Zinc in PDB 4d1v: A F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa

The structure of A F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa, PDB code: 4d1v 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)	24.730 / 1.70
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	69.947, 69.947, 46.936, 90.00, 90.00, 90.00
R / Rfree (%)	15.93 / 19.65

The binding sites of Zinc atom in the A F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa (pdb code 4d1v). 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 F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa, PDB code: 4d1v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the A F218Y Mutant of 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 F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1292 b:20.1 occ:1.00 ND1 A:HIS118 2.0 19.6 1.0 NE2 A:HIS196 2.0 17.8 1.0 NE2 A:HIS116 2.1 14.7 1.0 O A:HOH2102 2.1 24.6 1.0 HB2 A:HIS118 2.9 21.4 1.0 CE1 A:HIS118 3.0 21.2 1.0 O A:HOH2103 3.0 31.6 1.0 CE1 A:HIS116 3.0 16.6 1.0 CE1 A:HIS196 3.0 25.4 1.0 CG A:HIS118 3.0 20.2 1.0 CD2 A:HIS196 3.0 16.2 1.0 CD2 A:HIS116 3.0 15.1 1.0 HE1 A:HIS118 3.1 25.5 1.0 HE1 A:HIS116 3.2 19.9 1.0 HE1 A:HIS196 3.2 30.4 1.0 HD2 A:HIS196 3.2 19.4 1.0 HD2 A:HIS116 3.2 18.1 1.0 CB A:HIS118 3.4 17.8 1.0 HB3 A:HIS118 3.6 21.4 1.0 ZN A:ZN1293 3.7 30.4 1.0 OD1 A:ASP120 4.0 21.7 1.0 HB2 A:CYS221 4.0 23.5 1.0 O A:HOH2182 4.0 35.5 1.0 NE2 A:HIS118 4.1 21.6 1.0 ND1 A:HIS116 4.1 14.0 1.0 ND1 A:HIS196 4.1 18.4 1.0 CD2 A:HIS118 4.1 20.8 1.0 CG A:HIS196 4.2 17.7 1.0 CG A:HIS116 4.2 15.4 1.0 HB3 A:CYS221 4.3 23.5 1.0 CB A:CYS221 4.4 19.6 1.0 SG A:CYS221 4.5 24.0 1.0 H A:HIS118 4.5 17.1 1.0 OD2 A:ASP120 4.5 19.9 1.0 O A:HOH2109 4.5 34.9 1.0 CG A:ASP120 4.7 18.8 1.0 HD21 A:ASN233 4.7 45.9 1.0 CA A:HIS118 4.8 14.8 1.0 HB3 A:SER197 4.8 21.2 1.0 HG2 A:ARG121 4.8 16.4 1.0 HE2 A:HIS118 4.9 25.9 1.0 HD1 A:HIS116 4.9 16.8 1.0 HD1 A:HIS196 4.9 22.1 1.0 HE A:ARG121 4.9 19.3 1.0 HD2 A:HIS118 5.0 25.0 1.0

Zinc binding site 2 out of 2 in the A F218Y Mutant of 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 F218Y Mutant of Vim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:30.4 occ:1.00 NE2 A:HIS263 2.1 20.4 1.0 OD2 A:ASP120 2.1 19.9 1.0 O A:HOH2182 2.2 35.5 1.0 O A:HOH2102 2.3 24.6 1.0 SG A:CYS221 2.4 24.0 1.0 HH21 A:ARG121 3.0 26.6 1.0 CE1 A:HIS263 3.1 19.5 1.0 CD2 A:HIS263 3.1 22.6 1.0 CG A:ASP120 3.2 18.8 1.0 HD2 A:HIS263 3.3 27.1 1.0 HE1 A:HIS263 3.3 23.4 1.0 HB3 A:CYS221 3.3 23.5 1.0 HE1 A:HIS116 3.5 19.9 1.0 CB A:CYS221 3.5 19.6 1.0 HE A:ARG121 3.5 19.3 1.0 O A:HOH2109 3.6 34.9 1.0 OD1 A:ASP120 3.6 21.7 1.0 ZN A:ZN1292 3.7 20.1 1.0 NH2 A:ARG121 3.8 22.1 1.0 HB2 A:CYS221 3.9 23.5 1.0 O A:HOH2103 3.9 31.6 1.0 ND1 A:HIS263 4.2 18.1 1.0 CE1 A:HIS116 4.2 16.6 1.0 NE A:ARG121 4.2 16.1 1.0 CG A:HIS263 4.2 18.3 1.0 O A:HOH2181 4.3 36.5 1.0 NE2 A:HIS196 4.4 17.8 1.0 HH22 A:ARG121 4.4 26.6 1.0 HE1 A:HIS196 4.4 30.4 1.0 NE2 A:HIS116 4.4 14.7 1.0 CB A:ASP120 4.5 16.6 1.0 CZ A:ARG121 4.5 19.6 1.0 O A:HOH2056 4.5 43.3 1.0 CE1 A:HIS196 4.5 25.4 1.0 HB2 A:ASP120 4.6 19.9 1.0 HA3 A:GLY262 4.7 17.6 1.0 HB3 A:ASP120 4.7 19.9 1.0 HA A:CYS221 4.7 20.3 1.0 CA A:CYS221 4.8 16.9 1.0 HG2 A:ARG121 4.9 16.4 1.0 HD1 A:HIS263 5.0 21.8 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