:9.8 occ:1.00 O A:HOH2053 2.0 9.0 1.0 OD2 A:ASP120 2.0 4.7 1.0 NE2 A:HIS263 2.1 6.5 1.0 SG A:CYS221 2.3 6.7 1.0 CG A:ASP120 3.0 10.6 1.0 CD2 A:HIS263 3.1 7.1 1.0 CE1 A:HIS263 3.1 8.8 1.0 HD2 A:HIS263 3.2 8.5 1.0 HE1 A:HIS263 3.3 10.5 1.0 HB3 A:CYS221 3.3 8.1 1.0 HH21 A:ARG121 3.3 6.0 1.0 HE A:ARG121 3.4 5.9 1.0 OD1 A:ASP120 3.4 8.0 1.0 CB A:CYS221 3.4 6.8 1.0 ZN A:ZN1296 3.5 6.8 1.0 HE1 A:HIS116 3.5 4.4 1.0 O B:HOH2011 3.7 17.6 1.0 O B:GLY63 3.7 16.5 1.0 HB2 A:CYS221 3.7 8.1 1.0 NH2 A:ARG121 3.9 5.0 1.0 NE A:ARG121 3.9 4.9 1.0 ND1 A:HIS263 4.2 5.8 1.0 CE1 A:HIS116 4.2 3.7 1.0 CG A:HIS263 4.2 4.3 1.0 CZ A:ARG121 4.3 4.5 1.0 CB A:ASP120 4.3 6.3 1.0 NE2 A:HIS196 4.3 6.2 1.0 NE2 A:HIS116 4.3 3.6 1.0 HA3 A:GLY262 4.3 4.3 1.0 HB2 A:ASP120 4.4 7.5 1.0 HH22 A:ARG121 4.5 6.0 1.0 HG2 A:ARG121 4.5 3.6 1.0 HB3 A:ASP120 4.6 7.5 1.0 HE1 A:HIS196 4.6 18.8 1.0 O A:HOH2104 4.6 13.8 1.0 HA B:TYR64 4.7 12.9 1.0 CA A:CYS221 4.7 4.7 1.0 CE1 A:HIS196 4.7 15.7 1.0 HA A:CYS221 4.7 5.7 1.0 C B:GLY63 4.7 17.4 1.0 HD2 A:ARG121 4.8 4.6 1.0 HB2 A:HIS118 4.9 7.1 1.0 CD A:ARG121 4.9 3.8 1.0 HD1 A:HIS263 4.9 7.0 1.0

Zinc binding site 3 out of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1296 b:10.8 occ:1.00 ND1 B:HIS118 1.9 9.4 1.0 NE2 B:HIS196 2.0 6.5 1.0 O A:HOH2017 2.1 10.2 1.0 NE2 B:HIS116 2.1 8.2 1.0 CE1 B:HIS118 2.9 9.8 1.0 HB2 B:HIS118 2.9 12.9 1.0 CG B:HIS118 3.0 11.2 1.0 CE1 B:HIS116 3.0 10.5 1.0 CD2 B:HIS196 3.0 8.1 1.0 CE1 B:HIS196 3.0 16.1 1.0 CD2 B:HIS116 3.1 10.7 1.0 HE1 B:HIS118 3.1 11.8 1.0 HE1 B:HIS116 3.2 12.6 1.0 HD2 B:HIS196 3.2 9.7 1.0 HE1 B:HIS196 3.2 19.4 1.0 HD2 B:HIS116 3.3 12.9 1.0 CB B:HIS118 3.3 10.7 1.0 ZN B:ZN1297 3.5 13.3 1.0 HB3 B:HIS118 3.5 12.9 1.0 HB2 B:CYS221 3.7 10.9 1.0 O A:HOH2019 3.9 17.0 1.0 OD1 B:ASP120 3.9 9.9 1.0 HG21 B:THR197 3.9 16.8 1.0 HB3 B:CYS221 4.0 10.9 1.0 NE2 B:HIS118 4.0 16.2 1.0 CD2 B:HIS118 4.1 12.1 1.0 ND1 B:HIS116 4.1 8.1 1.0 HG22 B:THR197 4.1 16.8 1.0 CB B:CYS221 4.1 9.1 1.0 ND1 B:HIS196 4.1 9.6 1.0 CG B:HIS196 4.2 12.2 1.0 CG B:HIS116 4.2 5.9 1.0 SG B:CYS221 4.2 11.2 1.0 CG2 B:THR197 4.5 14.0 1.0 HG2 B:ARG121 4.5 12.1 1.0 OD2 B:ASP120 4.5 9.4 1.0 H B:HIS118 4.6 8.8 1.0 CG B:ASP120 4.7 8.2 1.0 HE2 B:HIS118 4.8 19.5 1.0 CA B:HIS118 4.8 8.7 1.0 HG3 B:ARG121 4.8 12.1 1.0 HG23 B:THR197 4.8 16.8 1.0 HD1 B:HIS116 4.9 9.7 1.0 HD2 B:HIS118 4.9 14.6 1.0 HD1 B:HIS196 4.9 11.5 1.0

Zinc binding site 4 out of 4 in the Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Gim-1-2MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1297 b:13.3 occ:1.00 O A:HOH2017 2.0 10.2 1.0 OD2 B:ASP120 2.0 9.4 1.0 NE2 B:HIS263 2.2 7.3 1.0 SG B:CYS221 2.3 11.2 1.0 CG B:ASP120 3.0 8.2 1.0 CD2 B:HIS263 3.1 15.0 1.0 CE1 B:HIS263 3.1 13.5 1.0 HD2 B:HIS263 3.3 18.0 1.0 HE1 B:HIS263 3.3 16.2 1.0 OD1 B:ASP120 3.3 9.9 1.0 HB3 B:CYS221 3.3 10.9 1.0 HE B:ARG121 3.3 9.7 1.0 HH21 B:ARG121 3.4 13.2 1.0 CB B:CYS221 3.4 9.1 1.0 ZN B:ZN1296 3.5 10.8 1.0 HE1 B:HIS116 3.6 12.6 1.0 O A:GLY63 3.7 14.8 1.0 HB2 B:CYS221 3.8 10.9 1.0 O A:HOH2019 3.8 17.0 1.0 NE B:ARG121 3.9 8.1 1.0 NH2 B:ARG121 3.9 11.0 1.0 ND1 B:HIS263 4.2 9.5 1.0 CG B:HIS263 4.2 10.7 1.0 CZ B:ARG121 4.2 11.4 1.0 CE1 B:HIS116 4.2 10.5 1.0 CB B:ASP120 4.3 8.7 1.0 NE2 B:HIS116 4.3 8.2 1.0 HA3 B:GLY262 4.3 8.3 1.0 HB2 B:ASP120 4.3 10.4 1.0 NE2 B:HIS196 4.4 6.5 1.0 HG2 B:ARG121 4.4 12.1 1.0 HH22 B:ARG121 4.5 13.2 1.0 HB3 B:ASP120 4.6 10.4 1.0 HA A:TYR64 4.6 13.9 1.0 HE1 B:HIS196 4.6 19.4 1.0 C A:GLY63 4.7 13.9 1.0 HD2 B:ARG121 4.7 14.1 1.0 CA B:CYS221 4.7 10.6 1.0 HA B:CYS221 4.8 12.7 1.0 O B:HOH2057 4.8 16.9 1.0 CE1 B:HIS196 4.8 16.1 1.0 CD B:ARG121 4.8 11.8 1.0 HB2 B:HIS118 4.8 12.9 1.0 HD1 B:HIS263 5.0 11.4 1.0 HG B:SER69 5.0 17.4 1.0 O B:GLY262 5.0 9.3 1.0

P.S.Borra, O.Samuelsen, J.Spencer, T.R.Walsh, M.S.Lorentzen, H.-K.S.Leiros. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active- Site Plasticity in Metallo-Beta-Lactamases. Antimicrob.Agents Chemother. V. 57 848 2013.
ISSN: ISSN 0066-4804
PubMed: 23208706
DOI: 10.1128/AAC.02227-12