Zinc in PDB 3e0l: Computationally Designed Ammelide Deaminase

All present enzymatic activity of Computationally Designed Ammelide Deaminase:
3.5.4.3;

The structure of Computationally Designed Ammelide Deaminase, PDB code: 3e0l was solved by P.M.Murphy, J.M.Bolduc, J.L.Gallaher, B.L.Stoddard, D.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	117.04 / 2.37
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.827, 107.315, 233.620, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.7

The binding sites of Zinc atom in the Computationally Designed Ammelide Deaminase (pdb code 3e0l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Computationally Designed Ammelide Deaminase, PDB code: 3e0l:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Computationally Designed Ammelide Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Computationally Designed Ammelide Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1452 b:38.8 occ:1.00 O A:HOH1463 1.9 42.2 1.0 NE2 A:HIS84 2.0 29.1 1.0 NE2 A:HIS238 2.1 43.0 1.0 NE2 A:HIS82 2.1 32.3 1.0 OD1 A:ASP328 2.3 35.8 1.0 CE1 A:HIS238 2.8 43.5 1.0 CE1 A:HIS82 2.9 30.2 1.0 CD2 A:HIS84 2.9 30.3 1.0 CE1 A:HIS84 3.0 29.6 1.0 CD2 A:HIS82 3.3 32.2 1.0 CD2 A:HIS238 3.3 42.6 1.0 CG A:ASP328 3.3 34.5 1.0 OD2 A:ASP328 3.7 32.0 1.0 ND1 A:HIS238 4.0 43.5 1.0 O A:HOH1464 4.0 33.0 1.0 NE2 A:HIS277 4.1 34.8 1.0 ND1 A:HIS84 4.1 31.9 1.0 ND1 A:HIS82 4.1 29.7 1.0 CG A:HIS84 4.1 31.3 1.0 CG A:HIS238 4.3 41.7 1.0 CG A:HIS82 4.3 33.9 1.0 CB A:ASP328 4.5 32.5 1.0 O A:HOH1465 4.6 43.8 1.0 CE1 A:HIS277 4.8 35.1 1.0

Zinc binding site 2 out of 2 in the Computationally Designed Ammelide Deaminase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Computationally Designed Ammelide Deaminase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1452 b:36.3 occ:1.00 NE2 B:HIS82 2.0 34.4 1.0 O B:HOH1468 2.1 23.7 1.0 NE2 B:HIS238 2.1 41.8 1.0 NE2 B:HIS84 2.1 22.6 1.0 OD1 B:ASP328 2.2 35.5 1.0 CE1 B:HIS82 2.8 32.9 1.0 CD2 B:HIS84 3.0 23.5 1.0 CE1 B:HIS238 3.0 42.5 1.0 CD2 B:HIS238 3.1 41.7 1.0 CE1 B:HIS84 3.1 25.4 1.0 CD2 B:HIS82 3.2 34.4 1.0 CG B:ASP328 3.2 35.5 1.0 OD2 B:ASP328 3.8 36.3 1.0 ND1 B:HIS82 4.0 33.2 1.0 NE2 B:HIS277 4.0 35.2 1.0 ND1 B:HIS238 4.2 40.6 1.0 CG B:HIS84 4.2 27.0 1.0 CG B:HIS82 4.2 33.6 1.0 ND1 B:HIS84 4.2 26.5 1.0 CG B:HIS238 4.2 39.0 1.0 O B:HOH1469 4.3 28.9 1.0 CB B:ASP328 4.4 34.0 1.0 CE1 B:HIS277 4.8 32.2 1.0 CA B:ASP328 4.9 34.2 1.0 CD2 B:HIS277 4.9 34.9 1.0

P.M.Murphy, J.M.Bolduc, J.L.Gallaher, B.L.Stoddard, D.Baker. Alteration of Enzyme Specificity By Computational Loop Remodeling and Design. Proc.Natl.Acad.Sci.Usa V. 106 9215 2009.
ISSN: ISSN 0027-8424
PubMed: 19470646
DOI: 10.1073/PNAS.0811070106