Zinc in PDB 5wcr: Phosphotriesterase Variant R0DELTAL7

Protein crystallography data

The structure of Phosphotriesterase Variant R0DELTAL7, PDB code: 5wcr 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) 39.46 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 86.051, 86.167, 88.779, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.1

Other elements in 5wcr:

The structure of Phosphotriesterase Variant R0DELTAL7 also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase Variant R0DELTAL7 (pdb code 5wcr). 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 R0DELTAL7, PDB code: 5wcr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5wcr

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Zinc binding site 1 out of 4 in the Phosphotriesterase Variant R0DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant R0DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:25.7
occ:0.92
O2 A:CAC2403 2.0 27.2 0.6
NE2 A:HIS55 2.1 28.0 1.0
OQ2 A:KCX169 2.1 29.9 1.0
NE2 A:HIS57 2.1 29.0 1.0
OD1 A:ASP292 2.2 27.2 1.0
CD2 A:HIS55 3.0 24.7 1.0
CX A:KCX169 3.0 27.7 1.0
CE1 A:HIS57 3.0 24.5 1.0
CG A:ASP292 3.0 30.6 1.0
CD2 A:HIS57 3.1 24.8 1.0
CE1 A:HIS55 3.1 28.7 1.0
AS A:CAC2403 3.3 37.9 0.6
OD2 A:ASP292 3.4 31.2 1.0
OQ1 A:KCX169 3.5 32.6 1.0
C1 A:CAC2403 3.7 33.5 0.6
ZN A:ZN2402 3.7 32.9 0.9
NZ A:KCX169 4.0 25.3 1.0
CG2 A:VAL101 4.1 22.3 1.0
CG A:HIS55 4.1 24.9 1.0
ND1 A:HIS57 4.2 24.4 1.0
ND1 A:HIS55 4.2 25.2 1.0
CG A:HIS57 4.2 25.8 1.0
CE1 A:HIS230 4.2 35.5 1.0
O1 A:CAC2403 4.3 36.4 0.6
CB A:ASP292 4.4 27.3 1.0
NE2 A:HIS230 4.4 35.8 1.0
C2 A:CAC2403 4.7 40.1 0.6
CA A:ASP292 4.9 27.1 1.0

Zinc binding site 2 out of 4 in 5wcr

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Zinc binding site 2 out of 4 in the Phosphotriesterase Variant R0DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant R0DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:32.9
occ:0.92
ND1 A:HIS201 1.9 31.9 1.0
OQ1 A:KCX169 1.9 32.6 1.0
NE2 A:HIS230 2.1 35.8 1.0
O1 A:CAC2403 2.4 36.4 0.6
O2 A:CAC2403 2.5 27.2 0.6
CE1 A:HIS201 2.8 34.4 1.0
CX A:KCX169 2.9 27.7 1.0
CG A:HIS201 3.0 30.4 1.0
CD2 A:HIS230 3.0 34.1 1.0
AS A:CAC2403 3.1 37.9 0.6
CE1 A:HIS230 3.1 35.5 1.0
OQ2 A:KCX169 3.2 29.9 1.0
CB A:HIS201 3.5 28.0 1.0
ZN A:ZN2401 3.7 25.7 0.9
NE1 A:TRP131 3.9 31.1 1.0
NE2 A:HIS201 3.9 34.6 1.0
CD2 A:HIS201 4.1 32.3 1.0
CE1 A:HIS55 4.1 28.7 1.0
NZ A:KCX169 4.1 25.3 1.0
NE2 A:HIS55 4.2 28.0 1.0
ND1 A:HIS230 4.2 33.4 1.0
CG A:HIS230 4.2 33.4 1.0
CA A:HIS201 4.3 25.2 1.0
C1 A:CAC2403 4.4 33.5 0.6
OD2 A:ASP292 4.5 31.2 1.0
C2 A:CAC2403 4.6 40.1 0.6
CD1 A:TRP131 4.6 29.2 1.0
CE A:KCX169 4.6 25.5 1.0
CE2 A:TRP131 5.0 33.3 1.0

Zinc binding site 3 out of 4 in 5wcr

Go back to Zinc Binding Sites List in 5wcr
Zinc binding site 3 out of 4 in the Phosphotriesterase Variant R0DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant R0DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2401

b:29.6
occ:0.90
O2 G:CAC2403 1.9 33.0 0.7
NE2 G:HIS57 2.0 37.1 1.0
NE2 G:HIS55 2.1 42.1 1.0
OQ1 G:KCX169 2.1 41.5 1.0
OD1 G:ASP292 2.3 42.9 1.0
CD2 G:HIS55 3.0 40.4 1.0
CE1 G:HIS57 3.0 34.8 1.0
CD2 G:HIS57 3.0 37.2 1.0
CX G:KCX169 3.1 41.3 1.0
CE1 G:HIS55 3.1 41.9 1.0
CG G:ASP292 3.2 41.6 1.0
AS G:CAC2403 3.3 40.4 0.7
OD2 G:ASP292 3.5 42.0 1.0
OQ2 G:KCX169 3.5 43.5 1.0
C1 G:CAC2403 3.7 38.5 0.7
ZN G:ZN2402 3.8 38.2 1.0
CG2 G:VAL101 4.1 32.3 1.0
ND1 G:HIS57 4.1 33.4 1.0
NZ G:KCX169 4.1 38.3 1.0
CG G:HIS57 4.2 32.8 1.0
CG G:HIS55 4.2 39.9 1.0
CE1 G:HIS230 4.2 46.8 1.0
ND1 G:HIS55 4.2 40.6 1.0
O1 G:CAC2403 4.2 39.8 0.7
NE2 G:HIS230 4.4 48.1 1.0
CB G:ASP292 4.5 36.0 1.0
C2 G:CAC2403 4.7 36.0 0.7
CA G:ASP292 5.0 35.6 1.0

Zinc binding site 4 out of 4 in 5wcr

Go back to Zinc Binding Sites List in 5wcr
Zinc binding site 4 out of 4 in the Phosphotriesterase Variant R0DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant R0DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2402

b:38.2
occ:0.97
OQ2 G:KCX169 2.0 43.5 1.0
ND1 G:HIS201 2.1 45.7 1.0
NE2 G:HIS230 2.1 48.1 1.0
O1 G:CAC2403 2.2 39.8 0.7
O2 G:CAC2403 2.8 33.0 0.7
CX G:KCX169 3.0 41.3 1.0
CE1 G:HIS201 3.0 44.6 1.0
CD2 G:HIS230 3.0 45.1 1.0
AS G:CAC2403 3.1 40.4 0.7
CE1 G:HIS230 3.1 46.8 1.0
CG G:HIS201 3.1 41.5 1.0
OQ1 G:KCX169 3.3 41.5 1.0
CB G:HIS201 3.5 35.1 1.0
ZN G:ZN2401 3.8 29.6 0.9
NE1 G:TRP131 3.9 36.4 1.0
NE2 G:HIS201 4.1 44.8 1.0
CE1 G:HIS55 4.2 41.9 1.0
NZ G:KCX169 4.2 38.3 1.0
CG G:HIS230 4.2 44.5 1.0
ND1 G:HIS230 4.2 45.3 1.0
CD2 G:HIS201 4.2 44.0 1.0
NE2 G:HIS55 4.3 42.1 1.0
CA G:HIS201 4.3 35.5 1.0
C1 G:CAC2403 4.5 38.5 0.7
C2 G:CAC2403 4.5 36.0 0.7
CD1 G:TRP131 4.5 33.3 1.0
CE G:KCX169 4.6 38.0 1.0
OD2 G:ASP292 4.7 42.0 1.0
CE2 G:TRP131 5.0 38.9 1.0

Reference:

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant R0DELTAL7 To Be Published.
Page generated: Wed Dec 16 11:16:00 2020

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