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Arsenic in PDB 4xd5: Phosphotriesterase Variant R2

Protein crystallography data

The structure of Phosphotriesterase Variant R2, PDB code: 4xd5 was solved by E.Campbell, M.Kaltenbach, N.Tokuriki, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.19 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.704, 85.869, 88.382, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.4

Other elements in 4xd5:

The structure of Phosphotriesterase Variant R2 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Phosphotriesterase Variant R2 (pdb code 4xd5). 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 R2, PDB code: 4xd5:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 4xd5

Go back to Arsenic Binding Sites List in 4xd5
Arsenic binding site 1 out of 2 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Phosphotriesterase Variant R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As2403

b:26.0
occ:0.68
AS A:CAC2403 0.0 26.0 0.7
O2 A:CAC2403 1.7 18.1 0.7
O1 A:CAC2403 1.8 9.9 0.7
C2 A:CAC2403 2.0 20.5 0.7
C1 A:CAC2403 2.0 26.3 0.7
ZN A:ZN2402 3.1 14.2 0.8
ZN A:ZN2401 3.3 13.8 1.0
NH2 A:ARG254 3.5 26.5 0.3
OQ2 A:KCX169 3.5 14.6 1.0
OQ1 A:KCX169 4.0 14.3 1.0
NE1 A:TRP131 4.0 21.5 1.0
OD2 A:ASP301 4.1 15.4 1.0
CX A:KCX169 4.2 17.0 1.0
O A:HOH2650 4.3 33.7 1.0
CZ2 A:TRP131 4.3 20.5 1.0
NE2 A:HIS57 4.3 12.5 1.0
OD1 A:ASP301 4.4 9.4 1.0
CE2 A:TRP131 4.4 17.3 1.0
ND1 A:HIS201 4.5 19.0 1.0
NE2 A:HIS230 4.6 12.7 1.0
CZ A:ARG254 4.7 23.5 0.3
CG A:ASP301 4.7 10.3 1.0
CE1 A:HIS57 4.8 10.7 1.0
CE1 A:HIS201 4.8 28.6 1.0

Arsenic binding site 2 out of 2 in 4xd5

Go back to Arsenic Binding Sites List in 4xd5
Arsenic binding site 2 out of 2 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Phosphotriesterase Variant R2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As401

b:26.3
occ:0.79
AS G:CAC401 0.0 26.3 0.8
O1 G:CAC401 1.7 17.9 0.8
O2 G:CAC401 1.7 22.3 0.8
C1 G:CAC401 2.0 26.7 0.8
C2 G:CAC401 2.0 19.7 0.8
ZN G:ZN403 3.1 18.0 0.9
ZN G:ZN402 3.3 14.9 0.9
OQ2 G:KCX169 3.5 16.1 1.0
NH2 G:ARG254 3.8 25.9 0.3
OD2 G:ASP301 4.0 23.6 1.0
OQ1 G:KCX169 4.1 17.1 1.0
CX G:KCX169 4.2 19.8 1.0
NE2 G:HIS57 4.3 12.5 1.0
NE1 G:TRP131 4.3 18.6 1.0
O G:HOH664 4.3 43.4 1.0
NE2 G:HIS230 4.4 18.7 1.0
OD1 G:ASP301 4.4 15.8 1.0
CZ2 G:TRP131 4.5 25.9 1.0
ND1 G:HIS201 4.5 15.1 1.0
CG G:ASP301 4.6 18.4 1.0
CE2 G:TRP131 4.7 21.1 1.0
CE1 G:HIS201 4.8 25.4 1.0
CZ G:ARG254 4.9 25.9 0.3
NH1 G:ARG254 4.9 29.2 0.7
CE1 G:HIS57 4.9 15.3 1.0
CE1 G:HIS230 4.9 19.8 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: Wed Jul 10 12:40:45 2024

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