Zinc in PDB 5tp4: Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria

All present enzymatic activity of Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria:
3.5.1.87;

The structure of Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria, PDB code: 5tp4 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)	43.99 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.530, 136.960, 164.580, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19.1

The binding sites of Zinc atom in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria (pdb code 5tp4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria, PDB code: 5tp4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase 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 Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:23.9 occ:0.42 O A:HOH972 2.1 35.0 1.0 NE2 A:HIS190 2.4 12.5 1.0 O A:HOH723 2.5 15.0 1.0 NE2 A:HIS84 2.6 13.7 1.0 CE1 A:HIS190 3.2 11.7 1.0 ZN A:ZN502 3.3 42.7 0.4 CD2 A:HIS190 3.4 11.0 1.0 N A:GLY96 3.5 10.2 1.0 CD2 A:HIS84 3.5 9.9 1.0 CE1 A:HIS84 3.5 11.8 1.0 O A:HOH738 3.9 17.8 1.0 CA A:GLY96 3.9 8.7 1.0 C A:ASP95 4.0 10.4 1.0 OE2 A:GLU129 4.1 19.6 1.0 CB A:ASP95 4.1 20.2 1.0 ND1 A:HIS358 4.2 13.8 1.0 NE2 A:GLN193 4.3 17.4 1.0 OE1 A:GLU129 4.3 14.1 1.0 CA A:ASP95 4.4 9.9 1.0 CD A:GLU129 4.4 15.1 1.0 ND1 A:HIS190 4.4 8.9 1.0 OD1 A:ASP95 4.4 38.3 1.0 OE2 A:GLU130 4.5 17.8 1.0 CG A:HIS190 4.5 8.9 1.0 CE1 A:HIS358 4.6 10.7 1.0 ND1 A:HIS84 4.6 12.9 1.0 CG A:HIS84 4.7 12.2 1.0 CG A:ASP95 4.7 34.3 1.0 O A:ASP95 4.8 11.5 1.0 O A:HOH631 4.8 11.2 1.0 CD A:GLN193 4.9 14.6 1.0 OE1 A:GLN193 5.0 16.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase 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 Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:42.7 occ:0.38 O A:HOH972 2.3 35.0 1.0 O A:HOH1016 2.5 52.4 1.0 OE2 A:GLU130 2.7 17.8 1.0 ZN A:ZN501 3.3 23.9 0.4 OE1 A:GLU130 3.4 17.8 1.0 CD A:GLU130 3.4 15.8 1.0 NE2 A:GLN193 3.6 17.4 1.0 CB A:ASP95 3.8 20.2 1.0 O A:HOH665 3.9 13.3 1.0 CG A:ASP95 3.9 34.3 1.0 O A:HOH738 4.0 17.8 1.0 OD2 A:ASP95 4.3 39.2 1.0 OD1 A:ASP95 4.3 38.3 1.0 O A:HOH835 4.3 28.3 1.0 NE2 A:HIS84 4.4 13.7 1.0 CE1 A:HIS84 4.4 11.8 1.0 OE1 A:GLU129 4.6 14.1 1.0 CD A:GLN193 4.8 14.6 1.0 CG A:GLU130 4.8 11.6 1.0 CA A:ASP95 5.0 9.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase 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 Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:24.2 occ:0.54 O B:HOH948 2.3 37.4 1.0 NE2 B:HIS190 2.4 12.6 1.0 O B:HOH708 2.4 13.3 1.0 NE2 B:HIS84 2.5 14.8 1.0 CE1 B:HIS190 3.2 14.3 1.0 ZN B:ZN502 3.3 27.1 0.3 CD2 B:HIS84 3.4 9.8 1.0 CD2 B:HIS190 3.5 13.1 1.0 CE1 B:HIS84 3.5 13.1 1.0 N B:GLY96 3.6 11.9 1.0 CA B:GLY96 3.9 9.5 1.0 OE2 B:GLU129 4.0 19.8 1.0 C B:ASP95 4.1 9.7 1.0 O B:HOH729 4.2 18.5 1.0 ND1 B:HIS358 4.2 15.2 1.0 OE1 B:GLU129 4.2 13.9 1.0 CD B:GLU129 4.2 16.6 1.0 CB B:ASP95 4.3 17.8 1.0 OE2 B:GLU130 4.3 22.5 1.0 NE2 B:GLN193 4.4 17.5 1.0 ND1 B:HIS190 4.4 10.4 1.0 CA B:ASP95 4.5 9.6 1.0 CE1 B:HIS358 4.5 12.6 1.0 CG B:HIS190 4.5 10.6 1.0 CG B:HIS84 4.6 12.0 1.0 ND1 B:HIS84 4.6 13.2 1.0 O B:HOH633 4.7 10.2 1.0 OD1 B:ASP95 4.8 43.5 1.0 CG B:ASP95 4.8 39.2 1.0 O B:ASP95 4.8 13.1 1.0 CD B:GLN193 5.0 14.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase 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 Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:27.1 occ:0.34 O B:HOH948 2.1 37.4 1.0 OE2 B:GLU130 2.4 22.5 1.0 OE1 B:GLU130 3.1 19.6 1.0 CD B:GLU130 3.1 22.0 1.0 ZN B:ZN501 3.3 24.2 0.5 NE2 B:GLN193 3.8 17.5 1.0 O B:HOH784 3.9 16.2 1.0 O B:HOH908 3.9 45.1 1.0 CB B:ASP95 4.0 17.8 1.0 CG B:ASP95 4.1 39.2 1.0 O B:HOH729 4.1 18.5 1.0 OD2 B:ASP95 4.2 44.5 1.0 NE2 B:HIS84 4.2 14.8 1.0 CE1 B:HIS84 4.3 13.1 1.0 OE1 B:GLU129 4.3 13.9 1.0 O B:HOH607 4.5 32.4 1.0 O B:HOH1038 4.5 46.1 1.0 CG B:GLU130 4.6 14.2 1.0 OD1 B:ASP95 4.6 43.5 1.0 OE2 B:GLU129 4.8 19.8 1.0 CG B:GLN88 5.0 17.1 1.0 CD B:GLN193 5.0 14.4 1.0 CD B:GLU129 5.0 16.6 1.0

D.G.Conrady, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Hydantoinase/Carbamoylase Family Amidase From Burkholderia Ambifaria To Be Published.