Zinc in PDB 3t00: Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate

All present enzymatic activity of Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate:
3.6.1.9;

The structure of Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate, PDB code: 3t00 was solved by V.Agarwal, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.123, 111.123, 72.441, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.1

The structure of Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Vanadium	(V)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate (pdb code 3t00). 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 Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate, PDB code: 3t00:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate


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 Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:34.0 occ:1.00 O4 A:VO4503 1.8 32.9 1.0 OD1 A:ASP29 2.0 24.6 1.0 NE2 A:HIS251 2.2 18.6 1.0 OD2 A:ASP250 2.3 17.6 1.0 OG1 A:THR68 2.3 21.2 1.0 CG A:ASP29 2.7 20.7 1.0 OD2 A:ASP29 2.9 23.6 1.0 CD2 A:HIS251 3.1 18.1 1.0 CE1 A:HIS251 3.1 17.5 1.0 CG A:ASP250 3.1 17.1 1.0 CB A:THR68 3.2 20.7 1.0 V A:VO4503 3.3 33.4 1.0 OD1 A:ASP250 3.4 17.4 1.0 CG2 A:THR68 3.5 20.4 1.0 O A:HOH465 3.6 29.4 1.0 CA A:THR68 3.6 20.2 1.0 OD2 A:ASP211 3.8 24.1 1.0 N A:THR68 4.0 19.9 1.0 CG A:ASP211 4.1 21.4 1.0 CB A:ASP29 4.1 18.0 1.0 O1 A:VO4503 4.1 32.2 1.0 ND1 A:HIS251 4.2 18.6 1.0 CG A:HIS251 4.2 17.6 1.0 O3 A:VO4503 4.2 31.3 1.0 ZN A:ZN502 4.3 30.9 1.0 N A:GLY30 4.4 17.3 1.0 CB A:ASP250 4.4 16.4 1.0 OD1 A:ASP211 4.5 21.8 1.0 CA A:ASP29 4.5 17.4 1.0 CE1 A:HIS377 4.5 18.9 1.0 CB A:ASP211 4.6 20.8 1.0 O2 A:VO4503 4.7 29.3 1.0 NE2 A:HIS377 4.7 19.6 1.0 C A:ASP29 4.8 17.5 1.0 C A:PHE67 4.8 20.3 1.0 C A:THR68 4.9 20.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate


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 Phosphonoacetate Hydrolase From Sinorhizobium Meliloti 1021 in Complex with Vanadate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:30.9 occ:1.00 OD2 A:ASP211 1.8 24.1 1.0 O2 A:VO4503 2.0 29.3 1.0 NE2 A:HIS377 2.1 19.6 1.0 NE2 A:HIS215 2.1 21.9 1.0 O4 A:VO4503 2.6 32.9 1.0 CG A:ASP211 2.6 21.4 1.0 OD1 A:ASP211 2.8 21.8 1.0 CE1 A:HIS377 3.0 18.9 1.0 CD2 A:HIS215 3.0 22.7 1.0 V A:VO4503 3.0 33.4 1.0 CD2 A:HIS377 3.1 20.2 1.0 CE1 A:HIS215 3.2 21.9 1.0 CE1 A:HIS251 3.9 17.5 1.0 CB A:ASP211 4.1 20.8 1.0 ND1 A:HIS377 4.1 20.1 1.0 NE2 A:HIS251 4.1 18.6 1.0 CG A:HIS215 4.2 21.8 1.0 O3 A:VO4503 4.2 31.3 1.0 CG A:HIS377 4.2 20.9 1.0 ND1 A:HIS215 4.2 22.3 1.0 CE A:MET253 4.3 18.9 1.0 ZN A:ZN501 4.3 34.0 1.0 O1 A:VO4503 4.5 32.2 1.0 OG1 A:THR68 4.5 21.2 1.0 OD1 A:ASP29 4.7 24.6 1.0 O A:HOH465 4.8 29.4 1.0

V.Agarwal, S.A.Borisova, W.W.Metcalf, W.A.Van Der Donk, S.K.Nair. Structural and Mechanistic Insights Into C-P Bond Hydrolysis By Phosphonoacetate Hydrolase. Chem.Biol. V. 18 1230 2011.
ISSN: ISSN 1074-5521
PubMed: 22035792
DOI: 10.1016/J.CHEMBIOL.2011.07.019