Zinc in PDB 2ynv: CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta- Lactamases

The structure of CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta- Lactamases, PDB code: 2ynv 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)	19.55 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.648, 131.712, 40.721, 90.00, 94.78, 90.00
R / Rfree (%)	19.7 / 24.7

The structure of CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta- Lactamases also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta- Lactamases (pdb code 2ynv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active Site Plasticity in Metallo-Beta- Lactamases, PDB code: 2ynv:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. 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 CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. 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:28.4 occ:1.00 ND1 A:HIS118 2.0 9.6 1.0 NE2 A:HIS196 2.1 21.0 1.0 NE2 A:HIS116 2.3 17.4 1.0 CE1 A:HIS118 2.8 16.2 1.0 HE1 A:HIS118 2.9 19.4 1.0 CE1 A:HIS196 3.0 16.8 1.0 CG A:HIS118 3.1 16.1 1.0 CD2 A:HIS196 3.1 21.7 1.0 HE1 A:HIS196 3.1 20.1 1.0 CD2 A:HIS116 3.1 19.2 1.0 HB2 A:HIS118 3.2 8.8 1.0 CE1 A:HIS116 3.2 15.8 1.0 HD2 A:HIS116 3.3 23.1 1.0 HD2 A:HIS196 3.3 26.1 1.0 HE1 A:HIS116 3.5 19.0 1.0 CB A:HIS118 3.6 7.3 1.0 HG21 A:THR197 3.7 22.4 1.0 OD2 A:OCS221 3.7 24.1 1.0 HB3 A:HIS118 3.7 8.8 1.0 HG22 A:THR197 3.8 22.4 1.0 HA2 B:GLY63 3.8 84.2 1.0 NE2 A:HIS118 4.0 14.0 1.0 OD1 A:ASP120 4.1 24.9 1.0 CG2 A:THR197 4.1 18.6 1.0 ND1 A:HIS196 4.1 16.5 1.0 CD2 A:HIS118 4.1 18.4 1.0 CG A:HIS196 4.2 12.4 1.0 CG A:HIS116 4.3 19.1 1.0 ND1 A:HIS116 4.3 14.9 1.0 HA3 B:GLY63 4.3 84.2 1.0 HG23 A:THR197 4.3 22.4 1.0 H B:GLY63 4.3 77.8 1.0 CA B:GLY63 4.4 70.2 1.0 SG A:OCS221 4.5 21.7 1.0 CB A:OCS221 4.6 16.3 1.0 OD1 A:OCS221 4.6 25.1 1.0 N B:GLY63 4.6 64.8 1.0 HE2 A:HIS118 4.7 16.8 1.0 OD2 A:ASP120 4.8 23.5 1.0 H A:HIS118 4.8 13.1 1.0 CG A:ASP120 4.9 22.5 1.0 HG2 A:ARG121 4.9 35.4 1.0 HD1 A:HIS196 4.9 19.8 1.0 HG3 A:ARG121 4.9 35.4 1.0

Zinc binding site 2 out of 2 in the CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. 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 CYS221 Oxidized, Mono Zinc Gim-1 - Gim-1-Ox. 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:57.3 occ:1.00 NE2 B:HIS116 2.2 39.1 1.0 HD2 B:HIS196 2.4 47.3 1.0 NE2 B:HIS196 2.5 42.3 1.0 CD2 B:HIS196 2.7 39.4 1.0 ND1 B:HIS118 2.9 55.2 1.0 CE1 B:HIS116 3.0 35.8 1.0 CD2 B:HIS116 3.1 39.1 1.0 HE1 B:HIS116 3.2 42.9 1.0 HB2 B:HIS118 3.2 64.3 1.0 HD2 B:HIS116 3.4 47.0 1.0 HG21 B:THR197 3.4 40.1 1.0 HB2 B:CYS221 3.5 42.6 1.0 HG22 B:THR197 3.6 40.1 1.0 CG B:HIS118 3.8 53.4 1.0 CE1 B:HIS196 3.8 41.5 1.0 CB B:HIS118 3.9 53.6 1.0 CE1 B:HIS118 3.9 52.1 1.0 CG2 B:THR197 3.9 33.4 1.0 HB3 B:CYS221 4.0 42.6 1.0 HE1 B:HIS118 4.0 62.5 1.0 CG B:HIS196 4.0 35.1 1.0 HB3 B:HIS118 4.0 64.3 1.0 CB B:CYS221 4.1 35.5 1.0 ND1 B:HIS116 4.1 37.4 1.0 HG23 B:THR197 4.1 40.1 1.0 CG B:HIS116 4.2 36.2 1.0 HE1 B:HIS196 4.3 49.8 1.0 OD1 B:ASP120 4.4 63.3 1.0 SG B:CYS221 4.4 46.9 1.0 OD2 B:ASP120 4.4 59.5 1.0 ND1 B:HIS196 4.5 38.8 1.0 HG2 B:ARG121 4.8 53.5 1.0 HD1 B:HIS116 4.8 44.9 1.0 H A:GLY63 4.9 70.8 1.0 HD2 B:TYR233 4.9 0.4 1.0 CG B:ASP120 4.9 59.5 1.0 HA A:GLU62 4.9 78.8 1.0 HG3 B:ARG121 4.9 53.5 1.0 CD2 B:HIS118 5.0 55.3 1.0 H B:HIS118 5.0 55.2 1.0 NE2 B:HIS118 5.0 55.2 1.0 HG3 A:GLU62 5.0 81.5 1.0 HB3 B:HIS196 5.0 37.6 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