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Zinc in PDB 5wj0: Phosphotriesterase Variant S5+254R

Protein crystallography data

The structure of Phosphotriesterase Variant S5+254R, PDB code: 5wj0 was solved by C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.43 / 1.65
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.327, 85.785, 88.280, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.8

Other elements in 5wj0:

The structure of Phosphotriesterase Variant S5+254R also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase Variant S5+254R (pdb code 5wj0). 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 S5+254R, PDB code: 5wj0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5wj0

Go back to Zinc Binding Sites List in 5wj0
Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S5+254R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S5+254R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:14.6
occ:0.94
O2 A:CAC2406 2.0 11.4 0.6
NE2 A:HIS57 2.1 14.8 1.0
NE2 A:HIS55 2.1 13.9 1.0
OD1 A:ASP301 2.1 15.0 1.0
OQ1 A:KCX169 2.1 16.1 1.0
CE1 A:HIS57 3.0 11.0 1.0
CG A:ASP301 3.0 15.7 1.0
CD2 A:HIS55 3.0 12.4 1.0
CD2 A:HIS57 3.1 11.7 1.0
CX A:KCX169 3.1 13.3 1.0
CE1 A:HIS55 3.1 14.3 1.0
AS A:CAC2406 3.3 40.0 0.6
OD2 A:ASP301 3.3 16.1 1.0
O1 A:CAC2406 3.5 37.7 0.6
ZN A:ZN2402 3.5 19.7 1.0
OQ2 A:KCX169 3.6 14.1 1.0
CG2 A:VAL101 4.1 15.3 1.0
CE1 A:HIS230 4.1 20.4 1.0
ND1 A:HIS57 4.1 13.3 1.0
CG A:HIS55 4.2 13.3 1.0
ND1 A:HIS55 4.2 14.3 1.0
CG A:HIS57 4.2 11.3 1.0
NZ A:KCX169 4.2 13.3 1.0
NE2 A:HIS230 4.3 14.9 1.0
CB A:ASP301 4.4 14.4 1.0
C1 A:CAC2406 4.4 43.4 0.6
C2 A:CAC2406 4.8 37.9 0.6
CA A:ASP301 4.9 15.8 1.0
O A:HOH2583 4.9 31.4 1.0

Zinc binding site 2 out of 4 in 5wj0

Go back to Zinc Binding Sites List in 5wj0
Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S5+254R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S5+254R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:19.7
occ:0.98
OQ2 A:KCX169 1.9 14.1 1.0
NE2 A:HIS230 2.0 14.9 1.0
O2 A:CAC2406 2.2 11.4 0.6
ND1 A:HIS201 2.4 24.9 1.0
C2 A:CAC2406 2.6 37.9 0.6
CX A:KCX169 2.9 13.3 1.0
AS A:CAC2406 2.9 40.0 0.6
CE1 A:HIS230 3.0 20.4 1.0
CD2 A:HIS230 3.0 18.3 1.0
OQ1 A:KCX169 3.2 16.1 1.0
CE1 A:HIS201 3.2 23.6 1.0
CG A:HIS201 3.4 23.1 1.0
ZN A:ZN2401 3.5 14.6 0.9
CB A:HIS201 3.8 20.8 1.0
O1 A:CAC2406 3.9 37.7 0.6
NE1 A:TRP131 3.9 15.1 1.0
CE1 A:HIS55 4.0 14.3 1.0
NE2 A:HIS55 4.1 13.9 1.0
ND1 A:HIS230 4.1 18.9 1.0
CG A:HIS230 4.2 16.1 1.0
NZ A:KCX169 4.2 13.3 1.0
OD2 A:ASP301 4.4 16.1 1.0
NE2 A:HIS201 4.4 24.5 1.0
CD1 A:TRP131 4.5 14.6 1.0
CD2 A:HIS201 4.5 23.4 1.0
CA A:HIS201 4.6 16.9 1.0
CE A:KCX169 4.6 15.8 1.0
C1 A:CAC2406 4.6 43.4 0.6
OD1 A:ASP301 5.0 15.0 1.0

Zinc binding site 3 out of 4 in 5wj0

Go back to Zinc Binding Sites List in 5wj0
Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S5+254R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S5+254R within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn403

b:21.9
occ:0.95
O2 G:CAC406 1.8 19.1 0.6
NE2 G:HIS57 2.1 22.3 1.0
OD1 G:ASP301 2.1 34.7 1.0
OQ2 G:KCX169 2.1 31.0 1.0
NE2 G:HIS55 2.1 25.1 1.0
CE1 G:HIS57 3.0 21.8 1.0
CG G:ASP301 3.0 28.1 1.0
CD2 G:HIS55 3.0 24.4 1.0
CX G:KCX169 3.0 29.0 1.0
CD2 G:HIS57 3.1 22.0 1.0
CE1 G:HIS55 3.2 24.2 1.0
AS G:CAC406 3.2 43.4 0.6
OD2 G:ASP301 3.3 29.5 1.0
OQ1 G:KCX169 3.5 23.8 1.0
ZN G:ZN404 3.5 28.0 0.9
C1 G:CAC406 3.7 37.4 0.6
CE1 G:HIS230 4.0 29.5 1.0
CG2 G:VAL101 4.1 24.6 1.0
ND1 G:HIS57 4.1 22.6 1.0
NZ G:KCX169 4.1 24.4 1.0
CG G:HIS57 4.2 20.1 1.0
CG G:HIS55 4.2 23.1 1.0
O1 G:CAC406 4.2 32.5 0.6
ND1 G:HIS55 4.2 24.3 1.0
NE2 G:HIS230 4.3 23.7 1.0
CB G:ASP301 4.4 23.3 1.0
C2 G:CAC406 4.6 41.1 0.6
CA G:ASP301 4.9 23.2 1.0

Zinc binding site 4 out of 4 in 5wj0

Go back to Zinc Binding Sites List in 5wj0
Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S5+254R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S5+254R within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn404

b:28.0
occ:0.94
OQ1 G:KCX169 1.7 23.8 1.0
NE2 G:HIS230 2.0 23.7 1.0
O1 G:CAC406 2.2 32.5 0.6
ND1 G:HIS201 2.2 37.5 1.0
O2 G:CAC406 2.3 19.1 0.6
CX G:KCX169 2.8 29.0 1.0
AS G:CAC406 2.8 43.4 0.6
CE1 G:HIS201 2.9 35.1 1.0
CE1 G:HIS230 3.0 29.5 1.0
CD2 G:HIS230 3.0 26.8 1.0
OQ2 G:KCX169 3.1 31.0 1.0
CG G:HIS201 3.3 30.3 1.0
ZN G:ZN403 3.5 21.9 0.9
CB G:HIS201 3.8 27.0 1.0
NE1 G:TRP131 4.0 25.5 1.0
ND1 G:HIS230 4.1 26.4 1.0
CE1 G:HIS55 4.1 24.2 1.0
NE2 G:HIS55 4.1 25.1 1.0
NZ G:KCX169 4.1 24.4 1.0
CG G:HIS230 4.1 26.6 1.0
NE2 G:HIS201 4.2 33.6 1.0
C2 G:CAC406 4.3 41.1 0.6
C1 G:CAC406 4.3 37.4 0.6
CD2 G:HIS201 4.4 33.0 1.0
OD2 G:ASP301 4.4 29.5 1.0
CD1 G:TRP131 4.6 26.4 1.0
CE G:KCX169 4.6 22.2 1.0
CA G:HIS201 4.7 24.1 1.0
OD1 G:ASP301 4.9 34.7 1.0

Reference:

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S5+254R To Be Published.
Page generated: Wed Dec 16 11:16:50 2020

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