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Zinc in PDB 5wcp: Phosphotriesterase Variant S7

Protein crystallography data

The structure of Phosphotriesterase Variant S7, PDB code: 5wcp 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) 29.48 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.598, 85.954, 88.443, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.5

Other elements in 5wcp:

The structure of Phosphotriesterase Variant S7 also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase Variant S7 (pdb code 5wcp). 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 S7, PDB code: 5wcp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5wcp

Go back to Zinc Binding Sites List in 5wcp
Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:16.1
occ:0.90
O2 A:CAC2403 1.9 14.6 0.8
NE2 A:HIS55 2.0 14.9 1.0
NE2 A:HIS57 2.0 15.8 1.0
OQ2 A:KCX169 2.1 17.4 1.0
OD1 A:ASP301 2.4 17.3 1.0
CE1 A:HIS57 3.0 14.9 1.0
CD2 A:HIS55 3.0 14.3 1.0
CE1 A:HIS55 3.1 16.5 1.0
CX A:KCX169 3.1 17.0 1.0
CD2 A:HIS57 3.1 15.7 1.0
AS A:CAC2403 3.3 18.1 0.8
CG A:ASP301 3.4 14.6 1.0
OQ1 A:KCX169 3.5 17.6 1.0
C1 A:CAC2403 3.6 18.0 0.8
OD2 A:ASP301 3.6 19.0 1.0
CG2 A:VAL101 4.0 15.8 1.0
ZN A:ZN2402 4.0 16.6 0.8
NZ A:KCX169 4.0 17.2 1.0
O1 A:CAC2403 4.1 14.7 0.8
CE1 A:HIS230 4.1 19.2 1.0
ND1 A:HIS57 4.1 15.6 1.0
CG A:HIS55 4.2 14.7 1.0
ND1 A:HIS55 4.2 17.2 1.0
CG A:HIS57 4.2 14.5 1.0
NE2 A:HIS230 4.4 21.2 1.0
CB A:ASP301 4.7 16.7 1.0
C2 A:CAC2403 4.8 18.3 0.8

Zinc binding site 2 out of 4 in 5wcp

Go back to Zinc Binding Sites List in 5wcp
Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:16.6
occ:0.81
OQ1 A:KCX169 2.0 17.6 1.0
O1 A:CAC2403 2.0 14.7 0.8
NE2 A:HIS230 2.0 21.2 1.0
ND1 A:HIS201 2.0 18.3 1.0
CE1 A:HIS201 2.9 21.2 1.0
CD2 A:HIS230 3.0 19.9 1.0
CX A:KCX169 3.0 17.0 1.0
CE1 A:HIS230 3.1 19.2 1.0
AS A:CAC2403 3.1 18.1 0.8
CG A:HIS201 3.1 17.3 1.0
O2 A:CAC2403 3.1 14.6 0.8
OQ2 A:KCX169 3.4 17.4 1.0
CB A:HIS201 3.5 17.9 1.0
NE1 A:TRP131 3.8 18.8 1.0
ZN A:ZN2401 4.0 16.1 0.9
NE2 A:HIS201 4.1 23.3 1.0
CG A:HIS230 4.1 22.2 1.0
NZ A:KCX169 4.2 17.2 1.0
ND1 A:HIS230 4.2 21.6 1.0
CD2 A:HIS201 4.2 19.0 1.0
C2 A:CAC2403 4.3 18.3 0.8
CE1 A:HIS55 4.3 16.5 1.0
CA A:HIS201 4.4 18.3 1.0
CD1 A:TRP131 4.4 18.0 1.0
C1 A:CAC2403 4.5 18.0 0.8
NE2 A:HIS55 4.5 14.9 1.0
CE A:KCX169 4.6 19.3 1.0
OD2 A:ASP301 5.0 19.0 1.0

Zinc binding site 3 out of 4 in 5wcp

Go back to Zinc Binding Sites List in 5wcp
Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2401

b:19.1
occ:0.87
O2 G:CAC2403 1.9 17.8 0.8
NE2 G:HIS57 2.0 20.8 1.0
NE2 G:HIS55 2.1 23.4 1.0
OQ1 G:KCX169 2.2 23.2 1.0
OD1 G:ASP301 2.5 23.7 1.0
CE1 G:HIS57 2.9 21.2 1.0
CE1 G:HIS55 3.0 22.2 1.0
CD2 G:HIS55 3.1 24.1 1.0
CD2 G:HIS57 3.1 20.3 1.0
CX G:KCX169 3.1 21.9 1.0
AS G:CAC2403 3.2 21.9 0.8
CG G:ASP301 3.4 23.3 1.0
OQ2 G:KCX169 3.5 23.2 1.0
C1 G:CAC2403 3.6 18.9 0.8
OD2 G:ASP301 3.7 24.6 1.0
ZN G:ZN2402 4.0 19.8 0.8
O1 G:CAC2403 4.0 19.8 0.8
CG2 G:VAL101 4.0 22.2 1.0
CE1 G:HIS230 4.0 23.7 1.0
NZ G:KCX169 4.1 22.5 1.0
ND1 G:HIS57 4.1 22.1 1.0
ND1 G:HIS55 4.2 22.4 1.0
CG G:HIS57 4.2 21.1 1.0
CG G:HIS55 4.2 22.3 1.0
NE2 G:HIS230 4.4 23.9 1.0
C2 G:CAC2403 4.7 23.5 0.8
CB G:ASP301 4.8 22.2 1.0

Zinc binding site 4 out of 4 in 5wcp

Go back to Zinc Binding Sites List in 5wcp
Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2402

b:19.8
occ:0.81
OQ2 G:KCX169 1.9 23.2 1.0
O1 G:CAC2403 1.9 19.8 0.8
NE2 G:HIS230 2.0 23.9 1.0
ND1 G:HIS201 2.1 24.5 1.0
CD2 G:HIS230 2.9 24.5 1.0
CX G:KCX169 3.0 21.9 1.0
CE1 G:HIS201 3.0 26.0 1.0
CE1 G:HIS230 3.0 23.7 1.0
O2 G:CAC2403 3.0 17.8 0.8
AS G:CAC2403 3.1 21.9 0.8
CG G:HIS201 3.1 23.9 1.0
OQ1 G:KCX169 3.3 23.2 1.0
CB G:HIS201 3.5 22.5 1.0
NE1 G:TRP131 3.8 22.3 1.0
ZN G:ZN2401 4.0 19.1 0.9
CG G:HIS230 4.1 24.7 1.0
ND1 G:HIS230 4.1 25.1 1.0
NE2 G:HIS201 4.1 28.1 1.0
NZ G:KCX169 4.2 22.5 1.0
CD2 G:HIS201 4.2 25.1 1.0
CE1 G:HIS55 4.3 22.2 1.0
CA G:HIS201 4.3 22.2 1.0
C2 G:CAC2403 4.3 23.5 0.8
CD1 G:TRP131 4.4 22.7 1.0
C1 G:CAC2403 4.5 18.9 0.8
NE2 G:HIS55 4.6 23.4 1.0
CE G:KCX169 4.6 23.8 1.0

Reference:

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S7 To Be Published.
Page generated: Wed Dec 16 11:15:58 2020

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