Zinc in PDB 1ko3: Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced

All present enzymatic activity of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced:
3.5.2.6;

The structure of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced, PDB code: 1ko3 was solved by I.Garcia-Saez, J.-D.Docquier, G.M.Rossolini, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.91
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	67.805, 78.040, 79.648, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25

The structure of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced (pdb code 1ko3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced, PDB code: 1ko3:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:21.8 occ:1.00 ND1 A:HIS118 2.1 18.4 1.0 O A:OH1001 2.1 17.0 1.0 NE2 A:HIS196 2.1 12.4 1.0 NE2 A:HIS116 2.2 11.5 1.0 O A:HOH1108 2.8 29.7 1.0 CG A:HIS118 3.0 18.7 1.0 CD2 A:HIS196 3.0 11.1 1.0 CE1 A:HIS118 3.1 19.6 1.0 CE1 A:HIS116 3.1 12.1 1.0 CD2 A:HIS116 3.1 13.1 1.0 CE1 A:HIS196 3.2 11.8 1.0 CB A:HIS118 3.3 19.0 1.0 OD1 A:ASP120 4.0 23.8 1.0 CD2 A:HIS118 4.1 18.4 1.0 NE2 A:HIS118 4.1 17.9 1.0 ZN A:ZN2 4.2 28.1 0.8 ND1 A:HIS116 4.2 13.1 1.0 CG A:HIS196 4.2 10.6 1.0 CG A:HIS116 4.3 13.4 1.0 ND1 A:HIS196 4.3 11.9 1.0 SG A:CYS221 4.5 20.7 1.0 CB A:CYS221 4.5 17.9 1.0 CA A:HIS118 4.7 19.4 1.0 CL A:CL402 4.8 36.8 1.0 CG A:ASP120 4.9 23.2 1.0 OD2 A:ASP120 4.9 22.9 1.0 O A:HOH1027 4.9 21.3 1.0

Zinc binding site 2 out of 3 in the Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:28.1 occ:0.80 NE2 A:HIS263 2.3 21.3 1.0 SG A:CYS221 2.3 20.7 1.0 OD2 A:ASP120 2.3 22.9 1.0 O A:OH1001 2.5 17.0 1.0 CL A:CL402 2.9 36.8 1.0 CE1 A:HIS263 3.2 21.4 1.0 CD2 A:HIS263 3.2 21.3 1.0 CG A:ASP120 3.4 23.2 1.0 CB A:CYS221 3.5 17.9 1.0 NH2 A:ARG121 3.7 21.9 1.0 OD1 A:ASP120 3.8 23.8 1.0 O A:HOH1002 4.0 41.9 1.0 ZN A:ZN1 4.2 21.8 1.0 NE A:ARG121 4.3 20.7 1.0 O A:HOH1073 4.3 30.3 1.0 ND1 A:HIS263 4.4 20.3 1.0 CG A:HIS263 4.4 20.3 1.0 CZ A:ARG121 4.4 21.6 1.0 NE2 A:HIS196 4.6 12.4 1.0 CB A:ASP120 4.6 23.1 1.0 CA A:CYS221 4.7 17.2 1.0 CE1 A:HIS116 4.7 12.1 1.0 CE1 A:HIS196 4.7 11.8 1.0 O A:HOH1108 4.8 29.7 1.0 NE2 A:HIS116 4.9 11.5 1.0

Zinc binding site 3 out of 3 in the Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa with CYS221 Reduced within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:21.7 occ:1.00 OXT A:ACT400 2.0 19.5 1.0 NE2 A:HIS170 2.1 17.0 1.0 OXT A:ACT401 2.2 19.5 1.0 O A:ACT401 2.7 19.1 1.0 C A:ACT401 2.7 19.3 1.0 C A:ACT400 2.9 20.3 1.0 CE1 A:HIS170 3.0 19.1 1.0 O A:ACT400 3.2 19.9 1.0 CD2 A:HIS170 3.2 17.6 1.0 ND1 A:HIS170 4.2 17.9 1.0 CH3 A:ACT401 4.2 19.0 1.0 CB A:ALA135 4.3 16.9 1.0 CH3 A:ACT400 4.3 19.1 1.0 CG A:HIS170 4.3 17.9 1.0 CA A:ALA135 4.8 16.9 1.0 O A:HOH1082 4.9 27.4 1.0

I.Garcia-Saez, J.-D.Docquier, G.M.Rossolini, O.Dideberg. The Three-Dimensional Structure of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa in Its Reduced and Oxidised Form J.Mol.Biol. V. 375 604 2008.
ISSN: ISSN 0022-2836
PubMed: 18061205
DOI: 10.1016/J.JMB.2007.11.012