Atomistry » Arsenic » PDB 5yvb-6i5n » 6gbl
Atomistry »
  Arsenic »
    PDB 5yvb-6i5n »
      6gbl »

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: Wed Jul 10 13:17:23 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy