Zinc in PDB 6fei: Phosphotriesterase PTE_A53_1
Protein crystallography data
The structure of Phosphotriesterase PTE_A53_1, PDB code: 6fei
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)
|
39.18 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.230,
81.249,
70.666,
90.00,
94.80,
90.00
|
R / Rfree (%)
|
15.5 /
18.5
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_1
(pdb code 6fei). 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: 6fei:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 6fei
Go back to
Zinc Binding Sites List in 6fei
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:20.2
occ:1.00
|
OAF
|
A:D6K404
|
2.0
|
27.2
|
1.0
|
NE2
|
A:HIS57
|
2.0
|
16.3
|
1.0
|
O1
|
A:FMT401
|
2.1
|
19.6
|
1.0
|
NE2
|
A:HIS55
|
2.1
|
18.5
|
1.0
|
OD1
|
A:ASP301
|
2.3
|
18.9
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
17.0
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
17.9
|
1.0
|
CAL
|
A:D6K404
|
3.0
|
22.2
|
1.0
|
CD2
|
A:HIS57
|
3.0
|
18.6
|
1.0
|
C
|
A:FMT401
|
3.1
|
17.9
|
1.0
|
CG
|
A:ASP301
|
3.1
|
18.8
|
1.0
|
CE1
|
A:HIS55
|
3.2
|
20.2
|
1.0
|
CAH
|
A:D6K404
|
3.3
|
21.7
|
1.0
|
OD2
|
A:ASP301
|
3.4
|
19.9
|
1.0
|
O2
|
A:FMT401
|
3.5
|
17.3
|
1.0
|
CAI
|
A:D6K404
|
3.8
|
31.7
|
1.0
|
ZN
|
A:ZN403
|
3.8
|
20.6
|
1.0
|
CG2
|
A:VAL101
|
4.1
|
17.8
|
1.0
|
CE1
|
A:HIS230
|
4.1
|
19.4
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
17.2
|
1.0
|
CG
|
A:HIS57
|
4.2
|
16.9
|
1.0
|
CG
|
A:HIS55
|
4.2
|
17.5
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
16.0
|
1.0
|
OAJ
|
A:D6K404
|
4.2
|
27.3
|
1.0
|
NE2
|
A:HIS230
|
4.4
|
19.0
|
1.0
|
NZ
|
A:LYS169
|
4.4
|
22.5
|
1.0
|
CB
|
A:ASP301
|
4.4
|
19.1
|
1.0
|
CAE
|
A:D6K404
|
4.5
|
29.6
|
1.0
|
CAK
|
A:D6K404
|
4.6
|
28.8
|
1.0
|
CAA
|
A:D6K404
|
4.8
|
26.8
|
1.0
|
OAG
|
A:D6K404
|
4.8
|
38.5
|
1.0
|
CA
|
A:ASP301
|
4.9
|
17.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 6fei
Go back to
Zinc Binding Sites List in 6fei
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:20.6
occ:1.00
|
O2
|
A:FMT401
|
2.0
|
17.3
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
19.0
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
24.2
|
1.0
|
CAL
|
A:D6K404
|
2.8
|
22.2
|
1.0
|
CD2
|
A:HIS230
|
3.0
|
18.4
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
19.4
|
1.0
|
CE1
|
A:HIS201
|
3.0
|
26.9
|
1.0
|
C
|
A:FMT401
|
3.0
|
17.9
|
1.0
|
OAF
|
A:D6K404
|
3.1
|
27.2
|
1.0
|
CG
|
A:HIS201
|
3.1
|
21.0
|
1.0
|
O1
|
A:FMT401
|
3.4
|
19.6
|
1.0
|
CB
|
A:HIS201
|
3.5
|
18.6
|
1.0
|
OAJ
|
A:D6K404
|
3.8
|
27.3
|
1.0
|
CAH
|
A:D6K404
|
3.8
|
21.7
|
1.0
|
ZN
|
A:ZN402
|
3.8
|
20.2
|
1.0
|
NE1
|
A:TRP131
|
3.9
|
24.3
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
18.8
|
1.0
|
CG
|
A:HIS230
|
4.1
|
18.3
|
1.0
|
NE2
|
A:HIS201
|
4.2
|
26.1
|
1.0
|
CD2
|
A:HIS201
|
4.2
|
23.2
|
1.0
|
CE1
|
A:HIS55
|
4.2
|
20.2
|
1.0
|
NE2
|
A:HIS55
|
4.3
|
18.5
|
1.0
|
O
|
A:HOH542
|
4.3
|
30.6
|
1.0
|
CA
|
A:HIS201
|
4.4
|
18.0
|
1.0
|
NZ
|
A:LYS169
|
4.5
|
22.5
|
1.0
|
CD1
|
A:TRP131
|
4.5
|
21.9
|
1.0
|
OD2
|
A:ASP301
|
4.7
|
19.9
|
1.0
|
CE
|
A:LYS169
|
4.8
|
18.4
|
1.0
|
|
Zinc binding site 3 out
of 4 in 6fei
Go back to
Zinc Binding Sites List in 6fei
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:23.6
occ:1.00
|
NE2
|
B:HIS57
|
2.0
|
21.0
|
1.0
|
O
|
B:HOH629
|
2.1
|
25.7
|
1.0
|
O1
|
B:FMT401
|
2.1
|
22.3
|
1.0
|
NE2
|
B:HIS55
|
2.2
|
18.7
|
1.0
|
OD1
|
B:ASP301
|
2.2
|
22.4
|
1.0
|
CE1
|
B:HIS57
|
3.0
|
21.3
|
1.0
|
CD2
|
B:HIS55
|
3.0
|
19.8
|
1.0
|
CD2
|
B:HIS57
|
3.0
|
20.7
|
1.0
|
CG
|
B:ASP301
|
3.1
|
24.1
|
1.0
|
C
|
B:FMT401
|
3.2
|
24.4
|
1.0
|
CE1
|
B:HIS55
|
3.2
|
22.0
|
1.0
|
OD2
|
B:ASP301
|
3.4
|
22.9
|
1.0
|
O2
|
B:FMT401
|
3.6
|
21.4
|
1.0
|
ZN
|
B:ZN403
|
3.8
|
24.9
|
1.0
|
O
|
B:HOH701
|
4.0
|
29.8
|
1.0
|
CE1
|
B:HIS230
|
4.1
|
24.6
|
1.0
|
ND1
|
B:HIS57
|
4.1
|
19.4
|
1.0
|
CG2
|
B:VAL101
|
4.1
|
19.8
|
1.0
|
CG
|
B:HIS57
|
4.1
|
18.7
|
1.0
|
CG
|
B:HIS55
|
4.2
|
19.5
|
1.0
|
ND1
|
B:HIS55
|
4.3
|
20.0
|
1.0
|
NE2
|
B:HIS230
|
4.3
|
21.7
|
1.0
|
CB
|
B:ASP301
|
4.4
|
19.9
|
1.0
|
NZ
|
B:LYS169
|
4.5
|
25.7
|
1.0
|
CA
|
B:ASP301
|
4.9
|
19.2
|
1.0
|
|
Zinc binding site 4 out
of 4 in 6fei
Go back to
Zinc Binding Sites List in 6fei
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:24.9
occ:1.00
|
O2
|
B:FMT401
|
2.0
|
21.4
|
1.0
|
NE2
|
B:HIS230
|
2.0
|
21.7
|
1.0
|
ND1
|
B:HIS201
|
2.1
|
27.2
|
1.0
|
O
|
B:HOH701
|
2.2
|
29.8
|
1.0
|
O
|
B:HOH629
|
2.5
|
25.7
|
1.0
|
CE1
|
B:HIS201
|
2.9
|
27.0
|
1.0
|
CD2
|
B:HIS230
|
3.0
|
23.1
|
1.0
|
C
|
B:FMT401
|
3.0
|
24.4
|
1.0
|
CE1
|
B:HIS230
|
3.0
|
24.6
|
1.0
|
CG
|
B:HIS201
|
3.1
|
24.9
|
1.0
|
O1
|
B:FMT401
|
3.3
|
22.3
|
1.0
|
CB
|
B:HIS201
|
3.5
|
22.3
|
1.0
|
ZN
|
B:ZN402
|
3.8
|
23.6
|
1.0
|
NE1
|
B:TRP131
|
3.9
|
24.6
|
1.0
|
NE2
|
B:HIS201
|
4.1
|
30.3
|
1.0
|
ND1
|
B:HIS230
|
4.1
|
23.8
|
1.0
|
CG
|
B:HIS230
|
4.1
|
20.7
|
1.0
|
CD2
|
B:HIS201
|
4.2
|
27.3
|
1.0
|
CE1
|
B:HIS55
|
4.3
|
22.0
|
1.0
|
NE2
|
B:HIS55
|
4.3
|
18.7
|
1.0
|
CA
|
B:HIS201
|
4.4
|
22.3
|
1.0
|
NZ
|
B:LYS169
|
4.5
|
25.7
|
1.0
|
CD1
|
B:TRP131
|
4.5
|
22.3
|
1.0
|
OD2
|
B:ASP301
|
4.8
|
22.9
|
1.0
|
CE
|
B:LYS169
|
4.8
|
22.6
|
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: Wed Dec 16 11:47:37 2020
|