Zinc in PDB 8p9t: Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2483

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2483, PDB code: 8p9t 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)	34.12 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.535, 67.89, 40.326, 90, 93.45, 90
R / Rfree (%)	11.2 / 12.7

The structure of Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2483 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2483 (pdb code 8p9t). 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 2483, PDB code: 8p9t:
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 2483


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 2483 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.4 occ:0.87 O A:HOH470 1.9 9.6 1.0 NE2 A:HIS179 2.0 10.0 1.0 ND1 A:HIS116 2.0 10.6 1.0 NE2 A:HIS114 2.1 8.9 1.0 HB2 A:HIS116 2.9 10.2 1.0 CE1 A:HIS116 3.0 10.6 1.0 CE1 A:HIS179 3.0 10.8 1.0 CD2 A:HIS179 3.0 9.8 1.0 CE1 A:HIS114 3.0 8.2 1.0 CG A:HIS116 3.0 9.8 1.0 CD2 A:HIS114 3.1 8.9 1.0 HE1 A:HIS116 3.1 12.8 1.0 HE1 A:HIS179 3.2 12.9 1.0 HE1 A:HIS114 3.2 9.9 1.0 HD2 A:HIS179 3.2 11.8 1.0 H121 A:XCQ303 3.2 12.3 1.0 HD2 A:HIS114 3.3 10.7 1.0 CB A:HIS116 3.4 8.5 1.0 ZN A:ZN302 3.5 8.9 0.8 O05 A:XCQ303 3.5 15.7 1.0 H021 A:XCQ303 3.6 14.3 1.0 HB3 A:HIS116 3.6 10.2 1.0 OD1 A:ASP118 3.8 10.4 1.0 HB2 A:CYS198 3.9 11.8 1.0 O15 A:XCQ303 4.0 11.0 1.0 NE2 A:HIS116 4.1 11.8 1.0 ND1 A:HIS179 4.1 11.1 1.0 ND1 A:HIS114 4.1 8.3 1.0 CG A:HIS179 4.1 10.7 1.0 HB3 A:CYS198 4.1 11.8 1.0 CD2 A:HIS116 4.1 11.2 1.0 CG A:HIS114 4.2 8.0 1.0 N12 A:XCQ303 4.2 10.3 1.0 CB A:CYS198 4.3 9.8 1.0 C04 A:XCQ303 4.3 14.9 1.0 SG A:CYS198 4.4 9.2 1.0 H A:HIS116 4.5 9.2 1.0 OD2 A:ASP118 4.5 10.1 1.0 CG A:ASP118 4.6 9.2 1.0 C02 A:XCQ303 4.6 11.9 1.0 HB3 A:SER180 4.7 13.1 1.0 HG2 A:ARG119 4.7 8.8 1.0 HE A:ARG119 4.8 9.7 1.0 C14 A:XCQ303 4.8 10.8 1.0 CA A:HIS116 4.8 8.0 1.0 HE2 A:HIS116 4.9 14.2 1.0 HD1 A:HIS179 4.9 13.3 1.0 O03 A:XCQ303 4.9 14.9 1.0 HD1 A:HIS114 4.9 10.0 1.0 O A:HOH544 4.9 14.1 0.9 H062 A:XCQ303 4.9 21.6 1.0 HG3 A:ARG119 4.9 8.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Metallo-Beta-Lactamase VIM1 with 2483


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 2483 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.9 occ:0.81 O A:HOH470 2.0 9.6 1.0 NE2 A:HIS240 2.1 9.7 1.0 O15 A:XCQ303 2.1 11.0 1.0 SG A:CYS198 2.3 9.2 1.0 OD2 A:ASP118 2.4 10.1 1.0 H121 A:XCQ303 2.7 12.3 1.0 CD2 A:HIS240 3.0 9.9 1.0 C14 A:XCQ303 3.1 10.8 1.0 HB3 A:CYS198 3.1 11.8 1.0 HD2 A:HIS240 3.1 11.9 1.0 CE1 A:HIS240 3.2 10.4 1.0 N12 A:XCQ303 3.2 10.3 1.0 HH21 A:ARG119 3.3 12.1 1.0 CB A:CYS198 3.3 9.8 1.0 CG A:ASP118 3.4 9.2 1.0 C13 A:XCQ303 3.4 10.7 1.0 HE1 A:HIS240 3.4 12.5 1.0 HE A:ARG119 3.5 9.7 1.0 ZN A:ZN301 3.5 9.4 0.9 HE1 A:HIS114 3.6 9.9 1.0 OD1 A:ASP118 3.7 10.4 1.0 HB2 A:CYS198 3.7 11.8 1.0 NH2 A:ARG119 3.9 10.1 1.0 H021 A:XCQ303 4.1 14.3 1.0 NE2 A:HIS179 4.1 10.0 1.0 NE A:ARG119 4.2 8.1 1.0 HE1 A:HIS179 4.2 12.9 1.0 CG A:HIS240 4.2 9.7 1.0 ND1 A:HIS240 4.2 10.2 1.0 O16 A:XCQ303 4.2 12.8 1.0 CE1 A:HIS114 4.2 8.2 1.0 CE1 A:HIS179 4.3 10.8 1.0 O A:HOH497 4.3 8.7 0.6 C11 A:XCQ303 4.3 10.5 1.0 NE2 A:HIS114 4.4 8.9 1.0 CZ A:ARG119 4.4 8.4 1.0 HH22 A:ARG119 4.5 12.1 1.0 HA A:CYS198 4.5 11.3 1.0 H191 A:XCQ303 4.5 17.5 1.0 CA A:CYS198 4.5 9.4 1.0 C17 A:XCQ303 4.6 11.2 1.0 HA3 A:GLY239 4.6 10.9 1.0 CB A:ASP118 4.7 8.8 1.0 HB2 A:ASP118 4.7 10.6 1.0 CD2 A:HIS179 4.9 9.8 1.0 HB3 A:ASP118 4.9 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 2483 To Be Published.