Zinc in PDB 5n5g: Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1

The structure of Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1, PDB code: 5n5g was solved by R.Salimraj, P.Hinchliffe, J.Spencer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.25 / 1.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.760, 67.940, 40.360, 90.00, 94.01, 90.00
R / Rfree (%)	14.5 / 15.6

The binding sites of Zinc atom in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1 (pdb code 5n5g). 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 Di-Zinc Metallo-Beta-Lactamase Vim-1, PDB code: 5n5g:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:13.3 occ:0.94 O A:HOH533 1.9 14.7 1.0 NE2 A:HIS179 2.0 10.3 1.0 ND1 A:HIS116 2.1 12.6 1.0 NE2 A:HIS114 2.1 10.5 1.0 HB2 A:HIS116 2.9 11.2 1.0 CD2 A:HIS179 2.9 8.6 1.0 CE1 A:HIS114 3.0 11.7 1.0 CE1 A:HIS179 3.0 11.6 1.0 CE1 A:HIS116 3.0 12.3 1.0 CD2 A:HIS114 3.1 8.5 1.0 CG A:HIS116 3.1 11.0 1.0 HD2 A:HIS179 3.1 10.3 1.0 HE1 A:HIS114 3.2 14.1 1.0 HE1 A:HIS116 3.2 14.8 1.0 HE1 A:HIS179 3.2 13.9 1.0 HD2 A:HIS114 3.3 10.2 1.0 CB A:HIS116 3.4 9.3 1.0 HB3 A:HIS116 3.6 11.2 1.0 ZN A:ZN302 3.6 24.6 0.7 OD1 A:ASP118 3.9 13.8 1.0 O A:HOH555 4.1 21.7 1.0 CG A:HIS179 4.1 8.6 1.0 ND1 A:HIS179 4.1 11.0 1.0 ND1 A:HIS114 4.1 9.5 1.0 NE2 A:HIS116 4.1 11.9 1.0 CG A:HIS114 4.2 8.8 1.0 CD2 A:HIS116 4.2 9.9 1.0 CB A:CYS198 4.3 10.7 1.0 SG A:CYS198 4.4 15.3 1.0 OD2 A:ASP118 4.5 17.5 1.0 H A:HIS116 4.5 10.2 1.0 CG A:ASP118 4.6 10.9 1.0 HD22 A:ASN210 4.7 49.5 1.0 HB3 A:SER180 4.7 10.6 1.0 HE A:ARG119 4.8 13.3 1.0 HG2 A:ARG119 4.8 12.1 1.0 CA A:HIS116 4.8 7.8 1.0 HD1 A:HIS114 4.9 11.4 1.0 HD1 A:HIS179 4.9 13.2 1.0 HG3 A:ARG119 4.9 12.1 1.0 HE2 A:HIS116 4.9 14.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:24.6 occ:0.73 O A:HOH555 2.1 21.7 1.0 OD2 A:ASP118 2.2 17.5 1.0 O A:HOH533 2.2 14.7 1.0 NE2 A:HIS240 2.2 13.2 1.0 SG A:CYS198 2.5 15.3 1.0 HH21 A:ARG119 3.0 24.5 1.0 CE1 A:HIS240 3.2 12.9 1.0 CD2 A:HIS240 3.2 14.2 1.0 CG A:ASP118 3.3 10.9 1.0 HE1 A:HIS240 3.3 15.5 1.0 HD2 A:HIS240 3.3 17.1 1.0 HE A:ARG119 3.4 13.3 1.0 CB A:CYS198 3.5 10.7 1.0 ZN A:ZN301 3.6 13.3 0.9 OD1 A:ASP118 3.6 13.8 1.0 HE1 A:HIS114 3.7 14.1 1.0 NH2 A:ARG119 3.9 20.4 1.0 NE A:ARG119 4.2 11.1 1.0 NE2 A:HIS179 4.2 10.3 1.0 ND1 A:HIS240 4.3 13.0 1.0 CG A:HIS240 4.3 12.2 1.0 HE1 A:HIS179 4.3 13.9 1.0 CE1 A:HIS114 4.4 11.7 1.0 HH22 A:ARG119 4.5 24.5 1.0 CE1 A:HIS179 4.5 11.6 1.0 O A:HOH595 4.5 24.8 1.0 NE2 A:HIS114 4.5 10.5 1.0 CZ A:ARG119 4.5 11.4 1.0 CB A:ASP118 4.6 9.6 1.0 HB2 A:ASP118 4.6 11.5 1.0 CA A:CYS198 4.8 10.3 1.0 HB3 A:ASP118 4.8 11.5 1.0 O A:HOH598 4.8 33.5 1.0 HA3 A:GLY239 4.8 11.4 1.0 HG2 A:ARG119 4.9 12.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Di-Zinc Metallo-Beta-Lactamase Vim-1


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 Di-Zinc Metallo-Beta-Lactamase Vim-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:10.5 occ:0.54 O A:HOH417 2.2 28.4 1.0 O A:HOH467 2.3 16.7 1.0 O22 A:BCN304 2.4 10.5 1.0 O A:HOH551 2.4 17.8 1.0 O4 A:BCN304 2.5 14.7 1.0 O A:HOH405 2.5 41.1 1.0 O6 A:BCN304 2.5 20.4 1.0 O A:HOH549 2.6 21.0 1.0 N1 A:BCN304 2.7 15.0 1.0 C2 A:BCN304 3.3 12.2 1.0 C1 A:BCN304 3.4 14.0 1.0 C3 A:BCN304 3.4 16.1 1.0 C6 A:BCN304 3.4 19.0 1.0 C4 A:BCN304 3.5 15.6 1.0 C5 A:BCN304 3.5 17.5 1.0 HA2 A:GLY88 3.6 11.3 1.0 H A:ALA89 3.8 10.6 1.0 HA3 A:GLY88 4.3 11.3 1.0 OE2 A:GLU149 4.3 17.8 1.0 OD2 A:ASP117 4.4 12.1 1.0 CA A:GLY88 4.4 9.4 1.0 O21 A:BCN304 4.5 12.9 1.0 O A:HOH671 4.5 22.8 1.0 OD1 A:ASP117 4.5 10.9 1.0 N A:ALA89 4.6 8.8 1.0 O A:HOH594 4.6 46.7 1.0 HB2 A:ALA89 4.8 13.2 1.0 CG A:ASP117 4.9 9.1 1.0 HB3 A:ALA89 5.0 13.2 1.0 HA3 A:GLY121 5.0 9.0 1.0

R.Salimraj, P.Hinchliffe, M.Kosmopoulou, J.M.Tyrrell, J.Brem, S.S.Van Berkel, A.Verma, R.J.Owens, M.A.Mcdonough, T.R.Walsh, C.J.Schofield, J.Spencer. Crystal Structures of Vim-1 Complexes Explain Active Site Heterogeneity in Vim-Class Metallo-Beta-Lactamases. Febs J. V. 286 169 2019.
ISSN: ISSN 1742-4658
PubMed: 30430727
DOI: 10.1111/FEBS.14695