Zinc in PDB 5eh9: Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function

All present enzymatic activity of Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function:
3.1.1.81;

The structure of Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function, PDB code: 5eh9 was solved by N.-S.Hong, C.J.Jackson, N.Tokuriki, G.Yang, F.Baier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.47 / 1.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.511, 55.473, 79.358, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 15.3

The binding sites of Zinc atom in the Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function (pdb code 5eh9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function, PDB code: 5eh9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.1 occ:1.00 O A:HOH420 2.0 14.9 1.0 OD2 A:ASP191 2.0 13.6 1.0 NE2 A:HIS109 2.1 12.7 1.0 NE2 A:HIS235 2.1 13.6 1.0 OD2 A:ASP108 2.2 14.9 1.0 CG A:ASP191 3.0 12.8 1.0 CD2 A:HIS109 3.0 13.1 1.0 CE1 A:HIS235 3.0 14.4 1.0 CD2 A:HIS235 3.1 14.1 1.0 CE1 A:HIS109 3.1 13.1 1.0 CG A:ASP108 3.2 14.6 1.0 OD1 A:ASP191 3.3 14.9 1.0 ZN A:ZN302 3.3 13.8 1.0 OD1 A:ASP108 3.5 15.0 1.0 O A:HOH423 3.7 25.0 1.0 O A:HOH427 3.9 16.4 1.0 O A:HOH564 4.1 41.4 1.0 NE2 A:HIS104 4.1 13.3 1.0 ND1 A:HIS235 4.1 14.5 1.0 CG A:HIS109 4.1 12.6 1.0 CE1 A:HIS104 4.2 13.6 1.0 ND1 A:HIS109 4.2 12.0 1.0 CG A:HIS235 4.2 14.5 1.0 CB A:ASP191 4.4 13.6 1.0 O A:HOH518 4.5 19.5 1.0 CB A:ASP108 4.6 13.8 1.0 CE1 A:TYR194 4.6 17.8 1.0 O A:HOH415 4.7 39.4 1.0 NE2 A:HIS169 4.7 13.6 1.0

Zinc binding site 2 out of 2 in the Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.8 occ:1.00 O A:HOH420 2.0 14.9 1.0 NE2 A:HIS169 2.0 13.6 1.0 NE2 A:HIS104 2.1 13.3 1.0 ND1 A:HIS106 2.1 14.2 1.0 OD2 A:ASP191 2.6 13.6 1.0 CD2 A:HIS104 3.0 12.6 1.0 CD2 A:HIS169 3.0 13.9 1.0 CE1 A:HIS169 3.0 15.7 1.0 CE1 A:HIS106 3.1 14.4 1.0 CE1 A:HIS104 3.2 13.6 1.0 CG A:HIS106 3.2 14.5 1.0 ZN A:ZN301 3.3 14.1 1.0 CB A:HIS106 3.6 12.5 1.0 CG A:ASP191 3.7 12.8 1.0 O A:HOH423 3.9 25.0 1.0 NE2 A:HIS109 4.0 12.7 1.0 CB A:ASP191 4.0 13.6 1.0 CD2 A:HIS109 4.0 13.1 1.0 ND1 A:HIS169 4.1 14.9 1.0 CG A:HIS169 4.2 14.0 1.0 NE2 A:HIS106 4.2 14.6 1.0 CG A:HIS104 4.2 12.5 1.0 ND1 A:HIS104 4.2 13.0 1.0 CD2 A:HIS106 4.3 14.4 1.0 OD1 A:ASP108 4.3 15.0 1.0 O A:HOH415 4.4 39.4 1.0 OH A:TYR194 4.7 21.6 1.0 OD2 A:ASP108 4.8 14.9 1.0 OD1 A:ASP191 4.8 14.9 1.0 CE1 A:TYR194 4.9 17.8 1.0 O A:HOH434 4.9 62.0 1.0 CG A:ASP108 5.0 14.6 1.0

G.Yang, N.Hong, F.Baier, C.J.Jackson, N.Tokuriki. Conformational Tinkering Drives Evolution of A Promiscuous Activity Through Indirect Mutational Effects. Biochemistry V. 55 4583 2016.
ISSN: ISSN 0006-2960
PubMed: 27444875
DOI: 10.1021/ACS.BIOCHEM.6B00561