Zinc in PDB 2ynt: Gim-1-3MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases

The structure of Gim-1-3MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynt 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)	19.987 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	110.922, 140.658, 41.069, 90.00, 90.00, 90.00
R / Rfree (%)	16.22 / 20.51

The binding sites of Zinc atom in the Gim-1-3MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases (pdb code 2ynt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Gim-1-3MOL Native. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta-Lactamases, PDB code: 2ynt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Gim-1-3MOL 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-1-3MOL 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:11.4 occ:1.00 O A:HOH2140 1.9 9.3 1.0 ND1 A:HIS118 2.0 8.0 1.0 NE2 A:HIS196 2.0 7.5 1.0 NE2 A:HIS116 2.1 9.8 1.0 CE1 A:HIS118 2.9 10.5 1.0 CD2 A:HIS196 3.0 8.8 1.0 CE1 A:HIS116 3.0 9.5 1.0 CG A:HIS118 3.0 10.0 1.0 CE1 A:HIS196 3.0 12.2 1.0 CD2 A:HIS116 3.0 6.6 1.0 CB A:HIS118 3.4 9.6 1.0 ZN A:ZN1297 3.5 12.8 1.0 O A:HOH2297 3.6 12.5 1.0 OD1 A:ASP120 4.0 13.5 1.0 NE2 A:HIS118 4.0 11.0 1.0 CB A:CYS221 4.1 9.0 1.0 CD2 A:HIS118 4.1 12.1 1.0 ND1 A:HIS116 4.1 8.4 1.0 ND1 A:HIS196 4.1 9.8 1.0 CG A:HIS196 4.1 7.9 1.0 CG A:HIS116 4.2 7.0 1.0 SG A:CYS221 4.3 8.7 1.0 CG2 A:THR197 4.4 10.1 1.0 OD2 A:ASP120 4.5 9.6 1.0 CG A:ASP120 4.7 13.0 1.0 CA A:HIS118 4.8 7.0 1.0

Zinc binding site 2 out of 6 in the Gim-1-3MOL 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-1-3MOL 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:12.8 occ:1.00 OD2 A:ASP120 2.0 9.6 1.0 O A:HOH2140 2.0 9.3 1.0 NE2 A:HIS263 2.1 9.2 1.0 SG A:CYS221 2.3 8.7 1.0 CD2 A:HIS263 3.0 11.8 1.0 CG A:ASP120 3.0 13.0 1.0 CE1 A:HIS263 3.1 10.2 1.0 OD1 A:ASP120 3.3 13.5 1.0 CB A:CYS221 3.3 9.0 1.0 ZN A:ZN1296 3.5 11.4 1.0 NE A:ARG121 3.9 8.6 1.0 O A:HOH2297 3.9 12.5 1.0 NH2 A:ARG121 4.0 8.3 1.0 CG A:HIS263 4.1 11.2 1.0 ND1 A:HIS263 4.1 9.2 1.0 CE1 A:HIS116 4.2 9.5 1.0 CZ A:ARG121 4.2 7.6 1.0 NE2 A:HIS116 4.3 9.8 1.0 CB A:ASP120 4.3 8.8 1.0 NE2 A:HIS196 4.4 7.5 1.0 CA A:CYS221 4.6 8.5 1.0 CE1 A:HIS196 4.7 12.2 1.0 CD A:ARG121 4.8 9.0 1.0 O A:HOH2229 4.9 12.9 1.0

Zinc binding site 3 out of 6 in the Gim-1-3MOL 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-1-3MOL 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:10.7 occ:1.00 O B:HOH2119 1.9 8.6 1.0 ND1 B:HIS118 2.0 8.5 1.0 NE2 B:HIS196 2.0 10.4 1.0 NE2 B:HIS116 2.0 7.3 1.0 CE1 B:HIS116 3.0 8.0 1.0 CE1 B:HIS118 3.0 7.1 1.0 CG B:HIS118 3.0 8.8 1.0 CD2 B:HIS196 3.0 8.2 1.0 CE1 B:HIS196 3.0 10.7 1.0 CD2 B:HIS116 3.1 9.6 1.0 CB B:HIS118 3.4 7.2 1.0 ZN B:ZN1298 3.5 12.6 1.0 OD1 B:ASP120 4.0 13.5 1.0 ND1 B:HIS116 4.1 7.0 1.0 NE2 B:HIS118 4.1 8.7 1.0 CB B:CYS221 4.1 8.5 1.0 CD2 B:HIS118 4.1 10.1 1.0 ND1 B:HIS196 4.1 9.4 1.0 CG B:HIS116 4.2 6.4 1.0 CG B:HIS196 4.2 6.7 1.0 SG B:CYS221 4.3 8.5 1.0 OD2 B:ASP120 4.5 9.0 1.0 CG2 B:THR197 4.5 8.8 1.0 CG B:ASP120 4.7 9.4 1.0 CA B:HIS118 4.8 8.3 1.0

Zinc binding site 4 out of 6 in the Gim-1-3MOL 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-1-3MOL 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:Zn1298 b:12.6 occ:1.00 NE2 B:HIS263 2.0 7.5 1.0 OD2 B:ASP120 2.0 9.0 1.0 O B:HOH2119 2.0 8.6 1.0 SG B:CYS221 2.3 8.5 1.0 CG B:ASP120 3.0 9.4 1.0 CD2 B:HIS263 3.0 7.0 1.0 CE1 B:HIS263 3.0 8.2 1.0 OD1 B:ASP120 3.3 13.5 1.0 CB B:CYS221 3.4 8.5 1.0 ZN B:ZN1297 3.5 10.7 1.0 NE B:ARG121 3.8 7.8 1.0 NH2 B:ARG121 4.0 10.3 1.0 ND1 B:HIS263 4.1 9.6 1.0 CG B:HIS263 4.1 9.1 1.0 CE1 B:HIS116 4.2 8.0 1.0 CZ B:ARG121 4.2 10.1 1.0 NE2 B:HIS116 4.3 7.3 1.0 CB B:ASP120 4.3 8.7 1.0 NE2 B:HIS196 4.4 10.4 1.0 CA B:CYS221 4.6 7.0 1.0 CD B:ARG121 4.6 6.6 1.0 CE1 B:HIS196 4.7 10.7 1.0 CG B:ARG121 5.0 7.5 1.0

Zinc binding site 5 out of 6 in the Gim-1-3MOL 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 5 of Gim-1-3MOL 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 C:Zn1299 b:14.9 occ:1.00 O C:HOH2069 1.9 12.1 1.0 ND1 C:HIS118 2.0 13.2 1.0 NE2 C:HIS196 2.0 9.3 1.0 NE2 C:HIS116 2.1 13.3 1.0 CE1 C:HIS118 2.9 14.8 1.0 CD2 C:HIS196 3.0 8.5 1.0 CG C:HIS118 3.0 15.9 1.0 CE1 C:HIS116 3.0 9.5 1.0 CD2 C:HIS116 3.1 7.9 1.0 CE1 C:HIS196 3.1 13.6 1.0 CB C:HIS118 3.4 15.6 1.0 ZN C:ZN1300 3.5 14.2 1.0 O A:HOH2052 3.9 17.8 1.0 OD1 C:ASP120 3.9 22.3 0.4 OD1 C:ASP120 3.9 22.5 0.6 NE2 C:HIS118 4.0 15.8 1.0 CD2 C:HIS118 4.1 20.9 1.0 CG C:HIS196 4.1 9.8 1.0 CB C:CYS221 4.1 9.8 1.0 ND1 C:HIS116 4.1 11.1 1.0 ND1 C:HIS196 4.1 11.7 1.0 CG C:HIS116 4.2 9.4 1.0 SG C:CYS221 4.2 10.6 1.0 CG2 C:THR197 4.4 12.8 1.0 OD2 C:ASP120 4.5 13.2 0.6 OD2 C:ASP120 4.5 13.2 0.4 CG C:ASP120 4.6 15.1 0.6 CG C:ASP120 4.6 15.1 0.4 CA C:HIS118 4.8 11.8 1.0

Zinc binding site 6 out of 6 in the Gim-1-3MOL 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 6 of Gim-1-3MOL 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 C:Zn1300 b:14.2 occ:1.00 OD2 C:ASP120 2.0 13.2 0.6 OD2 C:ASP120 2.0 13.2 0.4 O C:HOH2069 2.0 12.1 1.0 NE2 C:HIS263 2.1 11.3 1.0 SG C:CYS221 2.2 10.6 1.0 CG C:ASP120 3.0 15.1 0.6 CG C:ASP120 3.0 15.1 0.4 CD2 C:HIS263 3.0 12.1 1.0 CE1 C:HIS263 3.1 12.8 1.0 OD1 C:ASP120 3.3 22.3 0.4 OD1 C:ASP120 3.4 22.5 0.6 CB C:CYS221 3.4 9.8 1.0 ZN C:ZN1299 3.5 14.9 1.0 O A:HOH2052 3.8 17.8 1.0 NH2 C:ARG121 3.9 9.4 1.0 NE C:ARG121 3.9 11.9 1.0 ND1 C:HIS263 4.1 9.8 1.0 CG C:HIS263 4.1 11.0 1.0 CE1 C:HIS116 4.2 9.5 1.0 CZ C:ARG121 4.2 10.7 1.0 NE2 C:HIS196 4.3 9.3 1.0 NE2 C:HIS116 4.3 13.3 1.0 CB C:ASP120 4.3 10.9 0.6 CB C:ASP120 4.3 10.9 0.4 CE1 C:HIS196 4.6 13.6 1.0 CA C:CYS221 4.7 7.1 1.0 CD C:ARG121 4.9 9.1 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