Zinc in PDB 4d1w: A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa

The structure of A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa, PDB code: 4d1w was solved by H.-K.S.Leiros, S.Skagseth, K.S.W.Edvardsen, M.S.Lorentzen, G.E.K.Bjerga, I.Leiros, O.Samuelsen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.40
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	70.225, 70.225, 47.027, 90.00, 90.00, 90.00
R / Rfree (%)	11.776 / 15.636

The binding sites of Zinc atom in the A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa (pdb code 4d1w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa, PDB code: 4d1w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:11.9 occ:0.90 O A:HOH2118 1.9 16.1 1.0 NE2 A:HIS196 2.0 11.8 1.0 ND1 A:HIS118 2.0 10.8 1.0 NE2 A:HIS116 2.1 9.7 1.0 O A:HOH2119 2.8 23.6 1.0 CD2 A:HIS196 3.0 10.8 1.0 CE1 A:HIS118 3.0 12.8 1.0 CG A:HIS118 3.0 9.8 1.0 CE1 A:HIS116 3.0 11.1 1.0 CE1 A:HIS196 3.0 12.5 1.0 CD2 A:HIS116 3.0 9.1 1.0 CB A:HIS118 3.4 8.6 1.0 OD2 A:OCS221 3.4 16.6 0.4 ZN A:ZN1294 3.7 22.0 0.4 OD1 A:ASP120 4.0 18.2 1.0 NE2 A:HIS118 4.1 13.8 1.0 ND1 A:HIS196 4.2 11.6 1.0 CG A:HIS196 4.2 10.4 1.0 ND1 A:HIS116 4.2 11.0 1.0 CD2 A:HIS118 4.2 12.3 1.0 CG A:HIS116 4.2 8.9 1.0 SG A:OCS221 4.4 18.4 0.8 O A:HOH2211 4.5 28.4 1.0 CB A:OCS221 4.5 12.9 1.0 OD2 A:ASP120 4.6 20.2 1.0 OD1 A:OCS221 4.6 9.7 0.6 CG A:ASP120 4.7 14.8 1.0 CA A:HIS118 4.8 8.1 1.0 O A:HOH2126 4.8 37.9 1.0

Zinc binding site 2 out of 2 in the A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A H224Y Mutant For Vim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1294 b:22.0 occ:0.40 OD2 A:OCS221 1.6 16.6 0.4 O A:HOH2118 2.1 16.1 1.0 NE2 A:HIS263 2.2 18.1 1.0 OD2 A:ASP120 2.2 20.2 1.0 O A:HOH2126 2.3 37.9 1.0 SG A:OCS221 2.7 18.4 0.8 OD1 A:OCS221 3.1 9.7 0.6 CE1 A:HIS263 3.2 22.2 1.0 CD2 A:HIS263 3.2 21.0 1.0 CG A:ASP120 3.2 14.8 1.0 OD3 A:OCS221 3.3 17.7 0.4 O A:HOH2197 3.5 32.3 1.0 OD1 A:ASP120 3.6 18.2 1.0 ZN A:ZN1293 3.7 11.9 0.9 O A:HOH2249 3.8 30.0 1.0 O A:HOH2119 3.8 23.6 1.0 CB A:OCS221 4.0 12.9 1.0 NH2 A:ARG121 4.2 19.3 1.0 NE2 A:HIS196 4.4 11.8 1.0 ND1 A:HIS263 4.4 21.3 1.0 CG A:HIS263 4.4 14.9 1.0 CE1 A:HIS196 4.5 12.5 1.0 CB A:ASP120 4.5 13.2 1.0 CE1 A:HIS116 4.6 11.1 1.0 NE A:ARG121 4.6 13.2 1.0 NE2 A:HIS116 4.6 9.7 1.0 O A:HOH2196 4.9 24.5 1.0 CZ A:ARG121 4.9 13.0 1.0

H.-K.S.Leiros, S.Skagseth, K.S.W.Edvardsen, M.S.Lorentzen, G.E.K.Bjerga, I.Leiros, O.Samuelsen. HIS224 Alters the R2 Drug Binding Site and PHE218 Influences the Catalytic Efficiency in the Metallo-Beta-Lactamase Vim-7. Antimicrob.Agents Chemother. V. 58 4826 2014.
ISSN: ISSN 0066-4804
PubMed: 24913158
DOI: 10.1128/AAC.02735-13