Zinc in PDB 8p9p: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2408

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2408, PDB code: 8p9p 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)	29.01 / 1.14
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.51, 67.78, 40.21, 90, 93.42, 90
R / Rfree (%)	12 / 13.5

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2408 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2408 (pdb code 8p9p). 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 2408, PDB code: 8p9p:
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 2408


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 2408 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.6 occ:1.00 NE2 A:HIS179 2.0 9.9 1.0 NE2 A:HIS114 2.0 9.3 1.0 ND1 A:HIS116 2.0 9.8 1.0 HB2 A:HIS116 2.9 10.7 1.0 CE1 A:HIS114 3.0 8.8 1.0 CD2 A:HIS179 3.0 9.7 1.0 CE1 A:HIS116 3.0 10.7 1.0 CE1 A:HIS179 3.0 9.5 1.0 CD2 A:HIS114 3.0 8.1 1.0 CG A:HIS116 3.1 9.5 1.0 HE1 A:HIS114 3.1 10.6 1.0 HD2 A:HIS179 3.1 11.6 1.0 HE1 A:HIS116 3.1 12.8 1.0 H161 A:XB4303 3.2 12.2 1.0 HE1 A:HIS179 3.2 11.4 1.0 HD2 A:HIS114 3.3 9.7 1.0 CB A:HIS116 3.4 8.9 1.0 ZN A:ZN302 3.5 9.7 1.0 HB3 A:HIS116 3.7 10.7 1.0 H191 A:XB4303 3.7 13.2 1.0 HB2 A:CYS198 3.7 13.0 1.0 OD1 A:ASP118 3.9 9.8 1.0 O14 A:XB4303 3.9 10.1 1.0 H212 A:XB4303 4.1 16.6 1.0 ND1 A:HIS114 4.1 8.5 1.0 CG A:HIS179 4.1 10.0 1.0 NE2 A:HIS116 4.1 12.0 1.0 ND1 A:HIS179 4.1 10.2 1.0 N16 A:XB4303 4.1 10.2 1.0 CG A:HIS114 4.2 8.3 1.0 CD2 A:HIS116 4.2 10.8 1.0 HB3 A:CYS198 4.2 13.0 1.0 CB A:CYS198 4.2 10.8 1.0 SG A:CYS198 4.3 9.4 1.0 H A:HIS116 4.5 10.2 1.0 OD2 A:ASP118 4.5 10.0 1.0 CG A:ASP118 4.6 9.5 1.0 C19 A:XB4303 4.6 11.0 1.0 HG2 A:ARG119 4.7 10.6 1.0 HB3 A:SER180 4.7 12.8 1.0 C13 A:XB4303 4.7 10.4 1.0 C21 A:XB4303 4.7 13.9 1.0 H211 A:XB4303 4.7 16.6 1.0 HE A:ARG119 4.8 10.5 1.0 CA A:HIS116 4.8 8.6 1.0 HD1 A:HIS114 4.9 10.2 1.0 HE2 A:HIS116 4.9 14.4 1.0 HG3 A:ARG119 4.9 10.6 1.0 HD1 A:HIS179 4.9 12.3 1.0 C12 A:XB4303 4.9 11.2 1.0 O A:HOH547 4.9 12.8 0.9

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2408


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 2408 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.7 occ:0.97 NE2 A:HIS240 2.1 9.1 1.0 O14 A:XB4303 2.1 10.1 1.0 OD2 A:ASP118 2.3 10.0 1.0 SG A:CYS198 2.3 9.4 1.0 H161 A:XB4303 2.7 12.2 1.0 HB3 A:CYS198 3.1 13.0 1.0 CD2 A:HIS240 3.1 9.5 1.0 C13 A:XB4303 3.1 10.4 1.0 CE1 A:HIS240 3.1 10.3 1.0 HD2 A:HIS240 3.2 11.4 1.0 N16 A:XB4303 3.2 10.2 1.0 HH21 A:ARG119 3.2 12.7 1.0 CB A:CYS198 3.3 10.8 1.0 CG A:ASP118 3.3 9.5 1.0 HE1 A:HIS240 3.4 12.4 1.0 C12 A:XB4303 3.4 11.2 1.0 HE A:ARG119 3.5 10.5 1.0 ZN A:ZN301 3.5 9.6 1.0 OD1 A:ASP118 3.6 9.8 1.0 HB2 A:CYS198 3.6 13.0 1.0 HE1 A:HIS114 3.6 10.6 1.0 NH2 A:ARG119 3.9 10.6 1.0 H191 A:XB4303 4.1 13.2 1.0 NE2 A:HIS179 4.2 9.9 1.0 NE A:ARG119 4.2 8.8 1.0 CG A:HIS240 4.2 9.3 1.0 ND1 A:HIS240 4.2 10.0 1.0 HE1 A:HIS179 4.3 11.4 1.0 O15 A:XB4303 4.3 12.0 1.0 CE1 A:HIS114 4.3 8.8 1.0 O A:HOH510 4.3 11.3 0.9 CE1 A:HIS179 4.4 9.5 1.0 C17 A:XB4303 4.4 10.6 1.0 NE2 A:HIS114 4.4 9.3 1.0 HH22 A:ARG119 4.4 12.7 1.0 CZ A:ARG119 4.5 9.1 1.0 HA A:CYS198 4.5 12.4 1.0 H091 A:XB4303 4.5 14.5 1.0 CA A:CYS198 4.5 10.3 1.0 HA3 A:GLY239 4.5 11.3 1.0 C11 A:XB4303 4.6 10.4 1.0 CB A:ASP118 4.6 9.6 1.0 HB2 A:ASP118 4.7 11.5 1.0 HG A:SER69 4.8 18.9 0.2 OG A:SER69 4.8 15.8 0.2 HB3 A:ASP118 4.9 11.5 1.0 CD2 A:HIS179 5.0 9.7 1.0 HG2 A:ARG119 5.0 10.6 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 2408 To Be Published.