Atomistry » Zinc » PDB 4x3t-4xgm » 4xd3
Atomistry »
  Zinc »
    PDB 4x3t-4xgm »
      4xd3 »

Zinc 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:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase Variant E3 (pdb code 4xd3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Phosphotriesterase Variant E3, PDB code: 4xd3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4xd3

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:12.9
occ:0.68
O A:HOH2791 1.9 23.8 1.0
NE2 A:HIS57 2.1 13.2 1.0
OD1 A:ASP301 2.1 15.1 1.0
NE2 A:HIS55 2.2 16.1 1.0
OQ2 A:KCX169 2.2 18.8 1.0
CE1 A:HIS57 3.0 14.8 1.0
CG A:ASP301 3.0 16.5 1.0
CD2 A:HIS55 3.1 13.5 1.0
CX A:KCX169 3.1 23.9 1.0
CD2 A:HIS57 3.1 11.7 1.0
CE1 A:HIS55 3.2 14.3 1.0
O1 A:CAC2403 3.3 16.4 1.0
OD2 A:ASP301 3.3 20.8 1.0
OQ1 A:KCX169 3.5 19.0 1.0
O2 A:CAC2403 3.5 52.4 1.0
ZN A:ZN2402 3.6 15.3 0.5
NZ A:KCX169 4.1 19.4 1.0
AS A:CAC2403 4.1 0.1 1.0
ND1 A:HIS57 4.1 13.5 1.0
CG2 A:VAL101 4.2 15.4 1.0
CG A:HIS57 4.2 12.6 1.0
CE1 A:HIS230 4.2 18.1 1.0
CG A:HIS55 4.2 13.6 1.0
ND1 A:HIS55 4.3 17.2 1.0
CB A:ASP301 4.4 15.0 1.0
NE2 A:HIS230 4.5 19.4 1.0
O A:HOH2632 4.8 35.2 1.0
CA A:ASP301 4.8 12.7 1.0

Zinc binding site 2 out of 4 in 4xd3

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:15.3
occ:0.53
OQ1 A:KCX169 2.0 19.0 1.0
NE2 A:HIS230 2.1 19.4 1.0
O A:HOH2791 2.2 23.8 1.0
ND1 A:HIS201 2.3 23.2 1.0
O1 A:CAC2403 3.0 16.4 1.0
CX A:KCX169 3.0 23.9 1.0
CE1 A:HIS230 3.0 18.1 1.0
CD2 A:HIS230 3.1 20.0 1.0
CE1 A:HIS201 3.2 26.9 1.0
OQ2 A:KCX169 3.3 18.8 1.0
CG A:HIS201 3.3 25.0 1.0
ZN A:ZN2401 3.6 12.9 0.7
CB A:HIS201 3.7 20.6 1.0
NE1 A:TRP131 4.0 22.8 1.0
ND1 A:HIS230 4.2 23.6 1.0
NZ A:KCX169 4.2 19.4 1.0
CG A:HIS230 4.2 21.2 1.0
CE1 A:HIS55 4.3 14.3 1.0
NE2 A:HIS55 4.3 16.1 1.0
NE2 A:HIS201 4.3 26.1 1.0
OD2 A:ASP301 4.4 20.8 1.0
CD2 A:HIS201 4.4 23.1 1.0
AS A:CAC2403 4.6 0.1 1.0
CA A:HIS201 4.6 22.1 1.0
CD1 A:TRP131 4.7 16.8 1.0
CE A:KCX169 4.7 18.2 1.0
OD1 A:ASP301 5.0 15.1 1.0

Zinc binding site 3 out of 4 in 4xd3

Go back to Zinc Binding Sites List in 4xd3
Zinc binding site 3 out of 4 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn402

b:12.8
occ:0.67
O1 G:CAC401 1.9 28.4 1.0
NE2 G:HIS57 2.1 13.0 1.0
OD1 G:ASP301 2.1 17.6 1.0
NE2 G:HIS55 2.2 16.0 1.0
OQ2 G:KCX169 2.2 23.9 1.0
CE1 G:HIS57 3.0 19.7 1.0
CG G:ASP301 3.0 18.8 1.0
CD2 G:HIS55 3.1 16.3 1.0
CD2 G:HIS57 3.1 15.6 1.0
CX G:KCX169 3.2 27.9 1.0
CE1 G:HIS55 3.2 16.6 1.0
AS G:CAC401 3.3 85.7 1.0
OD2 G:ASP301 3.4 17.3 1.0
OQ1 G:KCX169 3.6 22.1 1.0
ZN G:ZN403 3.6 17.3 0.6
C2 G:CAC401 3.7 43.2 1.0
CE1 G:HIS230 4.1 18.9 1.0
ND1 G:HIS57 4.1 14.3 1.0
NZ G:KCX169 4.2 21.6 1.0
CG G:HIS57 4.2 16.6 1.0
CG2 G:VAL101 4.2 13.7 1.0
O2 G:CAC401 4.2 49.1 1.0
CG G:HIS55 4.3 12.8 1.0
NE2 G:HIS230 4.3 22.5 1.0
ND1 G:HIS55 4.3 16.1 1.0
CB G:ASP301 4.4 11.7 1.0
C1 G:CAC401 4.7 52.9 1.0
CA G:ASP301 4.8 11.1 1.0

Zinc binding site 4 out of 4 in 4xd3

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant E3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn403

b:17.3
occ:0.56
OQ1 G:KCX169 2.0 22.1 1.0
NE2 G:HIS230 2.0 22.5 1.0
O2 G:CAC401 2.4 49.1 1.0
CD2 G:HIS201 2.4 24.6 1.0
O1 G:CAC401 2.6 28.4 1.0
CX G:KCX169 2.9 27.9 1.0
CD2 G:HIS230 3.0 24.1 1.0
CE1 G:HIS230 3.1 18.9 1.0
AS G:CAC401 3.1 85.7 1.0
OQ2 G:KCX169 3.2 23.9 1.0
CG G:HIS201 3.3 21.9 1.0
NE2 G:HIS201 3.5 34.9 1.0
ZN G:ZN402 3.6 12.8 0.7
CB G:HIS201 3.7 22.6 1.0
CG G:HIS230 4.1 18.7 1.0
ND1 G:HIS230 4.1 19.2 1.0
NZ G:KCX169 4.2 21.6 1.0
NE1 G:TRP131 4.2 24.0 1.0
CE1 G:HIS55 4.2 16.6 1.0
NE2 G:HIS55 4.2 16.0 1.0
OD2 G:ASP301 4.4 17.3 1.0
C1 G:CAC401 4.4 52.9 1.0
ND1 G:HIS201 4.5 35.9 1.0
CE1 G:HIS201 4.6 29.4 1.0
O G:HOH809 4.6 54.0 1.0
CA G:HIS201 4.6 22.2 1.0
C2 G:CAC401 4.7 43.2 1.0
CE G:KCX169 4.7 19.2 1.0
CD1 G:TRP131 4.8 22.5 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: Sun Oct 27 10:27:15 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy