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Arsenic in PDB 4xd3: Phosphotriesterase Variant E3

Protein crystallography data

The structure of Phosphotriesterase Variant E3, PDB code: 4xd3 was solved by C.J.Jackson, E.Campbell, M.Kaltenbach, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.41 / 1.57
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.830, 85.882, 88.721, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.2

Other elements in 4xd3:

The structure of Phosphotriesterase Variant E3 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Phosphotriesterase Variant E3 (pdb code 4xd3). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Phosphotriesterase Variant E3, PDB code: 4xd3:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4xd3

Go back to Arsenic Binding Sites List in 4xd3
Arsenic binding site 1 out of 2 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2403

b:0.1
occ:1.00
AS A:CAC2403 0.0 0.1 1.0
O1 A:CAC2403 1.7 16.4 1.0
O2 A:CAC2403 1.7 52.4 1.0
C2 A:CAC2403 2.0 56.4 1.0
C1 A:CAC2403 2.0 40.4 1.0
O A:HOH2791 3.3 23.8 1.0
O A:HOH2632 3.5 35.2 1.0
ZN A:ZN2401 4.1 12.9 0.7
OD2 A:ASP301 4.5 20.8 1.0
ZN A:ZN2402 4.6 15.3 0.5
OD1 A:ASP301 4.6 15.1 1.0
NE2 A:HIS57 4.6 13.2 1.0
O A:HOH2735 4.7 48.4 1.0
OQ2 A:KCX169 4.7 18.8 1.0
CZ2 A:TRP131 4.8 28.1 1.0
NH1 A:ARG254 4.9 29.6 1.0
CG A:ASP301 4.9 16.5 1.0

Arsenic binding site 2 out of 2 in 4xd3

Go back to Arsenic Binding Sites List in 4xd3
Arsenic binding site 2 out of 2 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As401

b:85.7
occ:1.00
AS G:CAC401 0.0 85.7 1.0
O2 G:CAC401 1.7 49.1 1.0
O1 G:CAC401 1.8 28.4 1.0
C1 G:CAC401 2.0 52.9 1.0
C2 G:CAC401 2.0 43.2 1.0
ZN G:ZN403 3.1 17.3 0.6
ZN G:ZN402 3.3 12.8 0.7
OQ2 G:KCX169 3.4 23.9 1.0
OD2 G:ASP301 4.1 17.3 1.0
OQ1 G:KCX169 4.1 22.1 1.0
CX G:KCX169 4.2 27.9 1.0
NE2 G:HIS57 4.2 13.0 1.0
OD1 G:ASP301 4.3 17.6 1.0
NE1 G:TRP131 4.4 24.0 1.0
O G:HOH704 4.4 41.0 1.0
CZ2 G:TRP131 4.6 25.4 1.0
O G:HOH809 4.6 54.0 1.0
NE2 G:HIS230 4.6 22.5 1.0
CG G:ASP301 4.7 18.8 1.0
CE2 G:TRP131 4.7 22.2 1.0
CE1 G:HIS57 4.8 19.7 1.0
O G:HOH731 4.8 36.2 1.0
CD2 G:HIS201 4.8 24.6 1.0
CD2 G:HIS57 5.0 15.6 1.0

Reference:

E.Campbell, M.Kaltenbach, G.J.Correy, P.D.Carr, B.T.Porebski, E.K.Livingstone, L.Afriat-Jurnou, A.M.Buckle, M.Weik, F.Hollfelder, N.Tokuriki, C.J.Jackson. The Role of Protein Dynamics in the Evolution of New Enzyme Function. Nat.Chem.Biol. V. 12 944 2016.
ISSN: ESSN 1552-4469
PubMed: 27618189
DOI: 10.1038/NCHEMBIO.2175
Page generated: Sat Dec 12 01:45:50 2020

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