Zinc in PDB 6gbj: Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions

All present enzymatic activity of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions:
3.1.8.1;

The structure of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions, PDB code: 6gbj was solved by O.Khersonsky, R.Lipsh, Z.Avizemer, M.Goldsmith, Y.Ashani, H.Leader, O.Dym, S.Rogotner, D.Trudeau, D.S.Tawfik, S.J.Fleishman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.65 / 1.63
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.490, 69.490, 186.020, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 18.1

The binding sites of Zinc atom in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions (pdb code 6gbj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions, PDB code: 6gbj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.0 occ:1.00 O A:HOH530 2.0 15.4 1.0 NE2 A:HIS57 2.0 11.4 1.0 NE2 A:HIS55 2.1 11.2 1.0 O2 A:FMT401 2.1 12.9 1.0 OD1 A:ASP301 2.2 13.0 1.0 CD2 A:HIS55 3.0 13.0 1.0 CG A:ASP301 3.0 11.9 1.0 CE1 A:HIS57 3.0 12.0 1.0 CD2 A:HIS57 3.1 11.6 1.0 CE1 A:HIS55 3.1 13.2 1.0 C A:FMT401 3.1 12.8 1.0 O1 A:EDO405 3.2 24.3 0.8 OD2 A:ASP301 3.3 12.4 1.0 O1 A:FMT401 3.5 12.4 1.0 ZN A:ZN403 3.6 13.1 1.0 O A:HOH526 3.8 21.0 1.0 O2 A:EDO404 4.0 23.9 1.0 CG2 A:VAL101 4.0 12.5 1.0 C1 A:EDO405 4.1 25.0 0.8 NZ A:LYS169 4.1 12.8 1.0 CE1 A:HIS230 4.1 12.4 1.0 ND1 A:HIS57 4.2 11.8 1.0 CG A:HIS55 4.2 11.5 1.0 O A:HOH502 4.2 12.9 1.0 CG A:HIS57 4.2 12.2 1.0 ND1 A:HIS55 4.2 11.0 1.0 CB A:ASP301 4.3 12.1 1.0 NE2 A:HIS230 4.4 11.1 1.0 CA A:ASP301 4.9 12.9 1.0

Zinc binding site 2 out of 2 in the Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.1 occ:1.00 O1 A:FMT401 2.0 12.4 1.0 NE2 A:HIS230 2.1 11.1 1.0 O A:HOH502 2.1 12.9 1.0 ND1 A:HIS201 2.1 13.1 1.0 O A:HOH530 2.2 15.4 1.0 C A:FMT401 3.0 12.8 1.0 CE1 A:HIS201 3.0 13.1 1.0 CE1 A:HIS230 3.0 12.4 1.0 CD2 A:HIS230 3.1 13.1 1.0 CG A:HIS201 3.2 12.3 1.0 O2 A:FMT401 3.3 12.9 1.0 ZN A:ZN402 3.6 13.0 1.0 CB A:HIS201 3.6 12.2 1.0 O1 A:EDO405 3.7 24.3 0.8 NH2 A:ARG254 3.7 13.6 1.0 NE1 A:TRP131 4.0 13.9 1.0 O A:HOH526 4.0 21.0 1.0 ND1 A:HIS230 4.2 11.8 1.0 NZ A:LYS169 4.2 12.8 1.0 OD2 A:ASP301 4.2 12.4 1.0 CE1 A:HIS55 4.2 13.2 1.0 CG A:HIS230 4.2 12.1 1.0 NE2 A:HIS201 4.2 12.9 1.0 NE2 A:HIS55 4.2 11.2 1.0 CD2 A:HIS201 4.3 14.3 1.0 O2 A:EDO407 4.3 20.1 1.0 CA A:HIS201 4.4 12.1 1.0 CZ A:ARG254 4.4 14.0 1.0 CD1 A:TRP131 4.6 12.8 1.0 CE A:LYS169 4.6 11.9 1.0 NE A:ARG254 4.8 13.3 1.0 CG A:ASP301 5.0 11.9 1.0

O.Khersonsky, R.Lipsh, Z.Avizemer, Y.Ashani, M.Goldsmith, H.Leader, O.Dym, S.Rogotner, D.L.Trudeau, J.Prilusky, P.Amengual-Rigo, V.Guallar, D.S.Tawfik, S.J.Fleishman. Automated Design of Efficient and Functionally Diverse Enzyme Repertoires. Mol. Cell V. 72 178 2018.
ISSN: ISSN 1097-4164
PubMed: 30270109
DOI: 10.1016/J.MOLCEL.2018.08.033