Zinc in PDB 5u8o: Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans

The structure of Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans, PDB code: 5u8o was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.10 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.520, 106.830, 144.330, 90.00, 91.30, 90.00
R / Rfree (%)	16.3 / 22.2

The structure of Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans (pdb code 5u8o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans, PDB code: 5u8o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:57.4 occ:1.00 ND1 A:HIS96 2.4 58.1 1.0 NE2 A:HIS205 2.4 33.1 1.0 NE2 A:HIS94 2.4 30.1 1.0 OD2 A:ASP224 2.5 27.2 1.0 O A:HOH537 2.7 36.3 1.0 CE1 A:HIS205 3.1 25.7 1.0 CE1 A:HIS96 3.2 59.7 1.0 CD2 A:HIS94 3.3 27.6 1.0 CG A:HIS96 3.4 52.7 1.0 CE1 A:HIS94 3.5 26.2 1.0 CG A:ASP224 3.5 27.8 1.0 CD2 A:HIS205 3.5 31.1 1.0 O A:HOH598 3.6 42.9 1.0 ZN A:ZN402 3.7 51.7 1.0 CB A:HIS96 3.7 32.5 1.0 CB A:ASP224 3.8 25.0 1.0 NE2 A:HIS99 4.2 21.8 1.0 ND1 A:HIS205 4.4 36.2 1.0 NE2 A:HIS96 4.4 63.0 1.0 CD2 A:HIS99 4.4 19.0 1.0 CD2 A:HIS96 4.4 60.0 1.0 CG A:HIS94 4.5 27.3 1.0 ND1 A:HIS94 4.6 27.5 1.0 CG A:HIS205 4.6 35.0 1.0 UNK A:UNX403 4.6 30.0 1.0 OD1 A:ASP224 4.6 37.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:51.7 occ:1.00 OD2 A:ASP224 2.2 27.2 1.0 NE2 A:HIS269 2.4 25.5 1.0 NE2 A:HIS99 2.5 21.8 1.0 OD1 A:ASP98 2.6 40.2 1.0 O A:HOH537 2.9 36.3 1.0 CG A:ASP224 3.0 27.8 1.0 OD1 A:ASP224 3.1 37.9 1.0 CD2 A:HIS99 3.4 19.0 1.0 CD2 A:HIS269 3.4 23.7 1.0 CE1 A:HIS269 3.4 24.0 1.0 CG A:ASP98 3.6 45.1 1.0 CE1 A:HIS99 3.6 17.7 1.0 ZN A:ZN401 3.7 57.4 1.0 OD2 A:ASP98 3.9 47.3 1.0 CB A:ASP224 4.5 25.0 1.0 ND1 A:HIS269 4.5 29.0 1.0 CG A:HIS269 4.5 28.5 1.0 CG A:HIS99 4.6 28.0 1.0 NE2 A:HIS94 4.6 30.1 1.0 ND1 A:HIS99 4.6 20.3 1.0 CE1 A:HIS94 4.7 26.2 1.0 CD1 A:ILE43 4.8 23.6 1.0 CB A:SER268 4.9 21.6 1.0 CB A:ASP98 4.9 44.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:40.1 occ:0.69 OD2 B:ASP224 2.1 34.8 1.0 NE2 B:HIS205 2.2 28.4 1.0 NE2 B:HIS94 2.3 28.9 1.0 ND1 B:HIS96 2.4 50.2 1.0 O B:HOH549 2.8 39.3 1.0 CE1 B:HIS205 3.0 21.1 1.0 CD2 B:HIS94 3.1 32.1 1.0 CG B:ASP224 3.3 31.6 1.0 CE1 B:HIS96 3.3 54.6 1.0 CG B:HIS96 3.3 53.5 1.0 CD2 B:HIS205 3.4 25.3 1.0 CE1 B:HIS94 3.5 28.9 1.0 ZN B:ZN402 3.5 59.2 1.0 CB B:HIS96 3.6 33.8 1.0 CB B:ASP224 3.8 27.7 1.0 NE2 B:HIS99 4.1 24.0 1.0 ND1 B:HIS205 4.2 29.4 1.0 OD1 B:ASP224 4.3 30.5 1.0 CD2 B:HIS99 4.3 24.4 1.0 CG B:HIS94 4.3 32.7 1.0 NE2 B:HIS96 4.4 57.1 1.0 CG B:HIS205 4.4 28.8 1.0 CD2 B:HIS96 4.4 56.2 1.0 ND1 B:HIS94 4.5 31.3 1.0 UNK B:UNX403 4.8 30.0 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:59.2 occ:1.00 OD2 B:ASP224 2.4 34.8 1.0 NE2 B:HIS99 2.4 24.0 1.0 NE2 B:HIS269 2.6 30.7 1.0 OD1 B:ASP224 2.8 30.5 1.0 OD1 B:ASP98 2.8 45.5 1.0 CG B:ASP224 2.9 31.6 1.0 O B:HOH549 3.1 39.3 1.0 CD2 B:HIS99 3.3 24.4 1.0 CE1 B:HIS99 3.4 33.5 1.0 CE1 B:HIS269 3.4 25.5 1.0 ZN B:ZN401 3.5 40.1 0.7 CD2 B:HIS269 3.6 23.6 1.0 CG B:ASP98 3.7 45.9 1.0 OD2 B:ASP98 3.9 42.5 1.0 NE2 B:HIS94 4.3 28.9 1.0 CB B:ASP224 4.4 27.7 1.0 CE1 B:HIS94 4.5 28.9 1.0 CG B:HIS99 4.5 31.7 1.0 ND1 B:HIS99 4.5 23.2 1.0 ND1 B:HIS269 4.6 30.5 1.0 CG B:HIS269 4.7 34.0 1.0 CD1 B:ILE43 4.8 25.8 1.0 CB B:SER268 4.8 21.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:63.9 occ:1.00 NE2 C:HIS205 2.3 34.2 1.0 OD2 C:ASP224 2.4 39.8 1.0 ND1 C:HIS96 2.5 56.1 1.0 NE2 C:HIS94 2.5 35.9 1.0 CE1 C:HIS205 3.1 30.1 1.0 CD2 C:HIS205 3.3 30.7 1.0 CD2 C:HIS94 3.4 31.6 1.0 CE1 C:HIS96 3.4 57.5 1.0 CG C:HIS96 3.4 51.8 1.0 CG C:ASP224 3.5 38.5 1.0 CE1 C:HIS94 3.5 33.1 1.0 ZN C:ZN402 3.6 46.0 0.8 CB C:HIS96 3.7 35.6 1.0 CB C:ASP224 3.8 28.7 1.0 NE2 C:HIS99 4.3 24.8 1.0 UNK C:UNX403 4.3 30.0 1.0 ND1 C:HIS205 4.3 35.4 1.0 CG C:HIS205 4.4 38.2 1.0 CD2 C:HIS99 4.5 25.2 1.0 NE2 C:HIS96 4.5 59.9 1.0 OD1 C:ASP224 4.5 47.2 1.0 CG C:HIS94 4.6 34.0 1.0 CD2 C:HIS96 4.6 57.6 1.0 ND1 C:HIS94 4.6 36.5 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


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 Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:46.0 occ:0.81 OD2 C:ASP224 2.1 39.8 1.0 NE2 C:HIS269 2.4 36.3 1.0 OD1 C:ASP98 2.6 38.5 1.0 NE2 C:HIS99 2.6 24.8 1.0 CG C:ASP224 2.8 38.5 1.0 OD1 C:ASP224 2.9 47.2 1.0 CE1 C:HIS269 3.4 26.3 1.0 CD2 C:HIS269 3.4 31.8 1.0 CD2 C:HIS99 3.5 25.2 1.0 ZN C:ZN401 3.6 63.9 1.0 CG C:ASP98 3.6 41.8 1.0 CE1 C:HIS99 3.6 23.8 1.0 OD2 C:ASP98 3.9 47.6 1.0 UNK C:UNX403 4.3 30.0 1.0 CB C:ASP224 4.3 28.7 1.0 ND1 C:HIS269 4.5 39.7 1.0 CG C:HIS269 4.5 38.8 1.0 NE2 C:HIS94 4.6 35.9 1.0 CE1 C:HIS94 4.6 33.1 1.0 CG C:HIS99 4.7 25.6 1.0 ND1 C:HIS99 4.7 23.5 1.0 CB C:SER268 4.8 28.5 1.0 CD1 C:ILE43 4.9 32.1 1.0 CB C:ASP98 4.9 40.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:68.3 occ:1.00 OD2 D:ASP224 2.0 66.4 1.0 NE2 D:HIS205 2.4 35.9 1.0 NE2 D:HIS94 2.5 42.9 1.0 ND1 D:HIS96 2.8 50.8 1.0 O D:HOH538 2.8 42.5 1.0 CE1 D:HIS205 3.1 33.5 1.0 CG D:ASP224 3.2 51.1 1.0 ZN D:ZN402 3.3 62.2 1.0 CD2 D:HIS94 3.4 39.5 1.0 CD2 D:HIS205 3.6 34.7 1.0 CG D:HIS96 3.6 44.2 1.0 CE1 D:HIS94 3.6 39.4 1.0 CB D:HIS96 3.7 36.8 1.0 CE1 D:HIS96 3.8 55.1 1.0 CB D:ASP224 3.8 45.2 1.0 NE2 D:HIS99 4.0 32.5 1.0 OD1 D:ASP224 4.1 49.6 1.0 CD2 D:HIS99 4.2 31.2 1.0 ND1 D:HIS205 4.3 36.9 1.0 CG D:HIS94 4.6 39.4 1.0 CG D:HIS205 4.6 38.4 1.0 ND1 D:HIS94 4.7 42.8 1.0 CD2 D:HIS96 4.8 50.9 1.0 UNK D:UNX403 4.8 30.0 1.0 NE2 D:HIS96 4.8 53.0 1.0 OD2 D:ASP98 5.0 46.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:62.2 occ:1.00 NE2 D:HIS99 2.5 32.5 1.0 OD2 D:ASP224 2.5 66.4 1.0 NE2 D:HIS269 2.5 39.0 1.0 OD1 D:ASP98 2.8 53.8 1.0 OD1 D:ASP224 2.9 49.6 1.0 CG D:ASP224 3.0 51.1 1.0 O D:HOH538 3.0 42.5 1.0 CD2 D:HIS99 3.3 31.2 1.0 CE1 D:HIS269 3.3 36.7 1.0 ZN D:ZN401 3.3 68.3 1.0 CE1 D:HIS99 3.5 32.3 1.0 CG D:ASP98 3.6 52.4 1.0 CD2 D:HIS269 3.6 37.3 1.0 OD2 D:ASP98 3.7 46.6 1.0 NE2 D:HIS94 4.5 42.9 1.0 CG D:HIS99 4.5 30.2 1.0 CB D:ASP224 4.5 45.2 1.0 ND1 D:HIS269 4.5 43.8 1.0 ND1 D:HIS99 4.6 33.9 1.0 CE1 D:HIS94 4.6 39.4 1.0 CG D:HIS269 4.7 46.9 1.0 CD1 D:ILE43 4.9 41.5 1.0 CB D:SER268 5.0 47.2 1.0

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), S.L.Delker, D.G.Conrady, D.Lorimer, T.E.Edwards. Crystal Structure of Beta-Lactamase Domain Protein, From Burkholderia Multivorans To Be Published.