Zinc in PDB 4xd6: Phosphotriesterase Variant E2A
Protein crystallography data
The structure of Phosphotriesterase Variant E2A, PDB code: 4xd6
was solved by
C.J.Jackson,
E.Campbell,
M.Kaltenbach,
N.Tokuriki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.28 /
1.75
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.739,
85.759,
88.372,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.4 /
26.9
|
Other elements in 4xd6:
The structure of Phosphotriesterase Variant E2A also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant E2A
(pdb code 4xd6). 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 E2A, PDB code: 4xd6:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4xd6
Go back to
Zinc Binding Sites List in 4xd6
Zinc binding site 1 out
of 4 in the Phosphotriesterase Variant E2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant E2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:8.4
occ:1.00
|
NE2
|
A:HIS57
|
2.0
|
8.9
|
1.0
|
OD1
|
A:ASP301
|
2.1
|
6.1
|
1.0
|
NE2
|
A:HIS55
|
2.1
|
5.8
|
1.0
|
O2
|
A:CAC403
|
2.1
|
15.1
|
1.0
|
OQ2
|
A:KCX169
|
2.2
|
9.8
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
6.1
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
8.1
|
1.0
|
CG
|
A:ASP301
|
3.0
|
13.2
|
1.0
|
CX
|
A:KCX169
|
3.0
|
9.6
|
1.0
|
CD2
|
A:HIS57
|
3.0
|
8.1
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
6.5
|
1.0
|
AS
|
A:CAC403
|
3.3
|
79.7
|
1.0
|
C1
|
A:CAC403
|
3.4
|
33.3
|
1.0
|
OD2
|
A:ASP301
|
3.4
|
13.2
|
1.0
|
OQ1
|
A:KCX169
|
3.4
|
7.8
|
1.0
|
ZN
|
A:ZN402
|
3.5
|
13.0
|
1.0
|
CG2
|
A:VAL101
|
4.1
|
6.8
|
1.0
|
NZ
|
A:KCX169
|
4.1
|
11.7
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
8.3
|
1.0
|
O
|
A:HOH859
|
4.2
|
22.9
|
1.0
|
CG
|
A:HIS57
|
4.2
|
7.0
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
10.5
|
1.0
|
CG
|
A:HIS55
|
4.2
|
13.0
|
1.0
|
CE1
|
A:HIS230
|
4.2
|
13.3
|
1.0
|
CB
|
A:ASP301
|
4.3
|
9.0
|
1.0
|
NE2
|
A:HIS230
|
4.4
|
8.5
|
1.0
|
O1
|
A:CAC403
|
4.5
|
56.4
|
1.0
|
C2
|
A:CAC403
|
4.7
|
43.6
|
1.0
|
CA
|
A:ASP301
|
4.8
|
8.6
|
1.0
|
O
|
A:HOH679
|
4.9
|
28.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4xd6
Go back to
Zinc Binding Sites List in 4xd6
Zinc binding site 2 out
of 4 in the Phosphotriesterase Variant E2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant E2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:13.0
occ:1.00
|
OQ1
|
A:KCX169
|
2.0
|
7.8
|
1.0
|
NE2
|
A:HIS230
|
2.0
|
8.5
|
1.0
|
O2
|
A:CAC403
|
2.2
|
15.1
|
1.0
|
ND1
|
A:HIS201
|
2.2
|
18.5
|
1.0
|
CE1
|
A:HIS230
|
2.9
|
13.3
|
1.0
|
CX
|
A:KCX169
|
3.0
|
9.6
|
1.0
|
O1
|
A:CAC403
|
3.0
|
56.4
|
1.0
|
CD2
|
A:HIS230
|
3.1
|
10.3
|
1.0
|
CE1
|
A:HIS201
|
3.1
|
18.3
|
1.0
|
AS
|
A:CAC403
|
3.2
|
79.7
|
1.0
|
CG
|
A:HIS201
|
3.2
|
13.2
|
1.0
|
OQ2
|
A:KCX169
|
3.3
|
9.8
|
1.0
|
O
|
A:HOH859
|
3.4
|
22.9
|
1.0
|
ZN
|
A:ZN401
|
3.5
|
8.4
|
1.0
|
CB
|
A:HIS201
|
3.6
|
15.2
|
1.0
|
CE1
|
A:HIS55
|
3.9
|
6.5
|
1.0
|
NE2
|
A:HIS55
|
4.0
|
5.8
|
1.0
|
NE1
|
A:TRP131
|
4.0
|
15.2
|
1.0
|
ND1
|
A:HIS230
|
4.1
|
12.3
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
11.7
|
1.0
|
CG
|
A:HIS230
|
4.2
|
9.2
|
1.0
|
NE2
|
A:HIS201
|
4.2
|
18.0
|
1.0
|
CD2
|
A:HIS201
|
4.3
|
15.3
|
1.0
|
OD2
|
A:ASP301
|
4.4
|
13.2
|
1.0
|
CA
|
A:HIS201
|
4.4
|
11.2
|
1.0
|
CE
|
A:KCX169
|
4.6
|
7.3
|
1.0
|
C1
|
A:CAC403
|
4.6
|
33.3
|
1.0
|
C2
|
A:CAC403
|
4.7
|
43.6
|
1.0
|
CD1
|
A:TRP131
|
4.7
|
11.1
|
1.0
|
OD1
|
A:ASP301
|
4.8
|
6.1
|
1.0
|
CG
|
A:ASP301
|
4.9
|
13.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 4xd6
Go back to
Zinc Binding Sites List in 4xd6
Zinc binding site 3 out
of 4 in the Phosphotriesterase Variant E2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant E2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn401
b:22.2
occ:1.00
|
OQ1
|
G:KCX169
|
2.0
|
16.7
|
1.0
|
NE2
|
G:HIS230
|
2.0
|
24.1
|
1.0
|
ND1
|
G:HIS201
|
2.2
|
25.8
|
1.0
|
O1
|
G:CAC402
|
2.2
|
20.0
|
1.0
|
CX
|
G:KCX169
|
2.9
|
17.4
|
1.0
|
CD2
|
G:HIS230
|
3.0
|
18.0
|
1.0
|
O2
|
G:CAC402
|
3.1
|
72.2
|
1.0
|
CE1
|
G:HIS230
|
3.1
|
28.4
|
1.0
|
CE1
|
G:HIS201
|
3.1
|
23.3
|
1.0
|
OQ2
|
G:KCX169
|
3.2
|
15.1
|
1.0
|
CG
|
G:HIS201
|
3.2
|
24.3
|
1.0
|
AS
|
G:CAC402
|
3.2
|
63.6
|
1.0
|
ZN
|
G:ZN403
|
3.5
|
18.6
|
1.0
|
CB
|
G:HIS201
|
3.5
|
17.2
|
1.0
|
O
|
G:HOH815
|
3.6
|
25.4
|
1.0
|
NE1
|
G:TRP131
|
4.0
|
23.4
|
1.0
|
NE2
|
G:HIS55
|
4.0
|
23.2
|
1.0
|
CE1
|
G:HIS55
|
4.0
|
15.2
|
1.0
|
NZ
|
G:KCX169
|
4.1
|
17.5
|
1.0
|
ND1
|
G:HIS230
|
4.2
|
22.3
|
1.0
|
CG
|
G:HIS230
|
4.2
|
27.3
|
1.0
|
NE2
|
G:HIS201
|
4.2
|
24.9
|
1.0
|
CD2
|
G:HIS201
|
4.3
|
23.5
|
1.0
|
C2
|
G:CAC402
|
4.4
|
28.4
|
1.0
|
CA
|
G:HIS201
|
4.4
|
11.7
|
1.0
|
CE
|
G:KCX169
|
4.5
|
12.7
|
1.0
|
CD1
|
G:TRP131
|
4.7
|
17.9
|
1.0
|
C1
|
G:CAC402
|
4.9
|
56.5
|
1.0
|
OD2
|
G:ASP301
|
4.9
|
27.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4xd6
Go back to
Zinc Binding Sites List in 4xd6
Zinc binding site 4 out
of 4 in the Phosphotriesterase Variant E2A
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant E2A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn403
b:18.6
occ:1.00
|
OQ2
|
G:KCX169
|
2.1
|
15.1
|
1.0
|
O1
|
G:CAC402
|
2.1
|
20.0
|
1.0
|
NE2
|
G:HIS55
|
2.1
|
23.2
|
1.0
|
OD1
|
G:ASP301
|
2.2
|
20.5
|
1.0
|
NE2
|
G:HIS57
|
2.2
|
15.2
|
1.0
|
CD2
|
G:HIS55
|
3.0
|
21.8
|
1.0
|
CD2
|
G:HIS57
|
3.0
|
13.4
|
1.0
|
CX
|
G:KCX169
|
3.1
|
17.4
|
1.0
|
CG
|
G:ASP301
|
3.1
|
25.2
|
1.0
|
CE1
|
G:HIS55
|
3.2
|
15.2
|
1.0
|
CE1
|
G:HIS57
|
3.3
|
15.3
|
1.0
|
AS
|
G:CAC402
|
3.3
|
63.6
|
1.0
|
OD2
|
G:ASP301
|
3.5
|
27.1
|
1.0
|
OQ1
|
G:KCX169
|
3.5
|
16.7
|
1.0
|
ZN
|
G:ZN401
|
3.5
|
22.2
|
1.0
|
C2
|
G:CAC402
|
3.6
|
28.4
|
1.0
|
O
|
G:HOH815
|
3.8
|
25.4
|
1.0
|
NZ
|
G:KCX169
|
4.1
|
17.5
|
1.0
|
CE1
|
G:HIS230
|
4.1
|
28.4
|
1.0
|
CG2
|
G:VAL101
|
4.1
|
9.9
|
1.0
|
CG
|
G:HIS55
|
4.2
|
19.4
|
1.0
|
CG
|
G:HIS57
|
4.2
|
10.8
|
1.0
|
NE2
|
G:HIS230
|
4.3
|
24.1
|
1.0
|
ND1
|
G:HIS55
|
4.3
|
20.6
|
1.0
|
ND1
|
G:HIS57
|
4.3
|
13.6
|
1.0
|
CB
|
G:ASP301
|
4.4
|
17.8
|
1.0
|
C1
|
G:CAC402
|
4.4
|
56.5
|
1.0
|
O2
|
G:CAC402
|
4.7
|
72.2
|
1.0
|
CA
|
G:ASP301
|
5.0
|
17.7
|
1.0
|
|
Reference:
E.Campbell,
M.Kaltenbach,
G.J.Correy,
P.D.Carr,
B.T.Porebski,
E.K.Livingstone,
L.Afriat-Jurnou,
A.M.Buckle,
M.Weik,
F.Hollfelder,
N.Tokuriki,
C.J.Jackson.
The Role of Protein Dynamics in the Evolution of New Enzyme Function. Nat.Chem.Biol. V. 12 944 2016.
ISSN: ESSN 1552-4469
PubMed: 27618189
DOI: 10.1038/NCHEMBIO.2175
Page generated: Sun Oct 27 10:28:10 2024
|