Zinc in PDB 8pgf: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941, PDB code: 8pgf was solved by K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.05 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.497, 67.627, 40.267, 90, 93.53, 90
R / Rfree (%)	11.7 / 13.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941 (pdb code 8pgf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941, PDB code: 8pgf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941


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 VIM1 with 2941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.2 occ:0.71 O A:HOH546 1.9 9.2 0.5 ND1 A:HIS116 2.0 15.7 1.0 NE2 A:HIS179 2.0 13.4 1.0 NE2 A:HIS114 2.1 13.6 1.0 CE1 A:HIS116 2.9 15.3 1.0 HB2 A:HIS116 2.9 14.4 1.0 CE1 A:HIS179 3.0 14.2 1.0 CD2 A:HIS179 3.0 13.2 1.0 CG A:HIS116 3.0 13.7 1.0 HE1 A:HIS116 3.1 18.4 1.0 CE1 A:HIS114 3.1 12.2 1.0 CD2 A:HIS114 3.1 12.7 1.0 HE1 A:HIS179 3.2 17.0 1.0 HD2 A:HIS179 3.2 15.8 1.0 H371 A:XMU303 3.2 16.3 0.7 HE1 A:HIS114 3.2 14.6 1.0 HD2 A:HIS114 3.3 15.2 1.0 CB A:HIS116 3.4 12.0 1.0 H021 A:XMU303 3.4 20.1 0.7 ZN A:ZN302 3.6 9.9 0.5 HB3 A:HIS116 3.6 14.4 1.0 O05 A:XMU303 3.8 31.4 0.7 HB2 A:CYS198 3.8 17.8 1.0 OD1 A:ASP118 3.9 17.0 1.0 O36 A:XMU303 4.0 13.9 0.7 NE2 A:HIS116 4.0 16.0 1.0 ND1 A:HIS179 4.1 14.6 1.0 CG A:HIS179 4.1 13.8 1.0 CD2 A:HIS116 4.1 15.6 1.0 N37 A:XMU303 4.2 13.6 0.7 ND1 A:HIS114 4.2 12.5 1.0 O A:HOH438 4.2 3.1 0.1 CG A:HIS114 4.3 11.8 1.0 HB3 A:CYS198 4.3 17.8 1.0 CB A:CYS198 4.4 14.8 1.0 C04 A:XMU303 4.4 32.6 0.7 SG A:CYS198 4.4 15.6 1.0 C02 A:XMU303 4.5 16.8 0.7 OD2 A:ASP118 4.6 17.0 1.0 H A:HIS116 4.6 12.7 1.0 HB3 A:SER180 4.7 16.3 1.0 CG A:ASP118 4.7 14.9 1.0 C34 A:XMU303 4.8 15.2 0.7 N03 A:XMU303 4.8 21.5 0.7 HE2 A:HIS116 4.8 19.2 1.0 CA A:HIS116 4.8 10.8 1.0 HD1 A:HIS179 4.8 17.6 1.0 HE A:ARG119 4.8 13.1 1.0 HG2 A:ARG119 4.9 12.3 1.0 H071 A:XMU303 4.9 60.2 0.7 C33 A:XMU303 4.9 13.4 0.7 HD1 A:HIS114 4.9 15.0 1.0 O A:HOH536 5.0 17.0 0.6 HD2 A:HIS116 5.0 18.8 1.0 H012 A:XMU303 5.0 16.9 0.7

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941


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 VIM1 with 2941 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.9 occ:0.47 O36 A:XMU303 2.0 13.9 0.7 O A:HOH546 2.0 9.2 0.5 NE2 A:HIS240 2.1 9.8 0.5 SG A:CYS198 2.3 15.6 1.0 OD2 A:ASP118 2.3 17.0 1.0 H371 A:XMU303 2.6 16.3 0.7 C34 A:XMU303 3.0 15.2 0.7 HB3 A:CYS198 3.0 17.8 1.0 CD2 A:HIS240 3.0 9.8 0.5 HD2 A:HIS240 3.1 11.7 0.5 HH21 A:ARG119 3.2 19.5 1.0 N37 A:XMU303 3.2 13.6 0.7 CE1 A:HIS240 3.2 10.9 0.5 CB A:CYS198 3.2 14.8 1.0 C33 A:XMU303 3.3 13.4 0.7 CG A:ASP118 3.4 14.9 1.0 HE1 A:HIS240 3.4 13.1 0.5 HE A:ARG119 3.5 13.1 1.0 HE1 A:HIS114 3.5 14.6 1.0 HB2 A:CYS198 3.6 17.8 1.0 ZN A:ZN301 3.6 12.2 0.7 O A:HOH438 3.6 3.1 0.1 OD1 A:ASP118 3.7 17.0 1.0 NH2 A:ARG119 3.9 16.3 1.0 H021 A:XMU303 4.1 20.1 0.7 NE2 A:HIS179 4.1 13.4 1.0 HE1 A:HIS179 4.1 17.0 1.0 O35 A:XMU303 4.2 18.6 0.7 CE1 A:HIS114 4.2 12.2 1.0 NE A:ARG119 4.2 10.9 1.0 CG A:HIS240 4.2 9.3 0.5 CE1 A:HIS179 4.2 14.2 1.0 ND1 A:HIS240 4.3 10.9 0.5 O A:HOH562 4.3 7.0 0.3 C38 A:XMU303 4.4 13.8 0.7 NE2 A:HIS114 4.4 13.6 1.0 HA A:CYS198 4.4 16.1 1.0 HH22 A:ARG119 4.4 19.5 1.0 CA A:CYS198 4.5 13.4 1.0 CZ A:ARG119 4.5 11.6 1.0 C19 A:XMU303 4.5 14.0 0.7 H211 A:XMU303 4.6 20.5 0.7 HA3 A:GLY239 4.7 15.1 1.0 CB A:ASP118 4.7 12.9 1.0 HB2 A:ASP118 4.9 15.5 1.0 HB3 A:HIS240 4.9 24.5 0.5 HB3 A:ASP118 4.9 15.5 1.0 CD2 A:HIS179 5.0 13.2 1.0 C02 A:XMU303 5.0 16.8 0.7

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2941 To Be Published.