Zinc in PDB 6fu0: Phosphotriesterase PTE_A53_4
Enzymatic activity of Phosphotriesterase PTE_A53_4
All present enzymatic activity of Phosphotriesterase PTE_A53_4:
3.1.8.1;
Protein crystallography data
The structure of Phosphotriesterase PTE_A53_4, PDB code: 6fu0
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)
|
77.87 /
3.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
88.890,
119.900,
161.490,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
24.9
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_4
(pdb code 6fu0). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Phosphotriesterase PTE_A53_4, PDB code: 6fu0:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 1 out
of 8 in the Phosphotriesterase PTE_A53_4
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_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:49.6
occ:1.00
|
O1
|
A:FMT401
|
2.0
|
46.1
|
1.0
|
O
|
A:HOH501
|
2.0
|
58.7
|
1.0
|
OD1
|
A:ASP301
|
2.0
|
58.8
|
1.0
|
NE2
|
A:HIS57
|
2.1
|
52.3
|
1.0
|
NE2
|
A:HIS55
|
2.2
|
43.1
|
1.0
|
C
|
A:FMT401
|
2.9
|
49.6
|
1.0
|
CG
|
A:ASP301
|
3.0
|
62.9
|
1.0
|
O2
|
A:FMT401
|
3.1
|
49.5
|
1.0
|
CE1
|
A:HIS57
|
3.1
|
51.8
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
49.2
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
44.7
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
40.8
|
1.0
|
OD2
|
A:ASP301
|
3.4
|
60.4
|
1.0
|
ZN
|
A:ZN403
|
3.6
|
51.8
|
1.0
|
CE1
|
A:HIS230
|
3.9
|
53.7
|
1.0
|
NZ
|
A:LYS169
|
4.0
|
43.5
|
1.0
|
NE2
|
A:HIS230
|
4.2
|
55.6
|
1.0
|
ND1
|
A:HIS57
|
4.2
|
50.5
|
1.0
|
CG
|
A:HIS57
|
4.2
|
48.5
|
1.0
|
ND1
|
A:HIS55
|
4.3
|
40.7
|
1.0
|
CG
|
A:HIS55
|
4.3
|
42.7
|
1.0
|
CG2
|
A:VAL101
|
4.3
|
36.8
|
1.0
|
CB
|
A:ASP301
|
4.3
|
61.0
|
1.0
|
CA
|
A:ASP301
|
4.9
|
56.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 2 out
of 8 in the Phosphotriesterase PTE_A53_4
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_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:51.8
occ:1.00
|
O2
|
A:FMT401
|
2.0
|
49.5
|
1.0
|
O
|
A:HOH501
|
2.0
|
58.7
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
55.6
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
52.6
|
1.0
|
CE1
|
A:HIS201
|
3.0
|
51.5
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
53.7
|
1.0
|
CD2
|
A:HIS230
|
3.0
|
55.4
|
1.0
|
C
|
A:FMT401
|
3.1
|
49.6
|
1.0
|
CG
|
A:HIS201
|
3.2
|
51.3
|
1.0
|
ZN
|
A:ZN402
|
3.6
|
49.6
|
1.0
|
CB
|
A:HIS201
|
3.6
|
49.3
|
1.0
|
NE1
|
A:TRP131
|
3.7
|
47.0
|
1.0
|
O1
|
A:FMT401
|
3.7
|
46.1
|
1.0
|
NZ
|
A:LYS169
|
4.0
|
43.5
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
54.3
|
1.0
|
CG
|
A:HIS230
|
4.1
|
54.0
|
1.0
|
NE2
|
A:HIS201
|
4.1
|
51.0
|
1.0
|
CD2
|
A:HIS201
|
4.2
|
50.3
|
1.0
|
CE1
|
A:HIS55
|
4.4
|
40.8
|
1.0
|
NE2
|
A:HIS55
|
4.4
|
43.1
|
1.0
|
CA
|
A:HIS201
|
4.5
|
47.6
|
1.0
|
OD2
|
A:ASP301
|
4.5
|
60.4
|
1.0
|
CD1
|
A:TRP131
|
4.5
|
44.4
|
1.0
|
CE2
|
A:TRP131
|
4.7
|
48.2
|
1.0
|
CE
|
A:LYS169
|
4.7
|
38.0
|
1.0
|
OD1
|
A:ASP301
|
4.8
|
58.8
|
1.0
|
CZ2
|
A:TRP131
|
4.9
|
50.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 3 out
of 8 in the Phosphotriesterase PTE_A53_4
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_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:34.9
occ:1.00
|
O1
|
B:FMT401
|
2.0
|
36.2
|
1.0
|
OD1
|
B:ASP301
|
2.0
|
38.6
|
1.0
|
O
|
B:HOH501
|
2.0
|
40.7
|
1.0
|
NE2
|
B:HIS57
|
2.0
|
34.1
|
1.0
|
NE2
|
B:HIS55
|
2.2
|
32.4
|
1.0
|
C
|
B:FMT401
|
2.9
|
34.7
|
1.0
|
CE1
|
B:HIS57
|
3.0
|
34.0
|
1.0
|
CG
|
B:ASP301
|
3.0
|
38.1
|
1.0
|
CD2
|
B:HIS57
|
3.1
|
34.1
|
1.0
|
CD2
|
B:HIS55
|
3.1
|
30.7
|
1.0
|
O2
|
B:FMT401
|
3.2
|
36.0
|
1.0
|
CE1
|
B:HIS55
|
3.2
|
32.6
|
1.0
|
OD2
|
B:ASP301
|
3.4
|
38.9
|
1.0
|
ZN
|
B:ZN403
|
3.6
|
40.9
|
1.0
|
CE1
|
B:HIS230
|
3.9
|
40.7
|
1.0
|
NZ
|
B:LYS169
|
4.0
|
30.0
|
1.0
|
ND1
|
B:HIS57
|
4.1
|
33.6
|
1.0
|
CG
|
B:HIS57
|
4.2
|
33.6
|
1.0
|
NE2
|
B:HIS230
|
4.2
|
39.8
|
1.0
|
ND1
|
B:HIS55
|
4.3
|
32.2
|
1.0
|
CG
|
B:HIS55
|
4.3
|
30.4
|
1.0
|
CG2
|
B:VAL101
|
4.3
|
32.4
|
1.0
|
CB
|
B:ASP301
|
4.3
|
36.6
|
1.0
|
CA
|
B:ASP301
|
4.9
|
35.9
|
1.0
|
|
Zinc binding site 4 out
of 8 in 6fu0
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Zinc Binding Sites List in 6fu0
Zinc binding site 4 out
of 8 in the Phosphotriesterase PTE_A53_4
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_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:40.9
occ:1.00
|
NE2
|
B:HIS230
|
2.0
|
39.8
|
1.0
|
O2
|
B:FMT401
|
2.0
|
36.0
|
1.0
|
O
|
B:HOH501
|
2.0
|
40.7
|
1.0
|
ND1
|
B:HIS201
|
2.1
|
39.0
|
1.0
|
CE1
|
B:HIS230
|
2.9
|
40.7
|
1.0
|
CD2
|
B:HIS230
|
3.0
|
39.8
|
1.0
|
C
|
B:FMT401
|
3.0
|
34.7
|
1.0
|
CE1
|
B:HIS201
|
3.0
|
38.7
|
1.0
|
CG
|
B:HIS201
|
3.2
|
38.8
|
1.0
|
CB
|
B:HIS201
|
3.6
|
39.2
|
1.0
|
ZN
|
B:ZN402
|
3.6
|
34.9
|
1.0
|
NE1
|
B:TRP131
|
3.6
|
46.0
|
1.0
|
O1
|
B:FMT401
|
3.7
|
36.2
|
1.0
|
NZ
|
B:LYS169
|
3.9
|
30.0
|
1.0
|
ND1
|
B:HIS230
|
4.0
|
42.0
|
1.0
|
CG
|
B:HIS230
|
4.1
|
41.1
|
1.0
|
NE2
|
B:HIS201
|
4.2
|
38.6
|
1.0
|
CD2
|
B:HIS201
|
4.3
|
38.3
|
1.0
|
CE1
|
B:HIS55
|
4.4
|
32.6
|
1.0
|
NE2
|
B:HIS55
|
4.4
|
32.4
|
1.0
|
CA
|
B:HIS201
|
4.4
|
40.5
|
1.0
|
CD1
|
B:TRP131
|
4.5
|
46.7
|
1.0
|
OD2
|
B:ASP301
|
4.6
|
38.9
|
1.0
|
CE
|
B:LYS169
|
4.6
|
29.5
|
1.0
|
CE2
|
B:TRP131
|
4.7
|
46.3
|
1.0
|
OD1
|
B:ASP301
|
4.9
|
38.6
|
1.0
|
CZ2
|
B:TRP131
|
5.0
|
48.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 5 out
of 8 in the Phosphotriesterase PTE_A53_4
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Phosphotriesterase PTE_A53_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn402
b:32.8
occ:1.00
|
OD1
|
C:ASP301
|
2.0
|
40.0
|
1.0
|
O1
|
C:FMT401
|
2.0
|
41.0
|
1.0
|
O
|
C:HOH501
|
2.0
|
39.2
|
1.0
|
NE2
|
C:HIS55
|
2.0
|
28.2
|
1.0
|
NE2
|
C:HIS57
|
2.0
|
38.3
|
1.0
|
CD2
|
C:HIS55
|
2.9
|
28.1
|
1.0
|
CG
|
C:ASP301
|
3.0
|
41.6
|
1.0
|
CE1
|
C:HIS57
|
3.0
|
39.9
|
1.0
|
CE1
|
C:HIS55
|
3.0
|
27.7
|
1.0
|
CD2
|
C:HIS57
|
3.0
|
38.5
|
1.0
|
C
|
C:FMT401
|
3.1
|
41.8
|
1.0
|
O2
|
C:FMT401
|
3.4
|
40.4
|
1.0
|
OD2
|
C:ASP301
|
3.5
|
39.8
|
1.0
|
ZN
|
C:ZN403
|
3.7
|
40.8
|
1.0
|
CE1
|
C:HIS230
|
3.9
|
40.9
|
1.0
|
NZ
|
C:LYS169
|
4.0
|
37.5
|
1.0
|
CG
|
C:HIS55
|
4.1
|
27.8
|
1.0
|
ND1
|
C:HIS55
|
4.1
|
26.8
|
1.0
|
ND1
|
C:HIS57
|
4.1
|
40.7
|
1.0
|
CG2
|
C:VAL101
|
4.2
|
37.9
|
1.0
|
CG
|
C:HIS57
|
4.2
|
37.9
|
1.0
|
NE2
|
C:HIS230
|
4.3
|
40.2
|
1.0
|
CB
|
C:ASP301
|
4.3
|
39.1
|
1.0
|
CA
|
C:ASP301
|
4.8
|
38.8
|
1.0
|
|
Zinc binding site 6 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 6 out
of 8 in the Phosphotriesterase PTE_A53_4
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Phosphotriesterase PTE_A53_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn403
b:40.8
occ:1.00
|
NE2
|
C:HIS230
|
2.0
|
40.2
|
1.0
|
O2
|
C:FMT401
|
2.0
|
40.4
|
1.0
|
O
|
C:HOH501
|
2.0
|
39.2
|
1.0
|
ND1
|
C:HIS201
|
2.2
|
48.2
|
1.0
|
C
|
C:FMT401
|
2.9
|
41.8
|
1.0
|
CE1
|
C:HIS230
|
2.9
|
40.9
|
1.0
|
CD2
|
C:HIS230
|
3.0
|
40.1
|
1.0
|
CE1
|
C:HIS201
|
3.0
|
49.7
|
1.0
|
CG
|
C:HIS201
|
3.2
|
43.7
|
1.0
|
O1
|
C:FMT401
|
3.3
|
41.0
|
1.0
|
CB
|
C:HIS201
|
3.6
|
41.5
|
1.0
|
ZN
|
C:ZN402
|
3.7
|
32.8
|
1.0
|
NE1
|
C:TRP131
|
3.8
|
37.7
|
1.0
|
NZ
|
C:LYS169
|
4.0
|
37.5
|
1.0
|
ND1
|
C:HIS230
|
4.0
|
40.3
|
1.0
|
CG
|
C:HIS230
|
4.1
|
39.7
|
1.0
|
NE2
|
C:HIS201
|
4.2
|
47.4
|
1.0
|
CD2
|
C:HIS201
|
4.3
|
44.2
|
1.0
|
CE1
|
C:HIS55
|
4.3
|
27.7
|
1.0
|
NE2
|
C:HIS55
|
4.4
|
28.2
|
1.0
|
OD2
|
C:ASP301
|
4.4
|
39.8
|
1.0
|
CA
|
C:HIS201
|
4.5
|
41.9
|
1.0
|
CD1
|
C:TRP131
|
4.6
|
35.8
|
1.0
|
CE
|
C:LYS169
|
4.7
|
33.4
|
1.0
|
CE2
|
C:TRP131
|
4.8
|
36.0
|
1.0
|
OD1
|
C:ASP301
|
4.8
|
40.0
|
1.0
|
CG
|
C:ASP301
|
5.0
|
41.6
|
1.0
|
|
Zinc binding site 7 out
of 8 in 6fu0
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Zinc Binding Sites List in 6fu0
Zinc binding site 7 out
of 8 in the Phosphotriesterase PTE_A53_4
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Phosphotriesterase PTE_A53_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn402
b:37.6
occ:1.00
|
O1
|
D:FMT401
|
2.0
|
44.6
|
1.0
|
OD1
|
D:ASP301
|
2.0
|
45.2
|
1.0
|
O
|
D:HOH501
|
2.0
|
42.6
|
1.0
|
NE2
|
D:HIS55
|
2.1
|
31.9
|
1.0
|
NE2
|
D:HIS57
|
2.1
|
35.4
|
1.0
|
C
|
D:FMT401
|
3.0
|
43.2
|
1.0
|
CG
|
D:ASP301
|
3.0
|
45.1
|
1.0
|
CE1
|
D:HIS57
|
3.1
|
34.9
|
1.0
|
CD2
|
D:HIS55
|
3.1
|
31.0
|
1.0
|
CE1
|
D:HIS55
|
3.1
|
31.9
|
1.0
|
CD2
|
D:HIS57
|
3.1
|
35.9
|
1.0
|
O2
|
D:FMT401
|
3.2
|
46.7
|
1.0
|
OD2
|
D:ASP301
|
3.5
|
42.8
|
1.0
|
ZN
|
D:ZN403
|
3.7
|
41.2
|
1.0
|
CE1
|
D:HIS230
|
3.9
|
40.3
|
1.0
|
NZ
|
D:LYS169
|
4.0
|
31.7
|
1.0
|
ND1
|
D:HIS57
|
4.2
|
34.6
|
1.0
|
ND1
|
D:HIS55
|
4.2
|
30.2
|
1.0
|
NE2
|
D:HIS230
|
4.2
|
39.0
|
1.0
|
CG
|
D:HIS55
|
4.2
|
30.1
|
1.0
|
CG
|
D:HIS57
|
4.2
|
34.1
|
1.0
|
CG2
|
D:VAL101
|
4.2
|
36.8
|
1.0
|
CB
|
D:ASP301
|
4.3
|
43.4
|
1.0
|
CA
|
D:ASP301
|
4.8
|
41.7
|
1.0
|
|
Zinc binding site 8 out
of 8 in 6fu0
Go back to
Zinc Binding Sites List in 6fu0
Zinc binding site 8 out
of 8 in the Phosphotriesterase PTE_A53_4
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Phosphotriesterase PTE_A53_4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn403
b:41.2
occ:1.00
|
O2
|
D:FMT401
|
2.0
|
46.7
|
1.0
|
NE2
|
D:HIS230
|
2.0
|
39.0
|
1.0
|
O
|
D:HOH501
|
2.0
|
42.6
|
1.0
|
ND1
|
D:HIS201
|
2.0
|
45.1
|
1.0
|
CE1
|
D:HIS201
|
3.0
|
46.2
|
1.0
|
CD2
|
D:HIS230
|
3.0
|
38.5
|
1.0
|
CE1
|
D:HIS230
|
3.0
|
40.3
|
1.0
|
C
|
D:FMT401
|
3.0
|
43.2
|
1.0
|
CG
|
D:HIS201
|
3.1
|
44.5
|
1.0
|
CB
|
D:HIS201
|
3.5
|
42.7
|
1.0
|
O1
|
D:FMT401
|
3.6
|
44.6
|
1.0
|
NE1
|
D:TRP131
|
3.6
|
38.0
|
1.0
|
ZN
|
D:ZN402
|
3.7
|
37.6
|
1.0
|
NZ
|
D:LYS169
|
3.9
|
31.7
|
1.0
|
ND1
|
D:HIS230
|
4.1
|
40.2
|
1.0
|
NE2
|
D:HIS201
|
4.1
|
48.4
|
1.0
|
CG
|
D:HIS230
|
4.1
|
38.2
|
1.0
|
CD2
|
D:HIS201
|
4.2
|
46.0
|
1.0
|
CE1
|
D:HIS55
|
4.4
|
31.9
|
1.0
|
CA
|
D:HIS201
|
4.4
|
40.6
|
1.0
|
NE2
|
D:HIS55
|
4.5
|
31.9
|
1.0
|
CD1
|
D:TRP131
|
4.5
|
36.4
|
1.0
|
CE
|
D:LYS169
|
4.6
|
29.1
|
1.0
|
OD2
|
D:ASP301
|
4.6
|
42.8
|
1.0
|
CE2
|
D:TRP131
|
4.6
|
39.4
|
1.0
|
OD1
|
D:ASP301
|
4.9
|
45.2
|
1.0
|
CZ2
|
D:TRP131
|
4.9
|
42.9
|
1.0
|
|
Reference:
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.
Phosphotriesterase PTE_C23_1 To Be Published.
Page generated: Wed Dec 16 11:49:22 2020
|