Zinc in PDB 5td3: Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis

All present enzymatic activity of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis:
1.13.11.1;

The structure of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis, PDB code: 5td3 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)	40.51 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.410, 55.860, 85.690, 90.00, 116.30, 90.00
R / Rfree (%)	17.7 / 21

The structure of Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis (pdb code 5td3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis, PDB code: 5td3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Catechol 1,2-Dioxygenase 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 Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.2 occ:1.00 OH A:TYR175 1.9 20.4 1.0 NE2 A:HIS237 2.0 21.9 1.0 NE2 A:HIS235 2.1 22.8 1.0 CD2 A:HIS237 2.9 17.9 1.0 CE1 A:HIS237 3.0 20.2 1.0 CZ A:TYR175 3.0 22.1 1.0 CD2 A:HIS235 3.0 23.6 1.0 CE1 A:HIS235 3.1 24.8 1.0 NH1 A:ARG232 3.7 48.4 1.0 CE1 A:TYR175 3.8 20.6 1.0 CE2 A:TYR175 3.8 17.1 1.0 O A:HOH525 3.9 17.8 1.0 ND1 A:HIS237 4.0 21.9 1.0 CG A:HIS237 4.0 18.9 1.0 CG A:HIS235 4.2 20.8 1.0 ND1 A:HIS235 4.2 20.8 1.0 O A:HOH660 4.3 17.7 1.0 OE1 A:GLN251 4.9 19.4 0.5 CZ A:ARG232 4.9 41.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Catechol 1,2-Dioxygenase 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 Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:24.3 occ:1.00 OH B:TYR175 1.8 22.9 1.0 NE2 B:HIS237 2.0 20.9 1.0 NE2 B:HIS235 2.1 24.6 1.0 CD2 B:HIS237 2.9 23.8 1.0 CZ B:TYR175 3.0 24.9 1.0 CE1 B:HIS237 3.0 22.1 1.0 CD2 B:HIS235 3.0 23.6 1.0 CE1 B:HIS235 3.1 23.5 1.0 CE2 B:TYR175 3.7 21.7 1.0 CE1 B:TYR175 3.8 20.2 1.0 NH1 B:ARG232 3.9 60.0 1.0 O B:HOH517 3.9 20.6 1.0 CG B:HIS237 4.1 21.4 1.0 ND1 B:HIS237 4.1 23.8 1.0 CG B:HIS235 4.2 23.1 1.0 ND1 B:HIS235 4.2 23.7 1.0 O B:HOH617 4.4 17.0 1.0

D.G.Conrady, D.M.Dranow, D.Lorimer, T.E.Edwards. Crystal Structure of Catechol 1,2-Dioxygenase From Burkholderia Vietnamiensis To Be Published.