Zinc in PDB 8u00: Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides

The structure of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides, PDB code: 8u00 was solved by Y.Kim, N.Maltseva, M.Endres, A.Joachimiak, Center For Structural Biologyof Infectious Diseases (Csbid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.10 / 1.85
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	85.341, 85.341, 78.844, 90, 90, 90
R / Rfree (%)	18.9 / 22.5

The structure of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	4 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides (pdb code 8u00). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides, PDB code: 8u00:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


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 Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:47.0 occ:1.00 SG A:CYS176 2.3 43.7 1.0 SG A:CYS196 2.3 41.9 0.7 SG A:CYS196 2.3 43.2 0.3 CL A:CL307 2.4 39.2 1.0 O A:HOH446 2.8 38.5 1.0 CB A:CYS176 3.1 45.9 1.0 CB A:CYS196 3.1 41.9 0.3 CB A:CYS196 3.2 42.8 0.7 N A:LEU198 3.9 36.9 1.0 CB A:HIS172 4.0 41.7 1.0 N A:SER197 4.0 39.9 1.0 O A:THR169 4.1 44.7 1.0 CA A:CYS176 4.3 44.0 1.0 CA A:CYS196 4.4 40.6 0.3 CA A:CYS196 4.4 40.5 0.7 CA A:LEU198 4.5 35.5 1.0 C A:CYS196 4.5 41.6 0.3 C A:CYS196 4.5 41.7 0.7 CB A:HIS96 4.6 39.1 1.0 N A:HIS172 4.7 43.4 1.0 OG1 A:THR169 4.7 46.4 1.0 CG A:HIS172 4.8 40.0 1.0 CG A:HIS96 4.8 37.6 1.0 C A:SER197 4.8 42.3 1.0 ND1 A:HIS96 4.9 35.4 1.0 CD2 A:HIS172 4.9 38.9 1.0 CA A:SER197 4.9 41.2 1.0 N A:SER199 4.9 37.0 1.0 CA A:HIS172 4.9 45.9 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


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 Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:39.4 occ:1.00 OD2 A:ASP100 2.0 36.5 1.0 NE2 A:HIS101 2.2 36.8 1.0 NE2 A:HIS237 2.2 39.4 1.0 CL A:CL306 2.3 39.3 1.0 CG A:ASP100 3.0 37.1 1.0 CD2 A:HIS237 3.0 42.8 1.0 CD2 A:HIS101 3.1 35.3 1.0 CE1 A:HIS101 3.1 37.2 1.0 CE1 A:HIS237 3.3 45.6 1.0 OD1 A:ASP100 3.5 33.3 1.0 OG A:SER197 3.7 47.5 1.0 CE1 A:HIS96 4.1 42.4 1.0 ND1 A:HIS101 4.1 36.1 1.0 CG A:HIS101 4.2 35.4 1.0 CG A:HIS237 4.2 44.2 1.0 CB A:ASP100 4.3 35.5 1.0 ND1 A:HIS237 4.3 42.9 1.0 CB A:SER197 4.5 43.2 1.0 O2 A:GOL308 4.5 66.8 1.0 CD1 A:ILE49 4.9 35.9 1.0 NE2 A:HIS96 4.9 31.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:38.5 occ:1.00 ND1 A:HIS98 2.2 38.3 1.0 NE2 A:HIS172 2.2 38.7 1.0 NE2 A:HIS96 2.2 31.2 1.0 CD2 A:HIS172 3.0 38.9 1.0 CD2 A:HIS96 3.1 38.8 1.0 CE1 A:HIS98 3.2 43.5 1.0 CG A:HIS98 3.2 42.2 1.0 CE1 A:HIS96 3.3 42.4 1.0 CE1 A:HIS172 3.3 41.1 1.0 CB A:HIS98 3.5 41.4 1.0 CL A:CL306 4.2 39.3 1.0 CG A:HIS172 4.2 40.0 1.0 NE2 A:HIS98 4.3 43.1 1.0 CG A:HIS96 4.3 37.6 1.0 ND1 A:HIS96 4.3 35.4 1.0 CD2 A:HIS98 4.3 45.0 1.0 ND1 A:HIS172 4.4 37.5 1.0 OD1 A:ASP100 4.4 33.3 1.0 CA A:HIS98 4.9 43.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:47.0 occ:1.00 SG B:CYS176 2.3 43.9 1.0 SG B:CYS196 2.3 41.3 0.7 SG B:CYS196 2.3 44.6 0.3 CL B:CL307 2.4 39.2 1.0 O B:HOH462 2.8 39.0 1.0 CB B:CYS196 3.0 41.2 0.3 CB B:CYS176 3.1 45.6 1.0 CB B:CYS196 3.2 41.9 0.7 N B:LEU198 3.9 35.9 1.0 CB B:HIS172 4.0 42.0 1.0 N B:SER197 4.0 40.4 1.0 O B:THR169 4.2 44.9 1.0 CA B:CYS176 4.3 43.3 1.0 CA B:CYS196 4.3 41.1 0.3 CA B:CYS196 4.4 41.0 0.7 C B:CYS196 4.5 41.8 0.7 CA B:LEU198 4.5 35.4 1.0 C B:CYS196 4.5 41.7 0.3 CB B:HIS96 4.6 40.8 1.0 N B:HIS172 4.7 41.4 1.0 OG1 B:THR169 4.7 45.6 1.0 CG B:HIS172 4.8 39.1 1.0 ND1 B:HIS96 4.8 37.2 1.0 CD2 B:HIS172 4.8 38.3 1.0 CG B:HIS96 4.8 37.1 1.0 C B:SER197 4.9 41.0 1.0 CA B:HIS172 4.9 45.5 1.0 CA B:SER197 4.9 41.0 1.0 N B:SER199 4.9 39.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:40.5 occ:1.00 OD2 B:ASP100 2.0 35.4 1.0 NE2 B:HIS237 2.2 37.1 1.0 NE2 B:HIS101 2.2 37.2 1.0 CL B:CL306 2.3 38.5 1.0 CG B:ASP100 3.0 36.9 1.0 CD2 B:HIS237 3.0 40.6 1.0 CD2 B:HIS101 3.0 35.0 1.0 CE1 B:HIS101 3.1 36.1 1.0 CE1 B:HIS237 3.2 43.0 1.0 OD1 B:ASP100 3.4 34.2 1.0 OG B:SER197 3.8 48.1 1.0 CE1 B:HIS96 4.1 42.0 1.0 ND1 B:HIS101 4.1 36.4 1.0 CG B:HIS101 4.1 36.0 1.0 CG B:HIS237 4.2 42.0 1.0 CB B:ASP100 4.3 34.3 1.0 ND1 B:HIS237 4.3 41.4 1.0 CB B:SER197 4.5 44.2 1.0 NE2 B:HIS96 4.9 31.3 1.0 O2 B:EDO301 4.9 55.6 1.0 CD1 B:ILE49 4.9 35.1 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:38.3 occ:1.00 ND1 B:HIS98 2.2 37.4 1.0 NE2 B:HIS172 2.2 39.6 1.0 NE2 B:HIS96 2.3 31.3 1.0 CD2 B:HIS172 3.0 38.3 1.0 CD2 B:HIS96 3.1 39.3 1.0 CE1 B:HIS98 3.2 41.1 1.0 CG B:HIS98 3.2 37.5 1.0 CE1 B:HIS96 3.3 42.0 1.0 CE1 B:HIS172 3.3 39.3 1.0 CB B:HIS98 3.5 39.6 1.0 CL B:CL306 4.2 38.5 1.0 CG B:HIS172 4.2 39.1 1.0 NE2 B:HIS98 4.3 42.2 1.0 CG B:HIS96 4.3 37.1 1.0 CD2 B:HIS98 4.3 44.2 1.0 ND1 B:HIS172 4.3 38.0 1.0 ND1 B:HIS96 4.3 37.2 1.0 OD1 B:ASP100 4.4 34.2 1.0 CA B:HIS98 4.9 41.8 1.0

Y.Kim, N.Maltseva, M.Endres, A.Joachimiak. Crystal Structure of Metallo-Beta-Lactamase Superfamily Protein From Caulobacter Vibrioides To Be Published.