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

Enzymatic activity of 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;

Protein crystallography data

The structure of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions, PDB code: 6gbl 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) 41.61 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.797, 53.560, 89.339, 90.00, 107.21, 90.00
R / Rfree (%) 17.7 / 22

Other elements in 6gbl:

The structure of Repertoires of Functionally Diverse Enzymes Through Computational Design at Epistatic Active-Site Positions also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Arsenic Binding Sites:

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

Arsenic binding site 1 out of 2 in 6gbl

Go back to Arsenic Binding Sites List in 6gbl
Arsenic 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 Arsenic with other atoms in the As 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:As405

b:13.2
occ:1.00
AS A:CAC405 0.0 13.2 1.0
O2 A:CAC405 1.7 12.3 1.0
O1 A:CAC405 1.7 12.3 1.0
C2 A:CAC405 1.9 14.8 1.0
C1 A:CAC405 2.0 13.7 1.0
ZN A:ZN403 3.1 12.5 1.0
ZN A:ZN402 3.3 12.7 1.0
O2 A:EDO404 3.4 20.4 1.0
O2 A:FMT401 3.5 12.5 1.0
OD2 A:ASP301 3.8 10.6 1.0
O1 A:FMT401 4.1 12.4 1.0
NE1 A:TRP131 4.1 12.5 1.0
C A:FMT401 4.2 13.2 1.0
NE2 A:HIS230 4.2 12.8 1.0
OD1 A:ASP301 4.3 10.6 1.0
NE2 A:HIS57 4.3 11.7 1.0
CE1 A:HIS230 4.4 12.3 1.0
CG A:ASP301 4.5 11.4 1.0
CZ2 A:TRP131 4.5 12.3 1.0
CE2 A:TRP131 4.6 12.4 1.0
ND1 A:HIS201 4.6 11.1 1.0
C2 A:EDO404 4.8 22.1 1.0
C1 A:EDO404 4.9 27.6 1.0
CE1 A:HIS201 5.0 11.7 1.0
O1 A:EDO404 5.0 29.6 1.0
NE2 A:HIS55 5.0 11.6 1.0
CH2 A:TRP257 5.0 15.0 1.0

Arsenic binding site 2 out of 2 in 6gbl

Go back to Arsenic Binding Sites List in 6gbl
Arsenic 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 Arsenic with other atoms in the As 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
B:As404

b:14.9
occ:1.00
AS B:CAC404 0.0 14.9 1.0
O1 B:CAC404 1.7 14.5 1.0
O2 B:CAC404 1.7 14.0 1.0
C2 B:CAC404 1.9 15.6 1.0
C1 B:CAC404 2.0 14.7 1.0
O1 B:EDO405 3.1 28.6 1.0
ZN B:ZN403 3.1 15.7 1.0
ZN B:ZN402 3.3 13.1 1.0
O2 B:FMT401 3.5 13.4 1.0
C1 B:EDO405 3.7 24.9 1.0
OD2 B:ASP301 3.9 16.4 1.0
O1 B:FMT401 4.0 12.6 1.0
NE1 B:TRP131 4.0 12.6 1.0
O B:HOH592 4.1 24.3 1.0
NE2 B:HIS230 4.1 16.8 1.0
C B:FMT401 4.1 13.7 1.0
NE2 B:HIS57 4.2 13.4 1.0
OD1 B:ASP301 4.4 14.3 1.0
CZ2 B:TRP131 4.5 14.1 1.0
CE1 B:HIS230 4.5 15.4 1.0
ND1 B:HIS201 4.5 14.8 1.0
CE2 B:TRP131 4.6 13.7 1.0
CG B:ASP301 4.6 15.9 1.0
CE1 B:HIS201 4.8 15.7 1.0
C2 B:EDO405 4.9 27.6 1.0
CE1 B:HIS57 4.9 14.5 1.0
NE2 B:HIS55 4.9 12.6 1.0
CH2 B:TRP257 5.0 22.1 1.0
CD2 B:HIS57 5.0 14.1 1.0

Reference:

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
Page generated: Sat Dec 12 01:48:50 2020

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