Zinc in PDB 8p9q: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455, PDB code: 8p9q 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)	34.61 / 1.08
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.65, 67.88, 40.3, 90, 93.18, 90
R / Rfree (%)	12.7 / 14

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455 (pdb code 8p9q). 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 2455, PDB code: 8p9q:
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 2455


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 2455 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.5 occ:0.82 O A:HOH489 1.9 8.2 0.7 NE2 A:HIS179 2.0 12.0 1.0 ND1 A:HIS116 2.0 11.3 1.0 NE2 A:HIS114 2.1 10.9 1.0 HB2 A:HIS116 2.9 12.9 1.0 CE1 A:HIS116 3.0 13.2 1.0 CE1 A:HIS179 3.0 12.5 1.0 CD2 A:HIS179 3.0 11.9 1.0 CE1 A:HIS114 3.0 10.0 1.0 CG A:HIS116 3.0 11.6 1.0 CD2 A:HIS114 3.1 10.4 1.0 HE1 A:HIS116 3.1 15.8 1.0 HE1 A:HIS179 3.2 15.0 1.0 H091 A:XC6303 3.2 13.5 0.6 HD2 A:HIS179 3.2 14.2 1.0 HE1 A:HIS114 3.2 11.9 1.0 H091 A:XC6303 3.2 16.6 0.4 HD2 A:HIS114 3.2 12.5 1.0 O03 A:XC6303 3.4 19.7 0.4 CB A:HIS116 3.4 10.8 1.0 H051 A:XC6303 3.5 16.8 0.6 ZN A:ZN302 3.5 10.3 0.8 H051 A:XC6303 3.5 19.6 0.4 O03 A:XC6303 3.6 16.7 0.6 HB3 A:HIS116 3.6 12.9 1.0 OD1 A:ASP118 3.8 12.4 1.0 O13 A:XC6303 3.9 10.9 0.4 HB2 A:CYS198 3.9 13.5 1.0 O13 A:XC6303 4.0 12.6 0.6 ND1 A:HIS179 4.1 13.0 1.0 NE2 A:HIS116 4.1 13.8 1.0 HB3 A:CYS198 4.1 13.5 1.0 CG A:HIS179 4.1 12.2 1.0 ND1 A:HIS114 4.1 10.3 1.0 CD2 A:HIS116 4.2 13.5 1.0 N09 A:XC6303 4.2 11.2 0.6 CG A:HIS114 4.2 10.1 1.0 C02 A:XC6303 4.2 19.6 0.4 N09 A:XC6303 4.2 13.8 0.4 CB A:CYS198 4.3 11.3 1.0 C02 A:XC6303 4.3 17.9 0.6 SG A:CYS198 4.4 10.9 1.0 H A:HIS116 4.5 11.6 1.0 OD2 A:ASP118 4.5 11.8 1.0 C05 A:XC6303 4.5 14.0 0.6 C05 A:XC6303 4.6 16.3 0.4 CG A:ASP118 4.6 11.3 1.0 HB3 A:SER180 4.7 15.6 1.0 HG2 A:ARG119 4.7 11.2 1.0 HE A:ARG119 4.7 11.7 1.0 C11 A:XC6303 4.8 13.3 0.4 C11 A:XC6303 4.8 11.8 0.6 CA A:HIS116 4.8 10.0 1.0 O04 A:XC6303 4.8 17.3 0.6 O04 A:XC6303 4.8 18.7 0.4 HE2 A:HIS116 4.9 16.6 1.0 HD1 A:HIS179 4.9 15.6 1.0 O A:HOH560 4.9 14.7 0.9 HG3 A:ARG119 4.9 11.2 1.0 HD1 A:HIS114 4.9 12.4 1.0 C10 A:XC6303 5.0 14.1 0.4 C10 A:XC6303 5.0 11.6 0.6 H013 A:XC6303 5.0 25.4 0.4

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455


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 2455 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.3 occ:0.79 O A:HOH489 2.0 8.2 0.7 O13 A:XC6303 2.1 12.6 0.6 NE2 A:HIS240 2.1 12.2 1.0 O13 A:XC6303 2.1 10.9 0.4 SG A:CYS198 2.3 10.9 1.0 OD2 A:ASP118 2.3 11.8 1.0 H091 A:XC6303 2.7 13.5 0.6 H091 A:XC6303 2.8 16.6 0.4 CD2 A:HIS240 3.0 11.4 1.0 C11 A:XC6303 3.0 13.3 0.4 C11 A:XC6303 3.0 11.8 0.6 HB3 A:CYS198 3.1 13.5 1.0 HD2 A:HIS240 3.1 13.7 1.0 CE1 A:HIS240 3.2 12.5 1.0 N09 A:XC6303 3.2 11.2 0.6 HH21 A:ARG119 3.2 13.7 1.0 N09 A:XC6303 3.3 13.8 0.4 CB A:CYS198 3.3 11.3 1.0 CG A:ASP118 3.3 11.3 1.0 C10 A:XC6303 3.4 11.6 0.6 C10 A:XC6303 3.4 14.1 0.4 HE1 A:HIS240 3.4 15.0 1.0 HE A:ARG119 3.5 11.7 1.0 ZN A:ZN301 3.5 10.5 0.8 HE1 A:HIS114 3.6 11.9 1.0 OD1 A:ASP118 3.7 12.4 1.0 HB2 A:CYS198 3.7 13.5 1.0 NH2 A:ARG119 3.9 11.4 1.0 H051 A:XC6303 4.1 16.8 0.6 H051 A:XC6303 4.1 19.6 0.4 NE2 A:HIS179 4.2 12.0 1.0 O12 A:XC6303 4.2 15.5 0.4 HE1 A:HIS179 4.2 15.0 1.0 NE A:ARG119 4.2 9.8 1.0 CG A:HIS240 4.2 11.5 1.0 O12 A:XC6303 4.2 12.8 0.6 ND1 A:HIS240 4.2 11.8 1.0 CE1 A:HIS114 4.3 10.0 1.0 CE1 A:HIS179 4.3 12.5 1.0 C08 A:XC6303 4.3 12.1 0.6 O A:HOH536 4.3 12.3 0.7 C08 A:XC6303 4.4 14.2 0.4 NE2 A:HIS114 4.4 10.9 1.0 HH22 A:ARG119 4.4 13.7 1.0 CZ A:ARG119 4.4 9.9 1.0 H161 A:XC6303 4.4 20.8 0.4 HA A:CYS198 4.4 13.7 1.0 CA A:CYS198 4.5 11.4 1.0 HA3 A:GLY239 4.6 12.9 1.0 C14 A:XC6303 4.6 14.8 0.4 C14 A:XC6303 4.6 12.3 0.6 H261 A:XC6303 4.6 19.9 0.6 CB A:ASP118 4.7 10.9 1.0 HB2 A:ASP118 4.8 13.1 1.0 HB3 A:ASP118 4.9 13.1 1.0 CD2 A:HIS179 4.9 11.9 1.0 O03 A:XC6303 4.9 19.7 0.4

K.Calvopina, J.Brem, A.J.M.Farley, M.D.Allen, C.J.Schofield. Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2455 To Be Published.