Zinc in PDB 5i4m: Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis

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

The structure of Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis, PDB code: 5i4m 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)	47.94 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.460, 124.230, 77.040, 90.00, 101.94, 90.00
R / Rfree (%)	13.9 / 17.1

The binding sites of Zinc atom in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis (pdb code 5i4m). 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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis, PDB code: 5i4m:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:10.7 occ:0.75 OD1 A:ASP107 2.1 9.0 1.0 NE2 A:HIS96 2.2 9.7 1.0 O A:HOH792 2.2 10.0 1.0 O4P A:3PG503 2.2 15.1 0.8 NE2 A:HIS203 2.2 7.7 1.0 O2P A:3PG503 2.4 12.7 0.8 P A:3PG503 2.7 21.1 0.8 CE1 A:HIS203 3.1 9.2 1.0 CE1 A:HIS96 3.1 6.3 1.0 CD2 A:HIS96 3.2 6.4 1.0 CG A:ASP107 3.3 12.9 1.0 CD2 A:HIS203 3.3 6.6 1.0 N A:GLY108 3.7 7.6 1.0 O3P A:3PG503 3.8 7.4 0.8 OD2 A:ASP107 3.8 7.6 1.0 OE1 A:GLU141 3.9 10.9 1.0 ZN A:ZN502 3.9 9.2 0.8 O1P A:3PG503 4.0 10.2 0.8 ND1 A:HIS371 4.1 9.8 1.0 CA A:GLY108 4.1 7.0 1.0 OE2 A:GLU141 4.1 15.4 1.0 CD A:GLU141 4.2 15.1 1.0 ND1 A:HIS203 4.2 8.3 1.0 ND1 A:HIS96 4.2 5.8 1.0 NE2 A:GLN206 4.3 8.5 1.0 C A:ASP107 4.3 7.4 1.0 CG A:HIS96 4.3 5.6 1.0 CG A:HIS203 4.4 6.9 1.0 CE1 A:HIS371 4.4 11.3 1.0 CB A:ASP107 4.5 8.8 1.0 OE1 A:GLN206 4.6 9.5 1.0 OE2 A:GLU142 4.6 12.5 1.0 CA A:ASP107 4.7 7.1 1.0 O A:HOH619 4.7 8.3 1.0 CD A:GLN206 4.7 12.4 1.0 O A:GLY370 4.8 12.8 1.0 C3 A:3PG503 4.9 12.2 0.8 OG A:SER95 5.0 7.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:9.2 occ:0.83 O3P A:3PG503 2.0 7.4 0.8 OD2 A:ASP107 2.0 7.6 1.0 OE2 A:GLU142 2.1 12.5 1.0 NE2 A:HIS395 2.1 8.5 1.0 O2P A:3PG503 2.3 12.7 0.8 OE1 A:GLU142 2.4 8.0 1.0 CD A:GLU142 2.5 8.5 1.0 P A:3PG503 2.6 21.1 0.8 CG A:ASP107 3.0 12.9 1.0 CD2 A:HIS395 3.1 7.5 1.0 CE1 A:HIS395 3.2 9.0 1.0 OD1 A:ASP107 3.3 9.0 1.0 NE2 A:GLN206 3.8 8.5 1.0 O1P A:3PG503 3.8 10.2 0.8 O4P A:3PG503 3.8 15.1 0.8 ZN A:ZN501 3.9 10.7 0.8 O A:HOH757 3.9 7.4 1.0 C3 A:3PG503 4.0 12.2 0.8 CG A:GLU142 4.0 7.2 1.0 NE2 B:HIS239 4.2 10.7 1.0 ND1 A:HIS395 4.3 7.1 1.0 CG A:HIS395 4.3 7.3 1.0 CE1 A:HIS96 4.3 6.3 1.0 CB A:ASP107 4.3 8.8 1.0 CG A:GLN100 4.4 9.0 1.0 CD2 B:HIS239 4.5 9.6 1.0 NE2 A:HIS96 4.6 9.7 1.0 OE1 A:GLU141 4.6 10.9 1.0 NE2 A:GLN100 4.6 6.8 1.0 CB A:GLU142 4.9 9.2 1.0 CD A:GLN206 4.9 12.4 1.0 O A:HOH727 5.0 9.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:11.9 occ:0.75 OD1 B:ASP107 2.2 8.0 1.0 O4P B:3PG503 2.2 16.9 0.8 NE2 B:HIS96 2.2 8.4 1.0 NE2 B:HIS203 2.2 7.7 1.0 O B:HOH657 2.2 11.4 1.0 O3P B:3PG503 2.4 8.9 0.8 P B:3PG503 2.7 23.4 0.8 CE1 B:HIS203 3.1 10.0 1.0 CE1 B:HIS96 3.1 7.1 1.0 CD2 B:HIS96 3.2 9.2 1.0 CD2 B:HIS203 3.3 8.3 1.0 CG B:ASP107 3.3 11.7 1.0 N B:GLY108 3.8 7.7 1.0 O2P B:3PG503 3.8 10.5 0.8 OD2 B:ASP107 3.8 10.3 1.0 OE2 B:GLU141 3.8 13.1 1.0 ZN B:ZN502 3.9 10.4 0.8 O1P B:3PG503 4.0 10.8 0.8 ND1 B:HIS371 4.0 12.2 1.0 OE1 B:GLU141 4.1 15.9 1.0 CA B:GLY108 4.1 7.1 1.0 CD B:GLU141 4.2 12.5 1.0 ND1 B:HIS203 4.2 7.8 1.0 ND1 B:HIS96 4.3 6.9 1.0 CG B:HIS96 4.3 10.1 1.0 C B:ASP107 4.3 10.5 1.0 CG B:HIS203 4.4 10.8 1.0 CE1 B:HIS371 4.4 13.0 1.0 NE2 B:GLN206 4.4 7.8 1.0 CB B:ASP107 4.5 7.1 1.0 OE1 B:GLN206 4.6 9.5 1.0 OE2 B:GLU142 4.6 9.9 1.0 CA B:ASP107 4.7 7.2 1.0 O B:HOH631 4.7 11.6 1.0 O B:GLY370 4.8 14.3 1.0 CD B:GLN206 4.8 11.3 1.0 C3 B:3PG503 4.9 11.9 0.8 OG B:SER95 4.9 9.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis


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 Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:10.4 occ:0.82 O2P B:3PG503 2.0 10.5 0.8 OD2 B:ASP107 2.1 10.3 1.0 OE2 B:GLU142 2.2 9.9 1.0 NE2 B:HIS395 2.2 9.3 1.0 O3P B:3PG503 2.3 8.9 0.8 OE1 B:GLU142 2.3 11.1 1.0 CD B:GLU142 2.5 9.4 1.0 P B:3PG503 2.6 23.4 0.8 CG B:ASP107 3.0 11.7 1.0 CD2 B:HIS395 3.1 8.3 1.0 CE1 B:HIS395 3.2 10.2 1.0 OD1 B:ASP107 3.4 8.0 1.0 O1P B:3PG503 3.7 10.8 0.8 O4P B:3PG503 3.8 16.9 0.8 NE2 B:GLN206 3.8 7.8 1.0 O B:HOH760 3.9 9.2 1.0 ZN B:ZN501 3.9 11.9 0.8 C3 B:3PG503 3.9 11.9 0.8 CG B:GLU142 4.0 7.2 1.0 NE2 A:HIS239 4.3 10.0 1.0 CG B:HIS395 4.3 7.1 1.0 ND1 B:HIS395 4.3 6.2 1.0 CE1 B:HIS96 4.3 7.1 1.0 CB B:ASP107 4.4 7.1 1.0 CG B:GLN100 4.4 7.1 1.0 OE2 B:GLU141 4.5 13.1 1.0 NE2 B:HIS96 4.6 8.4 1.0 NE2 B:GLN100 4.6 8.2 1.0 CD2 A:HIS239 4.6 10.6 1.0 CB B:GLU142 4.9 9.3 1.0 O B:HOH747 5.0 11.8 1.0 CD B:GLN206 5.0 11.3 1.0

J.Abendroth, P.S.Horanyi, D.D.Lorimer, T.E.Edwards. Crystal Structure of Amidase, Hydantoinase/Carbamoylase Family From Burkholderia Vietnamiensis To Be Published.