Zinc in PDB 8pad: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2555

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2555, PDB code: 8pad 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)	34.60 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.48, 67.9, 40.28, 90, 93.5, 90
R / Rfree (%)	11.2 / 12.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2555 (pdb code 8pad). 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 2555, PDB code: 8pad:
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 2555


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 2555 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.7 occ:0.75 O A:HOH520 1.9 7.6 0.7 NE2 A:HIS179 2.0 10.6 1.0 ND1 A:HIS116 2.0 10.5 1.0 NE2 A:HIS114 2.1 9.8 1.0 O A:HOH401 2.9 38.4 0.8 HB2 A:HIS116 2.9 10.7 1.0 CE1 A:HIS116 3.0 11.1 1.0 CE1 A:HIS179 3.0 11.7 1.0 CD2 A:HIS179 3.0 9.3 1.0 CE1 A:HIS114 3.0 8.7 1.0 CG A:HIS116 3.1 9.6 1.0 CD2 A:HIS114 3.1 8.9 1.0 HE1 A:HIS116 3.1 13.3 1.0 HE1 A:HIS179 3.2 14.1 1.0 HD2 A:HIS179 3.2 11.2 1.0 HE1 A:HIS114 3.2 10.4 1.0 H371 A:XMU303 3.2 13.2 1.0 HD2 A:HIS114 3.3 10.7 1.0 CB A:HIS116 3.4 8.9 1.0 H021 A:XMU303 3.5 15.0 1.0 ZN A:ZN302 3.6 7.9 0.7 HB3 A:HIS116 3.7 10.7 1.0 HB2 A:CYS198 3.9 12.4 1.0 OD1 A:ASP118 3.9 10.5 1.0 O36 A:XMU303 4.0 11.5 1.0 O05 A:XMU303 4.0 22.9 1.0 ND1 A:HIS179 4.1 11.6 1.0 NE2 A:HIS116 4.1 12.6 1.0 CG A:HIS179 4.1 10.4 1.0 CD2 A:HIS116 4.2 11.9 1.0 ND1 A:HIS114 4.2 8.8 1.0 N37 A:XMU303 4.2 11.0 1.0 HB3 A:CYS198 4.2 12.4 1.0 CG A:HIS114 4.2 8.2 1.0 CB A:CYS198 4.3 10.3 1.0 SG A:CYS198 4.4 9.6 1.0 H A:HIS116 4.5 9.3 1.0 OD2 A:ASP118 4.5 10.8 1.0 C02 A:XMU303 4.6 12.5 1.0 CG A:ASP118 4.7 9.3 1.0 C04 A:XMU303 4.7 19.2 1.0 HB3 A:SER180 4.7 12.3 1.0 C34 A:XMU303 4.7 12.3 1.0 HE A:ARG119 4.8 9.6 1.0 HG2 A:ARG119 4.8 9.4 1.0 CA A:HIS116 4.8 8.2 1.0 HE2 A:HIS116 4.9 15.1 1.0 HD1 A:HIS179 4.9 13.9 1.0 HD1 A:HIS114 4.9 10.6 1.0 C33 A:XMU303 5.0 11.3 1.0 O A:HOH541 5.0 12.0 0.6 N03 A:XMU303 5.0 15.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2555


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 2555 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.9 occ:0.68 O A:HOH520 2.0 7.6 0.7 NE2 A:HIS240 2.1 10.3 1.0 O36 A:XMU303 2.1 11.5 1.0 SG A:CYS198 2.3 9.6 1.0 OD2 A:ASP118 2.3 10.8 1.0 H371 A:XMU303 2.6 13.2 1.0 CD2 A:HIS240 3.0 10.2 1.0 HB3 A:CYS198 3.1 12.4 1.0 C34 A:XMU303 3.1 12.3 1.0 HD2 A:HIS240 3.1 12.2 1.0 CE1 A:HIS240 3.2 10.5 1.0 N37 A:XMU303 3.2 11.0 1.0 HH21 A:ARG119 3.2 12.8 1.0 CB A:CYS198 3.3 10.3 1.0 CG A:ASP118 3.3 9.3 1.0 C33 A:XMU303 3.4 11.3 1.0 HE1 A:HIS240 3.4 12.6 1.0 HE A:ARG119 3.5 9.6 1.0 HE1 A:HIS114 3.5 10.4 1.0 ZN A:ZN301 3.6 8.7 0.8 HB2 A:CYS198 3.7 12.4 1.0 OD1 A:ASP118 3.7 10.5 1.0 NH2 A:ARG119 3.9 10.7 1.0 HE1 A:HIS179 4.1 14.1 1.0 H021 A:XMU303 4.1 15.0 1.0 NE2 A:HIS179 4.1 10.6 1.0 NE A:ARG119 4.2 8.0 1.0 CG A:HIS240 4.2 9.8 1.0 CE1 A:HIS114 4.2 8.7 1.0 ND1 A:HIS240 4.2 10.8 1.0 O35 A:XMU303 4.2 15.1 1.0 CE1 A:HIS179 4.2 11.7 1.0 C38 A:XMU303 4.3 11.7 1.0 O A:HOH556 4.4 8.7 0.6 NE2 A:HIS114 4.4 9.8 1.0 HH22 A:ARG119 4.4 12.8 1.0 HA A:CYS198 4.5 11.5 1.0 CZ A:ARG119 4.5 8.2 1.0 CA A:CYS198 4.5 9.6 1.0 HA3 A:GLY239 4.6 11.7 1.0 C19 A:XMU303 4.6 11.7 1.0 O A:HOH401 4.6 38.4 0.8 H211 A:XMU303 4.7 18.0 1.0 CB A:ASP118 4.7 9.3 1.0 HB2 A:ASP118 4.8 11.1 1.0 HB3 A:ASP118 4.9 11.1 1.0 CD2 A:HIS179 5.0 9.3 1.0

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2555 To Be Published.