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

Enzymatic activity of 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;

Protein crystallography data

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

Resolution Low / High (Å) 32.49 / 1.29
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.638, 55.735, 79.878, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 16.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Indirect Contributions of Mutations Underlie Optimization of New Enzyme Function (pdb code 5eht). 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: 5eht:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5eht

Go back to Zinc Binding Sites List in 5eht
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:11.9
occ:1.00
NE2 A:HIS109 2.0 9.7 1.0
O A:HOH432 2.1 12.5 1.0
OD2 A:ASP191 2.1 12.9 1.0
NE2 A:HIS235 2.1 11.5 1.0
OD2 A:ASP108 2.2 13.6 1.0
CD2 A:HIS109 3.0 9.8 1.0
CG A:ASP191 3.0 12.8 1.0
CE1 A:HIS235 3.0 11.4 1.0
CE1 A:HIS109 3.1 10.7 1.0
CD2 A:HIS235 3.1 12.1 1.0
CG A:ASP108 3.2 12.6 1.0
OD1 A:ASP191 3.3 12.0 1.0
ZN A:ZN302 3.3 11.7 1.0
OD1 A:ASP108 3.5 12.9 1.0
O A:HOH402 3.6 20.4 1.0
O A:HOH425 3.7 24.5 1.0
O A:HOH429 3.9 13.4 1.0
ND1 A:HIS235 4.1 11.8 1.0
CG A:HIS109 4.2 10.2 1.0
NE2 A:HIS104 4.2 10.3 1.0
O A:HOH561 4.2 39.3 1.0
CE1 A:HIS104 4.2 11.1 1.0
ND1 A:HIS109 4.2 10.9 1.0
CG A:HIS235 4.2 12.1 1.0
CB A:ASP191 4.4 11.9 1.0
O A:HOH528 4.5 15.9 1.0
CE1 A:TYR194 4.6 16.1 1.0
CB A:ASP108 4.6 11.5 1.0
NE2 A:HIS169 4.7 11.4 1.0

Zinc binding site 2 out of 2 in 5eht

Go back to Zinc Binding Sites List in 5eht
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:11.7
occ:1.00
O A:HOH432 2.0 12.5 1.0
NE2 A:HIS169 2.1 11.4 1.0
NE2 A:HIS104 2.1 10.3 1.0
ND1 A:HIS106 2.1 12.5 1.0
OD2 A:ASP191 2.6 12.9 1.0
CD2 A:HIS169 3.0 10.7 1.0
CE1 A:HIS106 3.0 12.9 1.0
CD2 A:HIS104 3.0 9.8 1.0
CE1 A:HIS169 3.1 11.9 1.0
CE1 A:HIS104 3.1 11.1 1.0
CG A:HIS106 3.2 12.5 1.0
ZN A:ZN301 3.3 11.9 1.0
CB A:HIS106 3.6 10.8 1.0
CG A:ASP191 3.7 12.8 1.0
O A:HOH402 3.8 20.4 1.0
O A:HOH425 3.9 24.5 1.0
CB A:ASP191 4.0 11.9 1.0
NE2 A:HIS109 4.0 9.7 1.0
CD2 A:HIS109 4.0 9.8 1.0
NE2 A:HIS106 4.1 14.2 1.0
CG A:HIS169 4.2 11.8 1.0
ND1 A:HIS169 4.2 13.8 1.0
CG A:HIS104 4.2 10.0 1.0
ND1 A:HIS104 4.2 10.2 1.0
CD2 A:HIS106 4.3 14.1 1.0
OD1 A:ASP108 4.3 12.9 1.0
O A:HOH606 4.6 55.0 1.0
OH A:TYR194 4.7 18.0 1.0
OD2 A:ASP108 4.8 13.6 1.0
OD1 A:ASP191 4.8 12.0 1.0
CE1 A:TYR194 4.8 16.1 1.0
CE1 A:HIS109 5.0 10.7 1.0
CG A:ASP108 5.0 12.6 1.0

Reference:

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
Page generated: Wed Dec 16 06:09:58 2020

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