Zinc in PDB 6fs3: Phosphotriesterase PTE_A53_1
Enzymatic activity of Phosphotriesterase PTE_A53_1
All present enzymatic activity of Phosphotriesterase PTE_A53_1:
3.1.8.1;
Protein crystallography data
The structure of Phosphotriesterase PTE_A53_1, PDB code: 6fs3
was solved by
O.Dym,
N.Aggarwal,
S.Albeck,
T.Unger,
S.Hamer Rogotner,
I.Silman,
H.Leader,
Y.Ashani,
M.Goldsmith,
P.Greisen,
D.Tawfik,
L.J.Sussman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.48 /
1.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.469,
81.460,
70.710,
90.00,
95.12,
90.00
|
R / Rfree (%)
|
16.7 /
20.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_1
(pdb code 6fs3). 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 PTE_A53_1, PDB code: 6fs3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6fs3
Go back to
Zinc Binding Sites List in 6fs3
Zinc binding site 1 out
of 4 in the Phosphotriesterase PTE_A53_1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:12.7
occ:1.00
|
O9
|
A:9ON404
|
2.0
|
14.3
|
1.0
|
NE2
|
A:HIS57
|
2.0
|
11.7
|
1.0
|
NE2
|
A:HIS55
|
2.1
|
16.3
|
1.0
|
O1
|
A:FMT401
|
2.1
|
12.4
|
1.0
|
OD1
|
A:ASP301
|
2.2
|
12.0
|
1.0
|
C1
|
A:9ON404
|
2.9
|
16.1
|
1.0
|
CD2
|
A:HIS55
|
2.9
|
11.7
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
12.7
|
1.0
|
CD2
|
A:HIS57
|
3.0
|
10.1
|
1.0
|
CG
|
A:ASP301
|
3.1
|
15.1
|
1.0
|
CE1
|
A:HIS55
|
3.2
|
14.0
|
1.0
|
C
|
A:FMT401
|
3.2
|
13.5
|
1.0
|
OD2
|
A:ASP301
|
3.4
|
14.9
|
1.0
|
C2
|
A:9ON404
|
3.4
|
18.4
|
1.0
|
C3
|
A:9ON404
|
3.5
|
22.9
|
1.0
|
O2
|
A:FMT401
|
3.7
|
13.0
|
1.0
|
ZN
|
A:ZN403
|
3.9
|
13.0
|
1.0
|
O8
|
A:9ON404
|
3.9
|
12.7
|
1.0
|
CG2
|
A:VAL101
|
4.0
|
12.6
|
1.0
|
C4
|
A:9ON404
|
4.1
|
28.8
|
1.0
|
CG
|
A:HIS55
|
4.1
|
15.5
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
11.6
|
1.0
|
CE1
|
A:HIS230
|
4.1
|
12.8
|
1.0
|
CG
|
A:HIS57
|
4.2
|
12.6
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
11.6
|
1.0
|
CB
|
A:ASP301
|
4.3
|
15.8
|
1.0
|
NE2
|
A:HIS230
|
4.5
|
10.2
|
1.0
|
O12
|
A:9ON404
|
4.5
|
25.1
|
1.0
|
NZ
|
A:LYS169
|
4.5
|
18.9
|
1.0
|
C7
|
A:9ON404
|
4.7
|
28.3
|
1.0
|
CA
|
A:ASP301
|
4.8
|
15.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6fs3
Go back to
Zinc Binding Sites List in 6fs3
Zinc binding site 2 out
of 4 in the Phosphotriesterase PTE_A53_1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:13.0
occ:1.00
|
O2
|
A:FMT401
|
2.0
|
13.0
|
1.0
|
O8
|
A:9ON404
|
2.0
|
12.7
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
10.2
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
16.1
|
1.0
|
O9
|
A:9ON404
|
2.5
|
14.3
|
1.0
|
C1
|
A:9ON404
|
2.6
|
16.1
|
1.0
|
CE1
|
A:HIS201
|
3.0
|
17.9
|
1.0
|
CD2
|
A:HIS230
|
3.0
|
13.1
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
12.8
|
1.0
|
C
|
A:FMT401
|
3.0
|
13.5
|
1.0
|
CG
|
A:HIS201
|
3.1
|
14.2
|
1.0
|
O1
|
A:FMT401
|
3.3
|
12.4
|
1.0
|
CB
|
A:HIS201
|
3.5
|
13.4
|
1.0
|
ZN
|
A:ZN402
|
3.9
|
12.7
|
1.0
|
NE1
|
A:TRP131
|
4.0
|
16.5
|
1.0
|
C2
|
A:9ON404
|
4.0
|
18.4
|
1.0
|
NE2
|
A:HIS201
|
4.1
|
22.5
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
13.3
|
1.0
|
CG
|
A:HIS230
|
4.1
|
11.8
|
1.0
|
CD2
|
A:HIS201
|
4.2
|
15.3
|
1.0
|
CE1
|
A:HIS55
|
4.2
|
14.0
|
1.0
|
NE2
|
A:HIS55
|
4.3
|
16.3
|
1.0
|
CA
|
A:HIS201
|
4.3
|
12.4
|
1.0
|
O12
|
A:9ON404
|
4.4
|
25.1
|
1.0
|
CD1
|
A:TRP131
|
4.5
|
16.8
|
1.0
|
O
|
A:HOH658
|
4.6
|
28.2
|
1.0
|
NZ
|
A:LYS169
|
4.7
|
18.9
|
1.0
|
CE
|
A:LYS169
|
4.8
|
13.7
|
1.0
|
OD2
|
A:ASP301
|
4.9
|
14.9
|
1.0
|
C7
|
A:9ON404
|
5.0
|
28.3
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6fs3
Go back to
Zinc Binding Sites List in 6fs3
Zinc binding site 3 out
of 4 in the Phosphotriesterase PTE_A53_1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:15.8
occ:1.00
|
O8
|
B:9ON404
|
1.9
|
17.6
|
1.0
|
NE2
|
B:HIS57
|
2.0
|
18.0
|
1.0
|
O1
|
B:FMT401
|
2.1
|
18.1
|
1.0
|
NE2
|
B:HIS55
|
2.2
|
19.6
|
1.0
|
OD1
|
B:ASP301
|
2.2
|
15.1
|
1.0
|
C1
|
B:9ON404
|
2.8
|
21.7
|
1.0
|
CE1
|
B:HIS57
|
2.9
|
14.3
|
1.0
|
CD2
|
B:HIS55
|
3.0
|
19.9
|
1.0
|
CD2
|
B:HIS57
|
3.0
|
18.9
|
1.0
|
CG
|
B:ASP301
|
3.1
|
19.3
|
1.0
|
CE1
|
B:HIS55
|
3.3
|
17.8
|
1.0
|
C
|
B:FMT401
|
3.3
|
17.5
|
1.0
|
C2
|
B:9ON404
|
3.4
|
24.2
|
1.0
|
OD2
|
B:ASP301
|
3.4
|
18.2
|
1.0
|
C3
|
B:9ON404
|
3.5
|
28.8
|
1.0
|
O2
|
B:FMT401
|
3.7
|
16.6
|
1.0
|
ZN
|
B:ZN403
|
3.9
|
18.0
|
1.0
|
O9
|
B:9ON404
|
3.9
|
22.0
|
1.0
|
CE1
|
B:HIS230
|
4.0
|
24.2
|
1.0
|
CG2
|
B:VAL101
|
4.0
|
13.9
|
1.0
|
ND1
|
B:HIS57
|
4.0
|
13.8
|
1.0
|
CG
|
B:HIS57
|
4.1
|
16.6
|
1.0
|
C4
|
B:9ON404
|
4.1
|
33.1
|
1.0
|
CG
|
B:HIS55
|
4.2
|
13.8
|
1.0
|
ND1
|
B:HIS55
|
4.3
|
16.4
|
1.0
|
NE2
|
B:HIS230
|
4.3
|
18.5
|
1.0
|
CB
|
B:ASP301
|
4.4
|
14.0
|
1.0
|
O10
|
B:9ON404
|
4.4
|
39.4
|
1.0
|
C7
|
B:9ON404
|
4.6
|
36.7
|
1.0
|
NZ
|
B:LYS169
|
4.7
|
20.3
|
1.0
|
CA
|
B:ASP301
|
4.8
|
12.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6fs3
Go back to
Zinc Binding Sites List in 6fs3
Zinc binding site 4 out
of 4 in the Phosphotriesterase PTE_A53_1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase PTE_A53_1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:18.0
occ:1.00
|
O2
|
B:FMT401
|
2.0
|
16.6
|
1.0
|
O9
|
B:9ON404
|
2.0
|
22.0
|
1.0
|
NE2
|
B:HIS230
|
2.0
|
18.5
|
1.0
|
ND1
|
B:HIS201
|
2.1
|
20.0
|
1.0
|
O8
|
B:9ON404
|
2.5
|
17.6
|
1.0
|
C1
|
B:9ON404
|
2.6
|
21.7
|
1.0
|
CD2
|
B:HIS230
|
2.9
|
18.6
|
1.0
|
C
|
B:FMT401
|
3.0
|
17.5
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
20.8
|
1.0
|
CE1
|
B:HIS230
|
3.1
|
24.2
|
1.0
|
CG
|
B:HIS201
|
3.1
|
17.0
|
1.0
|
O1
|
B:FMT401
|
3.3
|
18.1
|
1.0
|
CB
|
B:HIS201
|
3.5
|
14.3
|
1.0
|
ZN
|
B:ZN402
|
3.9
|
15.8
|
1.0
|
NE1
|
B:TRP131
|
3.9
|
18.0
|
1.0
|
C2
|
B:9ON404
|
4.0
|
24.2
|
1.0
|
CG
|
B:HIS230
|
4.1
|
18.2
|
1.0
|
ND1
|
B:HIS230
|
4.1
|
18.6
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
24.0
|
1.0
|
CD2
|
B:HIS201
|
4.2
|
22.5
|
1.0
|
CE1
|
B:HIS55
|
4.2
|
17.8
|
1.0
|
NE2
|
B:HIS55
|
4.3
|
19.6
|
1.0
|
CA
|
B:HIS201
|
4.3
|
18.8
|
1.0
|
O10
|
B:9ON404
|
4.3
|
39.4
|
1.0
|
NZ
|
B:LYS169
|
4.5
|
20.3
|
1.0
|
CD1
|
B:TRP131
|
4.5
|
16.6
|
1.0
|
CE
|
B:LYS169
|
4.8
|
19.1
|
1.0
|
OD2
|
B:ASP301
|
4.9
|
18.2
|
1.0
|
C7
|
B:9ON404
|
5.0
|
36.7
|
1.0
|
|
Reference:
O.Dym,
N.Aggarwal,
J.L.Sussman,
I.Silman.
Crystal Structures of Bacterail Phosphotriesterase Variant with High Catalytic Activity Towards Organophosphate Nerve Agents Developed By Use of Structure-Based Design and Molecular Evolution To Be Published.
Page generated: Mon Oct 28 21:23:43 2024
|