Zinc in PDB 4fr7: Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A, PDB code: 4fr7 was solved by K.Herzog, K.M.Hoffmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.07 / 1.61
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.600, 74.390, 78.720, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 18.6

The structure of Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A (pdb code 4fr7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A, PDB code: 4fr7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A


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-31 in Its Reduced Form at 1.61 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:17.5 occ:1.00 ND1 A:HIS249 2.1 16.1 1.0 CE1 A:HIS249 2.9 17.3 1.0 CG A:HIS249 3.1 16.0 1.0 CB A:HIS249 3.5 16.2 1.0 CA A:HIS249 3.8 18.4 1.0 NE2 A:HIS249 4.1 16.9 1.0 CD2 A:HIS249 4.2 17.5 1.0 ND2 A:ASN252 4.4 18.9 1.0 CD2 A:LEU201 4.5 20.0 1.0 O A:HIS249 4.7 17.0 1.0 C A:HIS249 4.7 16.0 1.0 N A:HIS249 4.8 17.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A


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-31 in Its Reduced Form at 1.61 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:22.2 occ:1.00 ND1 A:HIS114 1.9 19.9 1.0 NE2 A:HIS177 2.0 15.4 1.0 O A:HOH521 2.0 19.9 1.0 NE2 A:HIS112 2.1 21.0 1.0 O A:HOH608 2.6 39.8 1.0 CE1 A:HIS114 2.9 17.8 1.0 CD2 A:HIS177 3.0 16.6 1.0 O A:HOH511 3.0 28.6 1.0 CG A:HIS114 3.0 18.6 1.0 CE1 A:HIS177 3.0 18.6 1.0 CE1 A:HIS112 3.0 16.1 1.0 CD2 A:HIS112 3.1 18.0 1.0 CB A:HIS114 3.4 18.0 1.0 O A:HOH452 3.6 27.9 1.0 ZN A:ZN303 3.7 19.6 0.7 OD1 A:ASP116 3.9 21.8 1.0 O A:HOH512 4.0 29.9 1.0 NE2 A:HIS114 4.1 20.1 1.0 CD2 A:HIS114 4.1 18.8 1.0 ND1 A:HIS177 4.1 17.6 1.0 CG A:HIS177 4.1 16.4 1.0 ND1 A:HIS112 4.2 16.9 1.0 CG A:HIS112 4.2 15.4 1.0 CB A:OCS196 4.3 17.8 1.0 SG A:OCS196 4.3 20.6 1.0 O A:HOH528 4.5 37.6 1.0 OD2 A:ASP116 4.5 25.3 1.0 CG A:ASP116 4.6 18.0 1.0 CA A:HIS114 4.8 18.2 1.0 O A:HOH413 5.0 22.0 1.0 OD3 A:OCS196 5.0 15.7 0.3

Zinc binding site 3 out of 3 in the Crystal Structure of the Metallo-Beta-Lactamase Vim-31 in Its Reduced Form at 1.61 A


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-31 in Its Reduced Form at 1.61 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:19.6 occ:0.70 SG A:OCS196 2.0 20.6 1.0 OD1 A:OCS196 2.1 13.9 0.3 NE2 A:HIS238 2.2 23.8 1.0 O A:HOH521 2.2 19.9 1.0 O A:HOH512 2.3 29.9 1.0 OD2 A:ASP116 2.3 25.3 1.0 OD3 A:OCS196 3.0 15.7 0.3 CD2 A:HIS238 3.2 24.1 1.0 CE1 A:HIS238 3.2 23.5 1.0 CB A:OCS196 3.2 17.8 1.0 CG A:ASP116 3.4 18.0 1.0 O A:HOH608 3.6 39.8 1.0 ZN A:ZN302 3.7 22.2 1.0 OD1 A:ASP116 3.8 21.8 1.0 NH2 A:ARG117 3.8 25.2 1.0 O A:HOH452 4.0 27.9 1.0 NE A:ARG117 4.1 17.1 1.0 CE1 A:HIS112 4.2 16.1 1.0 O A:HOH445 4.2 32.7 1.0 ND1 A:HIS238 4.3 23.9 1.0 CG A:HIS238 4.3 22.2 1.0 NE2 A:HIS177 4.4 15.4 1.0 O A:HOH453 4.4 26.7 1.0 CZ A:ARG117 4.5 22.2 1.0 CA A:OCS196 4.5 16.9 1.0 NE2 A:HIS112 4.5 21.0 1.0 CE1 A:HIS177 4.5 18.6 1.0 CB A:ASP116 4.6 20.3 1.0 O A:HOH511 4.8 28.6 1.0 O A:HOH528 4.9 37.6 1.0

M.B.Kupper, K.Herzog, S.Bennink, P.Schlomer, P.Bogaerts, Y.Glupczynski, R.Fischer, C.Bebrone, K.M.Hoffmann. The Three-Dimensional Structure of Vim-31 - A Metallo-Beta-Lactamase From Enterobacter Cloacae in Its Native and Oxidized Form. Febs J. V. 282 2352 2015.
ISSN: ISSN 1742-464X
PubMed: 25825035
DOI: 10.1111/FEBS.13283