Zinc in PDB 5a87: Crystal Structure of the Metallo-Beta-Lactamase Vim-5

All present enzymatic activity of Crystal Structure of the Metallo-Beta-Lactamase Vim-5:
3.5.2.6;

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-5, PDB code: 5a87 was solved by J.Brem, A.O.Duzgun, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.270, 78.960, 64.030, 90.00, 104.82, 90.00
R / Rfree (%)	15.4 / 19.2

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5 (pdb code 5a87). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5, PDB code: 5a87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Metallo-Beta-Lactamase Vim-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1263 b:13.2 occ:1.00 O A:HOH2109 1.9 17.3 1.0 ND1 A:HIS116 2.0 12.2 1.0 NE2 A:HIS179 2.0 10.3 1.0 NE2 A:HIS114 2.0 11.4 1.0 CE1 A:HIS116 2.9 15.5 1.0 CD2 A:HIS179 3.0 9.9 1.0 CG A:HIS116 3.0 12.5 1.0 CE1 A:HIS114 3.0 11.8 1.0 CD2 A:HIS114 3.1 10.5 1.0 CE1 A:HIS179 3.1 12.8 1.0 CB A:HIS116 3.3 12.5 1.0 O2 A:GOL1262 3.5 48.6 1.0 ZN A:ZN1265 3.6 17.6 1.0 OD1 A:ASP118 3.9 16.0 1.0 O A:HOH2167 3.9 21.0 1.0 NE2 A:HIS116 4.0 16.9 1.0 CD2 A:HIS116 4.1 16.5 1.0 ND1 A:HIS114 4.1 11.8 1.0 CG A:HIS179 4.1 10.8 1.0 ND1 A:HIS179 4.1 13.3 1.0 CG A:HIS114 4.2 9.9 1.0 CB A:CYS198 4.3 12.1 1.0 SG A:CYS198 4.4 13.7 1.0 O A:HOH2219 4.4 62.4 1.0 OD2 A:ASP118 4.5 15.4 1.0 O3 A:GOL1262 4.6 47.7 1.0 CG A:ASP118 4.6 17.0 1.0 C2 A:GOL1262 4.7 48.6 1.0 CA A:HIS116 4.8 10.6 1.0 C3 A:GOL1262 4.8 47.8 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Metallo-Beta-Lactamase Vim-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1265 b:17.6 occ:1.00 O A:HOH2109 2.1 17.3 1.0 NE2 A:HIS240 2.1 12.8 1.0 OD2 A:ASP118 2.2 15.4 1.0 SG A:CYS198 2.3 13.7 1.0 O A:HOH2167 2.3 21.0 1.0 CD2 A:HIS240 3.0 12.3 1.0 CE1 A:HIS240 3.1 10.6 1.0 CG A:ASP118 3.3 17.0 1.0 CB A:CYS198 3.4 12.1 1.0 ZN A:ZN1263 3.6 13.2 1.0 OD1 A:ASP118 3.7 16.0 1.0 O A:HOH2219 3.8 62.4 1.0 NH2 A:ARG119 3.8 17.8 1.0 O2 A:GOL1262 3.9 48.6 1.0 C1 A:GOL1262 4.0 48.5 1.0 NE A:ARG119 4.1 14.2 1.0 CE1 A:HIS114 4.2 11.8 1.0 CG A:HIS240 4.2 10.4 1.0 ND1 A:HIS240 4.2 10.4 1.0 NE2 A:HIS179 4.3 10.3 1.0 NE2 A:HIS114 4.4 11.4 1.0 CZ A:ARG119 4.4 16.3 1.0 O A:HOH2176 4.4 17.4 1.0 C2 A:GOL1262 4.4 48.6 1.0 CE1 A:HIS179 4.5 12.8 1.0 CB A:ASP118 4.6 12.5 1.0 CA A:CYS198 4.6 11.0 1.0 O1 A:GOL1262 4.7 47.7 1.0 C3 A:GOL1262 4.8 47.8 1.0 O A:HOH2183 5.0 30.3 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Metallo-Beta-Lactamase Vim-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1267 b:17.3 occ:1.00 NE2 A:HIS153 2.1 13.8 1.0 O A:HOH2221 2.2 10.1 1.0 O A:HOH2222 2.4 10.8 1.0 CE1 A:HIS153 2.9 17.3 1.0 CD2 A:HIS153 3.2 13.2 1.0 O A:HOH2223 3.6 31.8 1.0 ND1 A:HIS153 4.1 17.4 1.0 CG A:HIS153 4.2 14.2 1.0 O A:HOH2121 4.4 14.8 1.0 CG2 A:THR152 4.4 17.6 1.0 CB A:ALA132 4.5 12.3 1.0 CA A:ALA132 4.6 11.7 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Metallo-Beta-Lactamase Vim-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1262 b:14.5 occ:1.00 O B:HOH2084 2.0 18.1 1.0 ND1 B:HIS116 2.0 13.2 1.0 NE2 B:HIS179 2.0 14.4 1.0 NE2 B:HIS114 2.0 11.9 1.0 CE1 B:HIS116 3.0 14.7 1.0 CD2 B:HIS179 3.0 15.8 1.0 CE1 B:HIS114 3.0 14.6 1.0 CG B:HIS116 3.0 12.7 1.0 CE1 B:HIS179 3.0 16.5 1.0 CD2 B:HIS114 3.1 13.2 1.0 CB B:HIS116 3.4 12.9 1.0 ZN B:ZN1264 3.5 19.9 1.0 OD1 B:ASP118 3.9 19.5 1.0 O B:HOH2142 4.0 23.7 1.0 NE2 B:HIS116 4.1 18.7 1.0 ND1 B:HIS114 4.1 14.2 1.0 CD2 B:HIS116 4.1 18.4 1.0 CG B:HIS179 4.1 12.7 1.0 ND1 B:HIS179 4.1 15.9 1.0 CG B:HIS114 4.2 13.2 1.0 CB B:CYS198 4.3 15.4 1.0 O B:HOH2045 4.3 46.4 1.0 SG B:CYS198 4.4 15.6 1.0 OD2 B:ASP118 4.5 18.9 1.0 CG B:ASP118 4.6 18.4 1.0 CA B:HIS116 4.8 11.9 1.0 ND2 B:ASN210 5.0 36.6 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Metallo-Beta-Lactamase Vim-5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1264 b:19.9 occ:1.00 O B:HOH2084 2.1 18.1 1.0 NE2 B:HIS240 2.1 13.1 1.0 SG B:CYS198 2.3 15.6 1.0 OD2 B:ASP118 2.3 18.9 1.0 O B:HOH2142 2.3 23.7 1.0 CD2 B:HIS240 3.0 14.3 1.0 CE1 B:HIS240 3.2 16.6 1.0 CG B:ASP118 3.3 18.4 1.0 CB B:CYS198 3.4 15.4 1.0 ZN B:ZN1262 3.5 14.5 1.0 OD1 B:ASP118 3.7 19.5 1.0 NH2 B:ARG119 3.9 21.6 1.0 CG B:HIS240 4.2 12.5 1.0 NE B:ARG119 4.2 16.2 1.0 CE1 B:HIS114 4.2 14.6 1.0 ND1 B:HIS240 4.2 13.0 1.0 NE2 B:HIS179 4.2 14.4 1.0 NE2 B:HIS114 4.4 11.9 1.0 CZ B:ARG119 4.5 19.3 1.0 O B:HOH2147 4.5 18.8 1.0 O B:HOH2045 4.5 46.4 1.0 CE1 B:HIS179 4.5 16.5 1.0 CA B:CYS198 4.6 13.1 1.0 CB B:ASP118 4.6 16.8 1.0 CD2 B:HIS179 5.0 15.8 1.0

A.Makena, A.O.Duzgun, J.Brem, M.A.Mcdonough, A.M.Rydzik, M.I.Abboud, A.Saral, A.C.Cicek, C.Sandalli, C.J.Schofield. Comparison of Verona Integron-Borne Metallo-Beta-Lactamase (Vim) Variants Reveals Differences in Stability and Inhibition Profiles. Antimicrob. Agents V. 60 1377 2015CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 26666919
DOI: 10.1128/AAC.01768-15