Zinc in PDB 4d1t: High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa

The structure of High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa, PDB code: 4d1t 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)	23.326 / 1.25
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	69.979, 69.979, 47.530, 90.00, 90.00, 90.00
R / Rfree (%)	13.07 / 14.83

The binding sites of Zinc atom in the High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa (pdb code 4d1t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa, PDB code: 4d1t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the High Resolution Structure of Native Tvim-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 High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1292 b:6.8 occ:1.00 O A:HOH2131 1.9 9.1 1.0 ND1 A:HIS118 2.0 6.5 1.0 NE2 A:HIS196 2.0 6.9 1.0 NE2 A:HIS116 2.0 5.9 1.0 HB2 A:HIS118 2.9 6.5 1.0 CE1 A:HIS118 3.0 6.8 1.0 CD2 A:HIS196 3.0 6.7 1.0 CE1 A:HIS116 3.0 5.9 1.0 CG A:HIS118 3.0 5.9 1.0 CE1 A:HIS196 3.0 7.5 1.0 CD2 A:HIS116 3.1 5.6 1.0 HE1 A:HIS118 3.1 8.2 1.0 HD2 A:HIS196 3.1 8.0 1.0 HE1 A:HIS116 3.2 7.1 1.0 HD2 A:HIS116 3.3 6.7 1.0 HE1 A:HIS196 3.3 9.0 1.0 O A:HOH2132 3.3 26.4 1.0 CB A:HIS118 3.4 5.4 1.0 ZN A:ZN1293 3.5 7.8 0.9 HB3 A:HIS118 3.6 6.5 1.0 O A:HOH2206 3.8 11.8 1.0 HB2 A:CYS221 3.8 7.4 1.0 OD1 A:ASP120 3.9 9.5 1.0 HB3 A:CYS221 4.0 7.4 1.0 NE2 A:HIS118 4.1 7.2 1.0 ND1 A:HIS116 4.1 5.7 1.0 ND1 A:HIS196 4.1 8.0 1.0 CD2 A:HIS118 4.1 7.2 1.0 CG A:HIS196 4.1 7.0 1.0 CG A:HIS116 4.2 5.3 1.0 CB A:CYS221 4.2 6.2 1.0 SG A:CYS221 4.3 6.7 1.0 OD2 A:ASP120 4.5 7.4 1.0 H A:HIS118 4.5 5.5 1.0 CG A:ASP120 4.6 7.2 1.0 HE A:ARG121 4.7 6.5 1.0 HB3 A:SER197 4.8 8.7 1.0 CA A:HIS118 4.8 5.0 1.0 HE2 A:HIS118 4.8 8.7 1.0 HG2 A:ARG121 4.9 5.6 1.0 HD1 A:HIS116 4.9 6.8 1.0 HD1 A:HIS196 4.9 9.6 1.0 HD21 A:ASN233 4.9 37.2 1.0 HG3 A:ARG121 4.9 5.6 1.0

Zinc binding site 2 out of 2 in the High Resolution Structure of Native Tvim-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 High Resolution Structure of Native Tvim-7 From Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1293 b:7.8 occ:0.90 O A:HOH2131 2.0 9.1 1.0 NE2 A:HIS263 2.1 7.6 1.0 OD2 A:ASP120 2.2 7.4 1.0 O A:HOH2206 2.2 11.8 1.0 SG A:CYS221 2.3 6.7 1.0 HH21 A:ARG121 3.0 8.6 1.0 CD2 A:HIS263 3.0 7.4 1.0 CE1 A:HIS263 3.1 7.0 1.0 HD2 A:HIS263 3.2 8.9 1.0 CG A:ASP120 3.2 7.2 1.0 HB3 A:CYS221 3.2 7.4 1.0 HE1 A:HIS263 3.3 8.4 1.0 CB A:CYS221 3.4 6.2 1.0 HE A:ARG121 3.5 6.5 1.0 ZN A:ZN1292 3.5 6.8 1.0 HE1 A:HIS116 3.5 7.1 1.0 OD1 A:ASP120 3.5 9.5 1.0 HB2 A:CYS221 3.8 7.4 1.0 NH2 A:ARG121 3.8 7.2 1.0 O A:HOH2132 4.2 26.4 1.0 ND1 A:HIS263 4.2 7.0 1.0 CG A:HIS263 4.2 6.9 1.0 CE1 A:HIS116 4.2 5.9 1.0 NE A:ARG121 4.2 5.4 1.0 NE2 A:HIS196 4.2 6.9 1.0 NE2 A:HIS116 4.3 5.9 1.0 HH22 A:ARG121 4.4 8.6 1.0 HE1 A:HIS196 4.5 9.0 1.0 CZ A:ARG121 4.5 5.4 1.0 HA3 A:GLY262 4.5 7.5 1.0 O A:HOH2218 4.5 17.9 1.0 CB A:ASP120 4.5 6.2 1.0 CE1 A:HIS196 4.5 7.5 1.0 HA A:CYS221 4.6 7.1 1.0 CA A:CYS221 4.6 5.9 1.0 HB2 A:ASP120 4.6 7.4 1.0 HB3 A:ASP120 4.8 7.4 1.0 HD1 A:HIS263 5.0 8.4 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