Zinc in PDB 3t1g: Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution

The structure of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution, PDB code: 3t1g was solved by R.Takeuchi, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.40 / 2.35
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.391, 77.592, 94.972, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25

The structure of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Zinc atom in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution (pdb code 3t1g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution, PDB code: 3t1g:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn353 b:22.8 occ:1.00 NE2 A:HIS17 2.0 19.5 1.0 NE2 A:HIS15 2.2 19.6 1.0 O A:HOH398 2.2 17.9 1.0 NE2 A:HIS214 2.3 18.6 1.0 OD1 A:ASP295 2.5 25.0 1.0 CD2 A:HIS17 3.0 18.8 1.0 CE1 A:HIS17 3.0 18.9 1.0 CE1 A:HIS15 3.2 19.8 1.0 CD2 A:HIS15 3.2 18.0 1.0 CE1 A:HIS214 3.2 18.0 1.0 CD2 A:HIS214 3.2 17.0 1.0 CG A:ASP295 3.4 22.8 1.0 OD2 A:ASP295 3.6 23.1 1.0 NE2 A:HIS238 3.7 21.8 1.0 ND1 A:HIS17 4.1 18.4 1.0 CG A:HIS17 4.1 18.0 1.0 ND1 A:HIS15 4.3 18.5 1.0 CG A:HIS15 4.3 18.8 1.0 ND1 A:HIS214 4.3 17.6 1.0 CG A:HIS214 4.4 18.9 1.0 CE1 A:HIS238 4.5 20.7 1.0 CD2 A:HIS238 4.6 21.3 1.0 CB A:ASP295 4.7 21.7 1.0 CD A:ARG101 5.0 17.4 1.0

Zinc binding site 2 out of 4 in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn354 b:82.6 occ:1.00 OE1 A:GLU45 2.6 44.7 1.0 OD2 A:ASP41 3.0 52.8 1.0 OE2 A:GLU45 3.1 47.9 1.0 CD A:GLU45 3.2 45.2 1.0 ZN A:ZN356 3.2 0.9 1.0 CG A:ASP41 4.0 52.1 1.0 N A:ASP41 4.3 48.0 1.0 OD1 A:ASP41 4.6 53.0 1.0 O A:ASP41 4.7 50.9 1.0 CG A:GLU45 4.7 43.2 1.0 C A:ASP41 4.8 48.9 1.0 CA A:ASP41 4.9 48.7 1.0

Zinc binding site 3 out of 4 in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn355 b:89.4 occ:1.00 O A:HOH469 2.5 19.8 1.0 O A:ASP123 2.5 39.6 1.0 OD2 A:ASP128 2.7 35.8 1.0 O A:HOH448 3.0 30.9 1.0 O A:HOH446 3.0 23.1 1.0 O A:HOH466 3.0 23.3 1.0 CG A:ASP128 3.4 35.4 1.0 OD1 A:ASP128 3.6 36.0 1.0 C A:ASP123 3.7 39.1 1.0 CB A:ASP123 4.4 43.3 1.0 CA A:VAL124 4.5 35.2 1.0 NH1 A:ARG76 4.5 43.8 1.0 N A:THR125 4.5 34.0 1.0 N A:VAL124 4.6 37.1 1.0 CG2 A:THR125 4.6 35.8 1.0 CG A:ASP123 4.6 44.1 1.0 CA A:ASP123 4.6 41.2 1.0 OD1 A:ASP123 4.7 43.0 1.0 CB A:ASP128 4.7 32.9 1.0 OG1 A:THR125 5.0 34.0 1.0

Zinc binding site 4 out of 4 in the Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Engineering of Organophosphate Hydrolase By Computational Design and Directed Evolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn356 b:0.9 occ:1.00 OD1 A:ASP41 2.8 53.0 1.0 OD2 A:ASP41 3.1 52.8 1.0 ZN A:ZN354 3.2 82.6 1.0 CG A:ASP41 3.3 52.1 1.0 N A:ASP41 4.4 48.0 1.0 CB A:ASP41 4.7 50.5 1.0 C A:ALA40 4.9 46.7 1.0 CA A:ALA40 5.0 46.2 1.0

S.D.Khare, Y.Kipnis, P.J.Greisen, R.Takeuchi, Y.Ashani, M.Goldsmith, Y.Song, J.L.Gallaher, I.Silman, H.Leader, J.L.Sussman, B.L.Stoddard, D.S.Tawfik, D.Baker. Computational Redesign of A Mononuclear Zinc Metalloenzyme For Organophosphate Hydrolysis. Nat.Chem.Biol. V. 8 294 2012.
ISSN: ISSN 1552-4450
PubMed: 22306579
DOI: 10.1038/NCHEMBIO.777