Zinc in PDB 5i0p: Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria

The structure of Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria, PDB code: 5i0p 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)	44.94 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.170, 141.230, 236.990, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 22.9

The binding sites of Zinc atom in the Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria (pdb code 5i0p). 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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria, PDB code: 5i0p:
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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:50.7 occ:1.00 ND1 A:HIS96 2.1 40.3 1.0 OD2 A:ASP224 2.1 39.7 1.0 NE2 A:HIS205 2.3 24.0 1.0 NE2 A:HIS94 2.4 24.4 1.0 CE1 A:HIS205 3.0 25.4 1.0 CE1 A:HIS96 3.0 36.0 1.0 CG A:HIS96 3.1 31.5 1.0 CG A:ASP224 3.2 23.9 1.0 CD2 A:HIS94 3.3 22.1 1.0 CD2 A:HIS205 3.4 27.1 1.0 CE1 A:HIS94 3.4 20.7 1.0 CB A:HIS96 3.4 25.8 1.0 ZN A:ZN401 3.5 37.1 1.0 CB A:ASP224 3.9 20.2 1.0 NE2 A:HIS96 4.2 33.2 1.0 OD1 A:ASP224 4.2 28.0 1.0 NE2 A:HIS99 4.2 24.0 1.0 CD2 A:HIS96 4.2 37.3 1.0 ND1 A:HIS205 4.2 25.9 1.0 CD2 A:HIS99 4.3 19.0 1.0 CG A:HIS205 4.4 25.2 1.0 CG A:HIS94 4.5 25.6 1.0 ND1 A:HIS94 4.5 25.5 1.0 OD2 A:ASP98 4.8 34.9 1.0 CA A:HIS96 4.9 27.6 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.1 occ:1.00 NE2 A:HIS269 2.3 26.4 1.0 NE2 A:HIS99 2.3 24.0 1.0 OD2 A:ASP224 2.4 39.7 1.0 OD1 A:ASP224 2.5 28.0 1.0 OD1 A:ASP98 2.7 39.9 1.0 CG A:ASP224 2.8 23.9 1.0 CD2 A:HIS99 3.1 19.0 1.0 CE1 A:HIS269 3.2 21.9 1.0 CD2 A:HIS269 3.3 21.2 1.0 CE1 A:HIS99 3.4 19.0 1.0 ZN A:ZN400 3.5 50.7 1.0 CG A:ASP98 3.6 34.7 1.0 OD2 A:ASP98 3.8 34.9 1.0 CB A:ASP224 4.3 20.2 1.0 CG A:HIS99 4.3 30.4 1.0 ND1 A:HIS269 4.4 26.6 1.0 ND1 A:HIS99 4.4 28.0 1.0 CG A:HIS269 4.4 26.5 1.0 CE1 A:HIS94 4.4 20.7 1.0 NE2 A:HIS94 4.4 24.4 1.0 CD2 A:LEU40 4.6 44.2 1.0 CD1 A:ILE43 4.7 18.7 1.0 CB A:SER268 4.8 25.5 1.0 CB A:ASP98 4.9 27.6 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn400 b:57.9 occ:1.00 ND1 B:HIS96 2.1 55.0 1.0 OD2 B:ASP224 2.1 48.6 1.0 NE2 B:HIS94 2.3 39.8 1.0 NE2 B:HIS205 2.3 30.6 1.0 CG B:HIS96 3.0 49.6 1.0 CE1 B:HIS96 3.1 45.5 1.0 CE1 B:HIS205 3.1 31.4 1.0 CE1 B:HIS94 3.2 35.6 1.0 CG B:ASP224 3.3 38.9 1.0 CD2 B:HIS94 3.3 35.0 1.0 CB B:HIS96 3.3 32.9 1.0 ZN B:ZN401 3.4 38.8 1.0 CD2 B:HIS205 3.4 30.2 1.0 NE2 B:HIS99 3.8 48.4 1.0 CB B:ASP224 3.9 23.6 1.0 CD2 B:HIS99 4.0 31.5 1.0 NE2 B:HIS96 4.2 44.9 1.0 CD2 B:HIS96 4.2 48.0 1.0 OD1 B:ASP224 4.3 36.8 1.0 ND1 B:HIS205 4.3 33.1 1.0 ND1 B:HIS94 4.4 34.6 1.0 CG B:HIS94 4.4 32.4 1.0 CG B:HIS205 4.4 32.2 1.0 OD2 B:ASP98 4.7 54.5 1.0 CA B:HIS96 4.8 35.1 1.0 CE1 B:HIS99 4.9 35.3 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:38.8 occ:1.00 NE2 B:HIS99 2.2 48.4 1.0 OD2 B:ASP224 2.3 48.6 1.0 NE2 B:HIS269 2.4 35.5 1.0 OD1 B:ASP98 2.5 50.7 1.0 OD1 B:ASP224 2.6 36.8 1.0 CG B:ASP224 2.8 38.9 1.0 CD2 B:HIS99 3.1 31.5 1.0 CE1 B:HIS99 3.2 35.3 1.0 CE1 B:HIS269 3.3 30.8 1.0 ZN B:ZN400 3.4 57.9 1.0 CD2 B:HIS269 3.4 33.8 1.0 CG B:ASP98 3.4 49.3 1.0 OD2 B:ASP98 3.7 54.5 1.0 CG B:HIS99 4.2 42.9 1.0 ND1 B:HIS99 4.3 36.8 1.0 CB B:ASP224 4.3 23.6 1.0 ND1 B:HIS269 4.4 32.8 1.0 CE1 B:HIS94 4.4 35.6 1.0 NE2 B:HIS94 4.5 39.8 1.0 CD1 B:ILE43 4.5 34.0 1.0 CG B:HIS269 4.5 34.3 1.0 CB B:SER268 4.7 37.8 1.0 CB B:ASP98 4.8 37.6 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn400 b:43.2 occ:1.00 OD2 C:ASP224 2.1 40.2 1.0 ND1 C:HIS96 2.1 43.2 1.0 NE2 C:HIS94 2.3 24.3 1.0 NE2 C:HIS205 2.3 27.0 1.0 CE1 C:HIS96 3.0 34.3 1.0 CG C:HIS96 3.1 39.0 1.0 CE1 C:HIS205 3.2 24.5 1.0 CD2 C:HIS94 3.2 20.5 1.0 CG C:ASP224 3.2 30.3 1.0 CE1 C:HIS94 3.2 19.8 1.0 O C:HOH593 3.2 54.6 1.0 CD2 C:HIS205 3.4 27.0 1.0 CB C:HIS96 3.5 32.2 1.0 ZN C:ZN401 3.5 36.8 1.0 CB C:ASP224 3.8 23.9 1.0 NE2 C:HIS99 4.1 21.5 1.0 NE2 C:HIS96 4.2 36.4 1.0 OD1 C:ASP224 4.2 29.3 1.0 CD2 C:HIS96 4.2 37.0 1.0 CD2 C:HIS99 4.3 23.0 1.0 ND1 C:HIS205 4.3 27.1 1.0 ND1 C:HIS94 4.3 19.1 1.0 CG C:HIS94 4.4 25.8 1.0 CG C:HIS205 4.5 24.2 1.0 OD2 C:ASP98 5.0 34.0 1.0 CA C:HIS96 5.0 28.7 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:36.8 occ:1.00 NE2 C:HIS269 2.3 19.2 1.0 NE2 C:HIS99 2.3 21.5 1.0 OD2 C:ASP224 2.4 40.2 1.0 OD1 C:ASP224 2.7 29.3 1.0 OD1 C:ASP98 2.8 36.3 1.0 CG C:ASP224 2.9 30.3 1.0 CD2 C:HIS99 3.1 23.0 1.0 CE1 C:HIS269 3.1 20.3 1.0 O C:HOH593 3.2 54.6 1.0 CD2 C:HIS269 3.3 24.2 1.0 CE1 C:HIS99 3.4 21.9 1.0 ZN C:ZN400 3.5 43.2 1.0 CG C:ASP98 3.6 33.4 1.0 OD2 C:ASP98 3.8 34.0 1.0 ND1 C:HIS269 4.3 27.4 1.0 CG C:HIS99 4.4 24.7 1.0 CB C:ASP224 4.4 23.9 1.0 CG C:HIS269 4.4 19.9 1.0 CE1 C:HIS94 4.4 19.8 1.0 ND1 C:HIS99 4.4 24.6 1.0 NE2 C:HIS94 4.5 24.3 1.0 CD1 C:ILE43 4.6 19.2 1.0 CB C:SER268 4.7 20.7 1.0 CD2 C:LEU40 4.8 42.0 1.0 CB C:ASP98 5.0 27.1 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn400 b:47.5 occ:1.00 ND1 D:HIS96 2.1 41.9 1.0 OD1 D:ASP224 2.1 45.4 1.0 NE2 D:HIS205 2.3 26.4 1.0 NE2 D:HIS94 2.3 22.7 1.0 CE1 D:HIS96 3.0 40.0 1.0 CE1 D:HIS205 3.1 16.8 1.0 CG D:HIS96 3.1 35.3 1.0 CD2 D:HIS94 3.2 26.2 1.0 CG D:ASP224 3.2 27.8 1.0 O D:HOH603 3.3 43.0 1.0 CE1 D:HIS94 3.3 21.9 1.0 ZN D:ZN401 3.3 38.4 1.0 CD2 D:HIS205 3.4 22.9 1.0 CB D:HIS96 3.5 27.2 1.0 CB D:ASP224 3.7 25.0 1.0 NE2 D:HIS99 3.9 31.4 1.0 NE2 D:HIS96 4.1 38.1 1.0 CD2 D:HIS99 4.2 24.6 1.0 CD2 D:HIS96 4.2 40.7 1.0 OD2 D:ASP224 4.2 35.9 1.0 ND1 D:HIS205 4.3 29.3 1.0 CG D:HIS94 4.4 25.9 1.0 ND1 D:HIS94 4.4 30.1 1.0 CG D:HIS205 4.4 23.0 1.0 CE1 D:HIS99 4.8 21.4 1.0 CA D:HIS96 4.9 23.1 1.0 OD2 D:ASP98 5.0 38.4 1.0

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


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 A Beta-Lactamase Domain Protein From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:38.4 occ:1.00 OD1 D:ASP224 2.1 45.4 1.0 NE2 D:HIS99 2.1 31.4 1.0 NE2 D:HIS269 2.3 22.5 1.0 OD2 D:ASP224 2.7 35.9 1.0 CG D:ASP224 2.7 27.8 1.0 OD1 D:ASP98 2.9 34.2 1.0 CD2 D:HIS99 3.0 24.6 1.0 CE1 D:HIS99 3.1 21.4 1.0 CE1 D:HIS269 3.2 20.0 1.0 CD2 D:HIS269 3.3 27.2 1.0 ZN D:ZN400 3.3 47.5 1.0 CG D:ASP98 3.8 37.6 1.0 O D:HOH603 3.8 43.0 1.0 OD2 D:ASP98 3.9 38.4 1.0 ND1 D:HIS99 4.2 27.9 1.0 CG D:HIS99 4.2 21.7 1.0 CB D:ASP224 4.2 25.0 1.0 NE2 D:HIS94 4.3 22.7 1.0 ND1 D:HIS269 4.3 26.8 1.0 CE1 D:HIS94 4.4 21.9 1.0 CG D:HIS269 4.4 30.5 1.0 CD1 D:ILE43 4.7 21.5 1.0 CB D:SER268 4.8 21.4 1.0

D.M.Dranow, J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of A Beta-Lactamase Domain Protein From Burkholderia Ambifaria To Be Published.