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Zinc in PDB 6bhl: Phosphotriesterase Variant S5DELTAL7

Protein crystallography data

The structure of Phosphotriesterase Variant S5DELTAL7, PDB code: 6bhl 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) 30.75 / 1.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.146, 85.485, 88.535, 90.00, 90.00, 90.00
R / Rfree (%) 13.4 / 16.1

Other elements in 6bhl:

The structure of Phosphotriesterase Variant S5DELTAL7 also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Phosphotriesterase Variant S5DELTAL7 (pdb code 6bhl). 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 S5DELTAL7, PDB code: 6bhl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6bhl

Go back to Zinc Binding Sites List in 6bhl
Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:9.9
occ:1.00
O2 A:CAC2407 1.9 10.6 0.6
NE2 A:HIS57 2.0 9.6 0.0
NE2 A:HIS57 2.0 7.7 1.0
NE2 A:HIS55 2.1 9.0 1.0
OQ2 A:KCX169 2.1 11.2 1.0
OD1 A:ASP292 2.3 10.5 1.0
CE1 A:HIS57 3.0 8.2 1.0
CE1 A:HIS57 3.0 9.5 0.0
CD2 A:HIS55 3.0 8.4 1.0
CD2 A:HIS57 3.0 9.5 0.0
CX A:KCX169 3.1 12.4 1.0
CD2 A:HIS57 3.1 8.2 1.0
CE1 A:HIS55 3.1 9.9 1.0
HE1 A:HIS57 3.1 9.8 1.0
HE1 A:HIS57 3.2 11.4 0.0
HD2 A:HIS55 3.2 10.1 1.0
CG A:ASP292 3.2 11.7 1.0
AS A:CAC2407 3.2 13.3 0.6
HD2 A:HIS57 3.2 11.4 0.0
HE1 A:HIS55 3.3 11.9 1.0
HD2 A:HIS57 3.3 9.8 1.0
HE1 A:HIS230 3.4 17.0 1.0
OQ1 A:KCX169 3.5 12.3 1.0
OD2 A:ASP292 3.5 12.4 1.0
HG23 A:VAL101 3.5 10.6 1.0
O A:HOH2501 3.5 8.0 1.0
C1 A:CAC2407 3.5 12.7 0.6
HG23 A:VAL101 3.5 11.4 0.0
HG21 A:VAL101 3.7 11.4 0.0
ZN A:ZN2402 3.7 12.6 0.9
HG21 A:VAL101 3.8 10.6 1.0
CG2 A:VAL101 4.0 9.5 0.0
CG2 A:VAL101 4.0 8.8 1.0
O1 A:CAC2407 4.1 12.0 0.6
CE1 A:HIS230 4.1 14.2 1.0
NZ A:KCX169 4.1 12.0 1.0
ND1 A:HIS57 4.1 8.8 1.0
ND1 A:HIS57 4.1 9.4 0.0
CG A:HIS57 4.2 9.4 0.0
HG22 A:VAL101 4.2 10.6 1.0
HG22 A:VAL101 4.2 11.4 0.0
ND1 A:HIS55 4.2 9.1 1.0
CG A:HIS55 4.2 8.5 1.0
CG A:HIS57 4.2 8.4 1.0
HZ A:KCX169 4.2 14.4 1.0
NE2 A:HIS230 4.3 13.6 1.0
CB A:ASP292 4.5 10.9 1.0
HA A:ASP292 4.5 12.3 1.0
HB2 A:ASP292 4.6 13.1 1.0
HD1 A:HIS57 4.9 10.6 1.0
HD1 A:HIS57 4.9 11.3 0.0
C2 A:CAC2407 4.9 14.5 0.6
HD1 A:HIS55 5.0 10.9 1.0
HD11 A:LEU106 5.0 12.9 0.0

Zinc binding site 2 out of 4 in 6bhl

Go back to Zinc Binding Sites List in 6bhl
Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:12.6
occ:0.86
OQ1 A:KCX169 1.9 12.3 1.0
O1 A:CAC2407 1.9 12.0 0.6
NE2 A:HIS230 2.0 13.6 1.0
ND1 A:HIS201 2.1 13.7 1.0
O2 A:CAC2407 2.8 10.6 0.6
CE1 A:HIS201 2.9 16.7 1.0
CX A:KCX169 3.0 12.4 1.0
AS A:CAC2407 3.0 13.3 0.6
HB2 A:HIS201 3.0 15.5 1.0
CD2 A:HIS230 3.0 13.2 1.0
CE1 A:HIS230 3.0 14.2 1.0
HE1 A:HIS201 3.1 20.0 1.0
HE1 A:TRP131 3.1 15.8 1.0
CG A:HIS201 3.1 14.2 1.0
HD2 A:HIS230 3.2 15.9 1.0
HE1 A:HIS230 3.3 17.0 1.0
OQ2 A:KCX169 3.3 11.2 1.0
HE1 A:HIS55 3.5 11.9 1.0
CB A:HIS201 3.5 12.9 1.0
O A:HOH2501 3.6 8.0 1.0
ZN A:ZN2401 3.7 9.9 1.0
NE1 A:TRP131 3.9 13.2 1.0
HA A:HIS201 4.0 14.8 1.0
NE2 A:HIS201 4.1 17.5 1.0
NZ A:KCX169 4.1 12.0 1.0
CE1 A:HIS55 4.1 9.9 1.0
ND1 A:HIS230 4.1 13.9 1.0
HD1 A:TRP131 4.1 14.5 1.0
CG A:HIS230 4.2 13.1 1.0
CD2 A:HIS201 4.2 16.3 1.0
HE2 A:KCX169 4.2 15.2 1.0
NE2 A:HIS55 4.3 9.0 1.0
HB3 A:HIS201 4.3 15.5 1.0
C1 A:CAC2407 4.3 12.7 0.6
CA A:HIS201 4.3 12.3 1.0
CD1 A:TRP131 4.4 12.1 1.0
C2 A:CAC2407 4.4 14.5 0.6
CE A:KCX169 4.6 12.7 1.0
HE3 A:KCX169 4.6 15.2 1.0
HM2 A:MPD2404 4.6 48.5 1.0
OD2 A:ASP292 4.7 12.4 1.0
H12 A:MPD2404 4.8 50.2 1.0
HE2 A:HIS201 4.9 20.9 1.0
HD1 A:HIS230 4.9 16.7 1.0
HZ A:KCX169 4.9 14.4 1.0
O2 A:MPD2404 5.0 37.1 1.0

Zinc binding site 3 out of 4 in 6bhl

Go back to Zinc Binding Sites List in 6bhl
Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2401

b:10.6
occ:1.00
O2 G:CAC2407 1.9 10.6 0.7
NE2 G:HIS57 2.0 9.3 1.0
NE2 G:HIS55 2.0 9.8 0.7
NE2 G:HIS55 2.1 9.5 0.3
OQ1 G:KCX169 2.1 11.6 1.0
OD1 G:ASP292 2.3 11.3 1.0
CE1 G:HIS57 2.9 9.0 1.0
CD2 G:HIS55 3.0 9.5 0.7
CD2 G:HIS55 3.0 9.5 0.3
CE1 G:HIS55 3.0 10.6 0.7
CX G:KCX169 3.1 11.7 1.0
HE1 G:HIS57 3.1 10.8 1.0
CD2 G:HIS57 3.1 8.8 1.0
CE1 G:HIS55 3.1 10.0 0.3
HD2 G:HIS55 3.1 11.4 0.7
HD2 G:HIS55 3.1 11.4 0.3
CG G:ASP292 3.2 10.8 1.0
AS G:CAC2407 3.2 12.8 0.7
HE1 G:HIS55 3.3 12.8 0.7
HE1 G:HIS55 3.3 12.0 0.3
HE1 G:HIS230 3.3 15.2 1.0
HD2 G:HIS57 3.3 10.5 1.0
OD2 G:ASP292 3.5 10.6 1.0
HG23 G:VAL101 3.5 11.2 0.7
OQ2 G:KCX169 3.5 11.3 1.0
O G:HOH2501 3.6 14.6 1.0
HG23 G:VAL101 3.6 14.8 0.3
C1 G:CAC2407 3.6 13.8 0.7
HG21 G:VAL101 3.7 14.8 0.3
ZN G:ZN2402 3.8 12.7 0.9
HG21 G:VAL101 3.9 11.2 0.7
CG2 G:VAL101 4.0 12.3 0.3
CG2 G:VAL101 4.0 9.3 0.7
CE1 G:HIS230 4.1 12.6 1.0
O1 G:CAC2407 4.1 11.6 0.7
HG22 G:VAL101 4.1 14.8 0.3
ND1 G:HIS57 4.1 8.5 1.0
NZ G:KCX169 4.1 10.5 1.0
ND1 G:HIS55 4.1 10.8 0.7
CG G:HIS55 4.1 9.9 0.7
HG22 G:VAL101 4.1 11.2 0.7
CG G:HIS55 4.2 9.8 0.3
ND1 G:HIS55 4.2 10.3 0.3
CG G:HIS57 4.2 8.6 1.0
HZ G:KCX169 4.2 12.6 1.0
NE2 G:HIS230 4.3 13.1 1.0
CB G:ASP292 4.5 9.9 1.0
HA G:ASP292 4.6 11.5 1.0
HB2 G:ASP292 4.7 11.9 1.0
C2 G:CAC2407 4.8 13.0 0.7
HD1 G:HIS57 4.9 10.2 1.0
HD1 G:HIS55 4.9 12.9 0.7
HD1 G:HIS55 5.0 12.3 0.3

Zinc binding site 4 out of 4 in 6bhl

Go back to Zinc Binding Sites List in 6bhl
Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn2402

b:12.7
occ:0.87
O1 G:CAC2407 2.0 11.6 0.7
OQ2 G:KCX169 2.0 11.3 1.0
NE2 G:HIS230 2.0 13.1 1.0
ND1 G:HIS201 2.1 13.5 1.0
O2 G:CAC2407 2.8 10.6 0.7
CE1 G:HIS201 2.9 15.6 1.0
CD2 G:HIS230 3.0 14.3 1.0
HB2 G:HIS201 3.0 15.5 1.0
CX G:KCX169 3.0 11.7 1.0
AS G:CAC2407 3.0 12.8 0.7
HE1 G:HIS201 3.1 18.8 1.0
HE1 G:TRP131 3.1 15.8 1.0
CE1 G:HIS230 3.1 12.6 1.0
HE1 G:TRP131 3.1 16.2 0.0
HD2 G:HIS230 3.1 17.2 1.0
CG G:HIS201 3.1 13.3 1.0
HE1 G:HIS230 3.3 15.2 1.0
OQ1 G:KCX169 3.3 11.6 1.0
CB G:HIS201 3.5 12.9 1.0
HE1 G:HIS55 3.6 12.8 0.7
HE1 G:HIS55 3.6 12.0 0.3
O G:HOH2501 3.7 14.6 1.0
ZN G:ZN2401 3.8 10.6 1.0
NE1 G:TRP131 3.9 13.2 1.0
HA G:HIS201 3.9 14.0 1.0
NE1 G:TRP131 3.9 13.5 0.0
NE2 G:HIS201 4.1 17.6 1.0
CG G:HIS230 4.1 13.8 1.0
ND1 G:HIS230 4.2 14.1 1.0
NZ G:KCX169 4.2 10.5 1.0
CE1 G:HIS55 4.2 10.6 0.7
CD2 G:HIS201 4.2 14.9 1.0
CE1 G:HIS55 4.2 10.0 0.3
HE2 G:KCX169 4.2 12.4 1.0
HD1 G:TRP131 4.2 14.7 1.0
CA G:HIS201 4.3 11.6 1.0
HB3 G:HIS201 4.3 15.5 1.0
NE2 G:HIS55 4.3 9.8 0.7
NE2 G:HIS55 4.4 9.5 0.3
C2 G:CAC2407 4.4 13.0 0.7
C1 G:CAC2407 4.4 13.8 0.7
CD1 G:TRP131 4.5 12.2 1.0
HD1 G:TRP131 4.5 15.9 0.0
CE G:KCX169 4.6 10.3 1.0
CD1 G:TRP131 4.6 13.2 0.0
HE3 G:KCX169 4.7 12.4 1.0
OD2 G:ASP292 4.8 10.6 1.0
HE2 G:HIS201 4.9 21.1 1.0
HZ2 G:TRP131 4.9 16.6 0.0
HD1 G:HIS230 5.0 16.9 1.0
HZ G:KCX169 5.0 12.6 1.0
CE2 G:TRP131 5.0 13.6 0.0

Reference:

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S5DELTAL7 To Be Published.
Page generated: Wed Dec 16 11:31:59 2020

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