Zinc in PDB 8ph0: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3637

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3637, PDB code: 8ph0 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)	34.62 / 1.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.46, 68.02, 40.29, 90, 93.45, 90
R / Rfree (%)	14.4 / 17.6

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3637 (pdb code 8ph0). 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 3637, PDB code: 8ph0:
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 3637


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 3637 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.9 occ:0.93 O A:HOH486 1.8 6.3 0.5 NE2 A:HIS179 2.1 13.5 1.0 ND1 A:HIS116 2.1 13.8 1.0 NE2 A:HIS114 2.2 13.3 1.0 O13 A:YVO303 2.8 16.6 1.0 HB2 A:HIS116 2.9 14.9 1.0 CD2 A:HIS179 3.1 12.9 1.0 CE1 A:HIS116 3.1 14.2 1.0 CE1 A:HIS179 3.1 11.9 1.0 CE1 A:HIS114 3.1 13.5 1.0 CG A:HIS116 3.1 13.2 1.0 CD2 A:HIS114 3.1 12.4 1.0 H161 A:YVO303 3.2 20.5 1.0 HE1 A:HIS116 3.2 17.0 1.0 HD2 A:HIS179 3.2 15.5 1.0 HE1 A:HIS179 3.3 14.3 1.0 HE1 A:HIS114 3.3 16.2 1.0 HD2 A:HIS114 3.3 14.8 1.0 CB A:HIS116 3.4 12.4 1.0 ZN A:ZN302 3.6 13.0 0.8 C12 A:YVO303 3.6 17.6 1.0 HB3 A:HIS116 3.7 14.9 1.0 H021 A:YVO303 3.7 21.9 1.0 OD1 A:ASP118 3.8 14.6 1.0 HB2 A:CYS198 4.0 18.3 1.0 O20 A:YVO303 4.0 16.1 1.0 ND1 A:HIS179 4.2 13.3 1.0 NE2 A:HIS116 4.2 14.4 1.0 CG A:HIS179 4.2 13.2 1.0 ND1 A:HIS114 4.2 12.6 1.0 N16 A:YVO303 4.2 17.1 1.0 CD2 A:HIS116 4.2 13.8 1.0 HB3 A:CYS198 4.2 18.3 1.0 CG A:HIS114 4.3 12.3 1.0 N03 A:YVO303 4.4 18.5 1.0 CB A:CYS198 4.4 15.3 1.0 C02 A:YVO303 4.5 18.3 1.0 SG A:CYS198 4.5 14.5 1.0 OD2 A:ASP118 4.5 15.6 1.0 H A:HIS116 4.6 15.2 1.0 CG A:ASP118 4.6 13.4 1.0 O11 A:YVO303 4.7 17.9 1.0 HB3 A:SER180 4.8 16.7 1.0 HG2 A:ARG119 4.8 14.0 1.0 C18 A:YVO303 4.8 16.4 1.0 HE A:ARG119 4.8 15.0 1.0 CA A:HIS116 4.9 12.2 1.0 O A:HOH557 4.9 11.8 0.7 HD1 A:HIS179 4.9 16.0 1.0 HE2 A:HIS116 4.9 17.3 1.0 HD1 A:HIS114 5.0 15.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 3637


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 3637 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.0 occ:0.77 O20 A:YVO303 2.1 16.1 1.0 O A:HOH486 2.1 6.3 0.5 NE2 A:HIS240 2.2 14.4 1.0 SG A:CYS198 2.3 14.5 1.0 OD2 A:ASP118 2.4 15.6 1.0 H161 A:YVO303 2.7 20.5 1.0 HB3 A:CYS198 3.0 18.3 1.0 C18 A:YVO303 3.0 16.4 1.0 CD2 A:HIS240 3.1 15.2 1.0 HD2 A:HIS240 3.2 18.2 1.0 N16 A:YVO303 3.2 17.1 1.0 HH21 A:ARG119 3.2 17.5 1.0 CB A:CYS198 3.2 15.3 1.0 CE1 A:HIS240 3.3 15.5 1.0 C17 A:YVO303 3.4 16.8 1.0 CG A:ASP118 3.5 13.4 1.0 HE1 A:HIS240 3.5 18.6 1.0 HE1 A:HIS114 3.5 16.2 1.0 HE A:ARG119 3.6 15.0 1.0 ZN A:ZN301 3.6 12.9 0.9 HB2 A:CYS198 3.7 18.3 1.0 OD1 A:ASP118 3.8 14.6 1.0 H021 A:YVO303 3.8 21.9 1.0 NH2 A:ARG119 3.9 14.6 1.0 NE2 A:HIS179 4.2 13.5 1.0 O19 A:YVO303 4.2 17.7 1.0 NE A:ARG119 4.2 12.5 1.0 CE1 A:HIS114 4.2 13.5 1.0 CG A:HIS240 4.3 15.3 1.0 C15 A:YVO303 4.3 17.3 1.0 HE1 A:HIS179 4.3 14.3 1.0 ND1 A:HIS240 4.3 15.5 1.0 CE1 A:HIS179 4.3 11.9 1.0 O A:HOH524 4.4 9.1 0.5 HA A:CYS198 4.4 16.8 1.0 NE2 A:HIS114 4.4 13.3 1.0 HH22 A:ARG119 4.4 17.5 1.0 CZ A:ARG119 4.5 13.2 1.0 CA A:CYS198 4.5 14.0 1.0 C21 A:YVO303 4.6 17.6 1.0 O13 A:YVO303 4.6 16.6 1.0 HA3 A:GLY239 4.6 15.8 1.0 H231 A:YVO303 4.7 23.8 1.0 CB A:ASP118 4.8 13.1 1.0 HB2 A:ASP118 4.9 15.8 1.0 C02 A:YVO303 4.9 18.3 1.0 CD2 A:HIS179 4.9 12.9 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 3637 To Be Published.