Zinc in PDB 8pa5: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2540

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2540, PDB code: 8pa5 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)	40.02 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.34, 67.85, 40.09, 90, 93.39, 90
R / Rfree (%)	11.4 / 12.9

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2540 (pdb code 8pa5). 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 2540, PDB code: 8pa5:
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 2540


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 2540 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.5 occ:0.94 O A:HOH508 1.9 6.5 0.9 ND1 A:HIS116 2.0 8.0 1.0 NE2 A:HIS179 2.0 8.0 1.0 NE2 A:HIS114 2.1 7.8 1.0 HB2 A:HIS116 2.9 9.1 1.0 CE1 A:HIS116 3.0 8.9 1.0 CD2 A:HIS179 3.0 7.6 1.0 CE1 A:HIS114 3.0 7.6 1.0 CE1 A:HIS179 3.0 8.3 1.0 CG A:HIS116 3.0 7.9 1.0 CD2 A:HIS114 3.0 7.5 1.0 HE1 A:HIS116 3.2 10.7 1.0 HD2 A:HIS179 3.2 9.1 1.0 HE1 A:HIS114 3.2 9.2 1.0 HE1 A:HIS179 3.2 10.0 1.0 HD2 A:HIS114 3.2 9.0 1.0 H161 A:XMZ303 3.3 9.4 1.0 CB A:HIS116 3.4 7.6 1.0 ZN A:ZN302 3.5 7.1 0.9 HB3 A:HIS116 3.7 9.1 1.0 H191 A:XMZ303 3.7 11.1 1.0 HB2 A:CYS198 3.8 10.3 1.0 OD1 A:ASP118 3.8 8.5 1.0 O14 A:XMZ303 4.0 8.2 1.0 HB3 A:CYS198 4.1 10.3 1.0 NE2 A:HIS116 4.1 10.3 1.0 ND1 A:HIS114 4.1 7.5 1.0 ND1 A:HIS179 4.1 8.4 1.0 CG A:HIS179 4.1 7.9 1.0 CD2 A:HIS116 4.1 9.6 1.0 CG A:HIS114 4.2 7.3 1.0 CB A:CYS198 4.2 8.6 1.0 N16 A:XMZ303 4.2 7.8 1.0 H212 A:XMZ303 4.2 14.7 1.0 SG A:CYS198 4.3 7.6 1.0 OD2 A:ASP118 4.5 8.5 1.0 H A:HIS116 4.5 8.6 1.0 CG A:ASP118 4.6 7.5 1.0 H211 A:XMZ303 4.6 14.7 1.0 C19 A:XMZ303 4.6 9.2 1.0 HG2 A:ARG119 4.7 9.0 1.0 C21 A:XMZ303 4.7 12.2 1.0 HE A:ARG119 4.7 9.1 1.0 HB3 A:SER180 4.7 11.4 1.0 C13 A:XMZ303 4.8 8.2 1.0 CA A:HIS116 4.8 7.4 1.0 HB3 A:ASN210 4.8 14.0 1.0 HE2 A:HIS116 4.9 12.3 1.0 HD1 A:HIS114 4.9 9.0 1.0 HD1 A:HIS179 4.9 10.1 1.0 HG3 A:ARG119 4.9 9.0 1.0 O A:HOH530 5.0 9.4 0.9 HD2 A:HIS116 5.0 11.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2540


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 2540 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.1 occ:0.86 O A:HOH508 2.0 6.5 0.9 NE2 A:HIS240 2.1 8.1 1.0 O14 A:XMZ303 2.2 8.2 1.0 OD2 A:ASP118 2.3 8.5 1.0 SG A:CYS198 2.3 7.6 1.0 H161 A:XMZ303 2.7 9.4 1.0 CD2 A:HIS240 3.0 8.0 1.0 HB3 A:CYS198 3.1 10.3 1.0 HD2 A:HIS240 3.1 9.6 1.0 CE1 A:HIS240 3.1 8.0 1.0 C13 A:XMZ303 3.2 8.2 1.0 HH21 A:ARG119 3.3 10.7 1.0 N16 A:XMZ303 3.3 7.8 1.0 CG A:ASP118 3.3 7.5 1.0 CB A:CYS198 3.3 8.6 1.0 HE1 A:HIS240 3.3 9.6 1.0 ZN A:ZN301 3.5 7.5 0.9 C12 A:XMZ303 3.6 8.3 1.0 HE A:ARG119 3.6 9.1 1.0 OD1 A:ASP118 3.6 8.5 1.0 HE1 A:HIS114 3.7 9.2 1.0 HB2 A:CYS198 3.7 10.3 1.0 NH2 A:ARG119 3.9 8.9 1.0 H191 A:XMZ303 4.1 11.1 1.0 HE1 A:HIS179 4.1 10.0 1.0 NE2 A:HIS179 4.2 8.0 1.0 CG A:HIS240 4.2 8.2 1.0 ND1 A:HIS240 4.2 8.0 1.0 NE A:ARG119 4.2 7.6 1.0 CE1 A:HIS179 4.3 8.3 1.0 O A:HOH566 4.3 7.7 0.7 O15 A:XMZ303 4.3 9.9 1.0 CE1 A:HIS114 4.4 7.6 1.0 C17 A:XMZ303 4.4 8.5 1.0 H091 A:XMZ303 4.4 14.1 1.0 NE2 A:HIS114 4.4 7.8 1.0 HH22 A:ARG119 4.5 10.7 1.0 HA A:CYS198 4.5 10.4 1.0 CZ A:ARG119 4.5 7.5 1.0 H093 A:XMZ303 4.6 14.1 1.0 CA A:CYS198 4.6 8.6 1.0 CB A:ASP118 4.6 8.0 1.0 HA3 A:GLY239 4.6 10.4 1.0 HB2 A:ASP118 4.7 9.6 1.0 C11 A:XMZ303 4.8 8.9 1.0 HB3 A:ASP118 4.8 9.6 1.0 HG A:SER69 4.9 13.6 0.1 HD1 A:HIS240 5.0 9.6 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 2540 To Be Published.