Zinc in PDB 4xd4: Phosphotriesterase Variant E2B
Protein crystallography data
The structure of Phosphotriesterase Variant E2B, PDB code: 4xd4
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)
|
39.31 /
1.90
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.560,
85.782,
88.443,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
24.3
|
Other elements in 4xd4:
The structure of Phosphotriesterase Variant E2B also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant E2B
(pdb code 4xd4). 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 E2B, PDB code: 4xd4:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4xd4
Go back to
Zinc Binding Sites List in 4xd4
Zinc binding site 1 out
of 4 in the Phosphotriesterase Variant E2B
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant E2B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2401
b:18.9
occ:1.00
|
O1
|
A:CAC2403
|
2.0
|
28.2
|
1.0
|
NE2
|
A:HIS57
|
2.0
|
13.4
|
1.0
|
OD1
|
A:ASP301
|
2.2
|
17.9
|
1.0
|
NE2
|
A:HIS55
|
2.2
|
12.9
|
1.0
|
OQ2
|
A:KCX169
|
2.2
|
18.4
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
17.7
|
1.0
|
CG
|
A:ASP301
|
3.0
|
16.9
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
14.7
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
11.8
|
1.0
|
CX
|
A:KCX169
|
3.1
|
24.1
|
1.0
|
CE1
|
A:HIS55
|
3.3
|
14.6
|
1.0
|
OD2
|
A:ASP301
|
3.3
|
24.6
|
1.0
|
AS
|
A:CAC2403
|
3.4
|
85.0
|
1.0
|
OQ1
|
A:KCX169
|
3.5
|
20.7
|
1.0
|
ZN
|
A:ZN2402
|
3.9
|
31.3
|
1.0
|
C2
|
A:CAC2403
|
3.9
|
42.3
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
12.9
|
1.0
|
CG2
|
A:VAL101
|
4.1
|
19.2
|
1.0
|
NZ
|
A:KCX169
|
4.1
|
18.9
|
1.0
|
CG
|
A:HIS57
|
4.2
|
12.1
|
1.0
|
CE1
|
A:HIS230
|
4.2
|
22.1
|
1.0
|
CG
|
A:HIS55
|
4.2
|
11.3
|
1.0
|
ND1
|
A:HIS55
|
4.3
|
13.8
|
1.0
|
CB
|
A:ASP301
|
4.4
|
17.3
|
1.0
|
NE2
|
A:HIS230
|
4.4
|
20.4
|
1.0
|
O2
|
A:CAC2403
|
4.4
|
43.8
|
1.0
|
C1
|
A:CAC2403
|
4.8
|
58.8
|
1.0
|
CA
|
A:ASP301
|
4.9
|
13.6
|
1.0
|
O
|
A:HOH2622
|
4.9
|
28.8
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4xd4
Go back to
Zinc Binding Sites List in 4xd4
Zinc binding site 2 out
of 4 in the Phosphotriesterase Variant E2B
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant E2B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2402
b:31.3
occ:1.00
|
OQ1
|
A:KCX169
|
2.0
|
20.7
|
1.0
|
ND1
|
A:HIS201
|
2.1
|
21.9
|
1.0
|
NE2
|
A:HIS230
|
2.2
|
20.4
|
1.0
|
O2
|
A:CAC2403
|
2.6
|
43.8
|
1.0
|
O1
|
A:CAC2403
|
2.8
|
28.2
|
1.0
|
CX
|
A:KCX169
|
3.0
|
24.1
|
1.0
|
CG
|
A:HIS201
|
3.1
|
27.2
|
1.0
|
CE1
|
A:HIS201
|
3.1
|
31.9
|
1.0
|
CD2
|
A:HIS230
|
3.1
|
28.1
|
1.0
|
CE1
|
A:HIS230
|
3.2
|
22.1
|
1.0
|
OQ2
|
A:KCX169
|
3.3
|
18.4
|
1.0
|
AS
|
A:CAC2403
|
3.3
|
85.0
|
1.0
|
CB
|
A:HIS201
|
3.4
|
22.0
|
1.0
|
NE1
|
A:TRP131
|
3.8
|
20.6
|
1.0
|
NH2
|
A:ARG254
|
3.8
|
31.5
|
0.5
|
ZN
|
A:ZN2401
|
3.9
|
18.9
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
18.9
|
1.0
|
NE2
|
A:HIS201
|
4.2
|
23.8
|
1.0
|
CD2
|
A:HIS201
|
4.2
|
30.9
|
1.0
|
CG
|
A:HIS230
|
4.3
|
23.1
|
1.0
|
ND1
|
A:HIS230
|
4.3
|
25.2
|
1.0
|
CE1
|
A:HIS55
|
4.4
|
14.6
|
1.0
|
NE2
|
A:HIS55
|
4.4
|
12.9
|
1.0
|
CA
|
A:HIS201
|
4.4
|
18.4
|
1.0
|
CD1
|
A:TRP131
|
4.5
|
18.7
|
1.0
|
CZ
|
A:ARG254
|
4.5
|
27.6
|
0.5
|
CE
|
A:KCX169
|
4.6
|
19.3
|
1.0
|
OD2
|
A:ASP301
|
4.6
|
24.6
|
1.0
|
C1
|
A:CAC2403
|
4.7
|
58.8
|
1.0
|
C2
|
A:CAC2403
|
4.8
|
42.3
|
1.0
|
CE2
|
A:TRP131
|
4.8
|
24.3
|
1.0
|
NE
|
A:ARG254
|
4.9
|
26.1
|
0.5
|
|
Zinc binding site 3 out
of 4 in 4xd4
Go back to
Zinc Binding Sites List in 4xd4
Zinc binding site 3 out
of 4 in the Phosphotriesterase Variant E2B
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant E2B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn402
b:22.8
occ:1.00
|
O1
|
G:CAC401
|
1.9
|
28.5
|
1.0
|
NE2
|
G:HIS55
|
2.1
|
19.9
|
1.0
|
NE2
|
G:HIS57
|
2.2
|
15.3
|
1.0
|
OQ2
|
G:KCX169
|
2.2
|
26.0
|
1.0
|
OD1
|
G:ASP301
|
2.3
|
19.6
|
1.0
|
CD2
|
G:HIS55
|
3.0
|
17.6
|
1.0
|
CD2
|
G:HIS57
|
3.1
|
13.4
|
1.0
|
CE1
|
G:HIS55
|
3.2
|
19.5
|
1.0
|
CE1
|
G:HIS57
|
3.2
|
16.2
|
1.0
|
CX
|
G:KCX169
|
3.2
|
25.8
|
1.0
|
CG
|
G:ASP301
|
3.2
|
24.4
|
1.0
|
AS
|
G:CAC401
|
3.3
|
50.3
|
1.0
|
OD2
|
G:ASP301
|
3.5
|
23.5
|
1.0
|
C2
|
G:CAC401
|
3.7
|
25.9
|
1.0
|
OQ1
|
G:KCX169
|
3.7
|
23.4
|
1.0
|
ZN
|
G:ZN403
|
3.8
|
32.7
|
1.0
|
CG2
|
G:VAL101
|
4.0
|
14.3
|
1.0
|
CE1
|
G:HIS230
|
4.1
|
24.9
|
1.0
|
NZ
|
G:KCX169
|
4.2
|
23.4
|
1.0
|
CG
|
G:HIS55
|
4.2
|
16.1
|
1.0
|
ND1
|
G:HIS55
|
4.2
|
16.5
|
1.0
|
ND1
|
G:HIS57
|
4.3
|
15.5
|
1.0
|
CG
|
G:HIS57
|
4.3
|
12.1
|
1.0
|
O2
|
G:CAC401
|
4.4
|
39.2
|
1.0
|
NE2
|
G:HIS230
|
4.4
|
19.9
|
1.0
|
CB
|
G:ASP301
|
4.5
|
15.4
|
1.0
|
C1
|
G:CAC401
|
4.6
|
37.5
|
1.0
|
CA
|
G:ASP301
|
4.9
|
18.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4xd4
Go back to
Zinc Binding Sites List in 4xd4
Zinc binding site 4 out
of 4 in the Phosphotriesterase Variant E2B
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant E2B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn403
b:32.7
occ:1.00
|
OQ1
|
G:KCX169
|
2.0
|
23.4
|
1.0
|
NE2
|
G:HIS230
|
2.1
|
19.9
|
1.0
|
O2
|
G:CAC401
|
2.2
|
39.2
|
1.0
|
ND1
|
G:HIS201
|
2.3
|
24.5
|
1.0
|
O1
|
G:CAC401
|
2.8
|
28.5
|
1.0
|
CX
|
G:KCX169
|
3.0
|
25.8
|
1.0
|
CD2
|
G:HIS230
|
3.0
|
20.7
|
1.0
|
AS
|
G:CAC401
|
3.0
|
50.3
|
1.0
|
CE1
|
G:HIS230
|
3.1
|
24.9
|
1.0
|
OQ2
|
G:KCX169
|
3.2
|
26.0
|
1.0
|
CE1
|
G:HIS201
|
3.2
|
23.3
|
1.0
|
CG
|
G:HIS201
|
3.2
|
20.4
|
1.0
|
CB
|
G:HIS201
|
3.5
|
20.3
|
1.0
|
ZN
|
G:ZN402
|
3.8
|
22.8
|
1.0
|
NE1
|
G:TRP131
|
4.0
|
20.9
|
1.0
|
CG
|
G:HIS230
|
4.2
|
22.7
|
1.0
|
NZ
|
G:KCX169
|
4.2
|
23.4
|
1.0
|
ND1
|
G:HIS230
|
4.2
|
22.5
|
1.0
|
CE1
|
G:HIS55
|
4.3
|
19.5
|
1.0
|
NE2
|
G:HIS55
|
4.3
|
19.9
|
1.0
|
C2
|
G:CAC401
|
4.3
|
25.9
|
1.0
|
NE2
|
G:HIS201
|
4.4
|
31.6
|
1.0
|
CD2
|
G:HIS201
|
4.4
|
24.1
|
1.0
|
CA
|
G:HIS201
|
4.4
|
18.6
|
1.0
|
C1
|
G:CAC401
|
4.6
|
37.5
|
1.0
|
CD1
|
G:TRP131
|
4.7
|
17.1
|
1.0
|
CE
|
G:KCX169
|
4.7
|
23.7
|
1.0
|
OD2
|
G:ASP301
|
4.7
|
23.5
|
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
|