Zinc in PDB 1m7j: Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases

All present enzymatic activity of Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases:
3.5.1.81;

The structure of Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases, PDB code: 1m7j was solved by S.-H.Liaw, S.-J.Chen, T.-P.Ko, C.-S.Hsu, A.H.-J.Wang, Y.-C.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.102, 77.167, 135.744, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 17.4

The binding sites of Zinc atom in the Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases (pdb code 1m7j). 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 D-Aminoacylase Defines A Novel Subset of Amidohydrolases, PDB code: 1m7j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases


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 D-Aminoacylase Defines A Novel Subset of Amidohydrolases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn801 b:7.3 occ:1.00 O A:ACT901 2.0 6.7 1.0 NE2 A:HIS250 2.0 6.3 1.0 ND1 A:HIS220 2.1 6.3 1.0 SG A:CYS96 2.2 6.9 1.0 OXT A:ACT901 2.6 8.7 1.0 C A:ACT901 2.6 8.0 1.0 CE1 A:HIS220 3.0 6.5 1.0 CE1 A:HIS250 3.0 5.5 1.0 CD2 A:HIS250 3.0 6.4 1.0 CG A:HIS220 3.1 6.9 1.0 ZN A:ZN802 3.2 19.3 0.2 CB A:CYS96 3.3 6.7 1.0 CB A:HIS220 3.4 6.6 1.0 NE2 A:HIS220 4.1 7.2 1.0 CH3 A:ACT901 4.1 8.6 1.0 OH A:TYR192 4.1 8.9 1.0 ND1 A:HIS250 4.1 6.1 1.0 CD2 A:HIS220 4.1 6.9 1.0 CH3 A:ACT902 4.2 10.4 1.0 CG A:HIS250 4.2 5.6 1.0 CE2 A:TYR192 4.3 7.8 1.0 CE1 A:HIS67 4.3 3.8 1.0 NE2 A:HIS67 4.3 10.2 1.0 CA A:HIS220 4.5 6.7 1.0 CA A:CYS96 4.5 6.2 1.0 CZ A:TYR192 4.7 7.7 1.0 NE2 A:HIS69 4.8 7.9 1.0 OD2 A:ASP366 4.9 11.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of D-Aminoacylase Defines A Novel Subset of Amidohydrolases


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 D-Aminoacylase Defines A Novel Subset of Amidohydrolases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:19.3 occ:0.25 NE2 A:HIS69 1.9 7.9 1.0 CE1 A:HIS67 2.0 3.8 1.0 SG A:CYS96 2.2 6.9 1.0 CE1 A:HIS69 2.4 7.7 1.0 OXT A:ACT901 2.5 8.7 1.0 NE2 A:HIS67 2.7 10.2 1.0 C A:ACT901 3.1 8.0 1.0 CD2 A:HIS69 3.2 7.5 1.0 ND1 A:HIS67 3.2 10.2 1.0 ZN A:ZN801 3.2 7.3 1.0 OD1 A:ASP366 3.4 8.8 1.0 CB A:CYS96 3.6 6.7 1.0 ND1 A:HIS69 3.6 6.8 1.0 O A:ACT901 3.7 6.7 1.0 CB A:ASN95 3.7 6.2 1.0 CD2 A:HIS67 4.0 4.6 1.0 CH3 A:ACT901 4.0 8.6 1.0 CG A:HIS69 4.0 6.2 1.0 CD2 A:HIS250 4.1 6.4 1.0 NE2 A:HIS250 4.2 6.3 1.0 CG A:HIS67 4.2 6.2 1.0 CG A:ASP366 4.2 8.1 1.0 C A:ASN95 4.3 6.3 1.0 N A:CYS96 4.4 5.8 1.0 O A:ASN95 4.5 6.5 1.0 OD2 A:ASP366 4.5 11.7 1.0 CA A:CYS96 4.6 6.2 1.0 CA A:ASN95 4.6 6.7 1.0 CG A:ASN95 4.8 6.5 1.0

S.-H.Liaw, S.-J.Chen, T.-P.Ko, C.-S.Hsu, C.J.Chen, A.H.Wang, Y.-C.Tsai. Crystal Structure of D-Aminoacylase From Alcaligenes Faecalis DA1. A Novel Subset of Amidohydrolases and Insights Into the Enzyme Mechanism. J.Biol.Chem. V. 278 4957 2003.
ISSN: ISSN 0021-9258
PubMed: 12454005
DOI: 10.1074/JBC.M210795200