Zinc in PDB 4xd5: Phosphotriesterase Variant R2
Protein crystallography data
The structure of Phosphotriesterase Variant R2, PDB code: 4xd5
was solved by
E.Campbell,
M.Kaltenbach,
N.Tokuriki,
C.J.Jackson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.19 /
1.85
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.704,
85.869,
88.382,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.1 /
20.4
|
Other elements in 4xd5:
The structure of Phosphotriesterase Variant R2 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant R2
(pdb code 4xd5). 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 R2, PDB code: 4xd5:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4xd5
Go back to
Zinc Binding Sites List in 4xd5
Zinc binding site 1 out
of 4 in the Phosphotriesterase Variant R2
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2401
b:13.8
occ:1.00
|
O1
|
A:CAC2403
|
2.0
|
9.9
|
0.7
|
NE2
|
A:HIS57
|
2.1
|
12.5
|
1.0
|
NE2
|
A:HIS55
|
2.1
|
10.8
|
1.0
|
OD1
|
A:ASP301
|
2.2
|
9.4
|
1.0
|
OQ2
|
A:KCX169
|
2.2
|
14.6
|
1.0
|
CD2
|
A:HIS55
|
3.0
|
10.1
|
1.0
|
CG
|
A:ASP301
|
3.0
|
10.3
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
10.7
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
10.9
|
1.0
|
CX
|
A:KCX169
|
3.1
|
17.0
|
1.0
|
CE1
|
A:HIS55
|
3.1
|
10.7
|
1.0
|
OD2
|
A:ASP301
|
3.3
|
15.4
|
1.0
|
AS
|
A:CAC2403
|
3.3
|
26.0
|
0.7
|
OQ1
|
A:KCX169
|
3.5
|
14.3
|
1.0
|
ZN
|
A:ZN2402
|
3.7
|
14.2
|
0.8
|
C2
|
A:CAC2403
|
3.8
|
20.5
|
0.7
|
CG2
|
A:VAL101
|
4.1
|
10.0
|
1.0
|
NZ
|
A:KCX169
|
4.1
|
16.2
|
1.0
|
ND1
|
A:HIS57
|
4.2
|
8.6
|
1.0
|
CG
|
A:HIS55
|
4.2
|
11.6
|
1.0
|
CE1
|
A:HIS230
|
4.2
|
16.2
|
1.0
|
ND1
|
A:HIS55
|
4.2
|
9.2
|
1.0
|
CG
|
A:HIS57
|
4.2
|
8.8
|
1.0
|
O2
|
A:CAC2403
|
4.3
|
18.1
|
0.7
|
CB
|
A:ASP301
|
4.4
|
10.5
|
1.0
|
NE2
|
A:HIS230
|
4.5
|
12.7
|
1.0
|
C1
|
A:CAC2403
|
4.8
|
26.3
|
0.7
|
CA
|
A:ASP301
|
4.8
|
10.1
|
1.0
|
O
|
A:HOH2650
|
4.9
|
33.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 4xd5
Go back to
Zinc Binding Sites List in 4xd5
Zinc binding site 2 out
of 4 in the Phosphotriesterase Variant R2
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2402
b:14.2
occ:0.77
|
OQ1
|
A:KCX169
|
2.0
|
14.3
|
1.0
|
NE2
|
A:HIS230
|
2.1
|
12.7
|
1.0
|
O2
|
A:CAC2403
|
2.1
|
18.1
|
0.7
|
ND1
|
A:HIS201
|
2.2
|
19.0
|
1.0
|
O1
|
A:CAC2403
|
2.7
|
9.9
|
0.7
|
CX
|
A:KCX169
|
3.0
|
17.0
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
16.2
|
1.0
|
AS
|
A:CAC2403
|
3.1
|
26.0
|
0.7
|
CD2
|
A:HIS230
|
3.1
|
17.3
|
1.0
|
CE1
|
A:HIS201
|
3.1
|
28.6
|
1.0
|
CG
|
A:HIS201
|
3.2
|
23.0
|
1.0
|
NH2
|
A:ARG254
|
3.2
|
26.5
|
0.3
|
OQ2
|
A:KCX169
|
3.3
|
14.6
|
1.0
|
CB
|
A:HIS201
|
3.5
|
20.3
|
1.0
|
ZN
|
A:ZN2401
|
3.7
|
13.8
|
1.0
|
NE1
|
A:TRP131
|
3.9
|
21.5
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
16.2
|
1.0
|
CE1
|
A:HIS55
|
4.2
|
10.7
|
1.0
|
ND1
|
A:HIS230
|
4.2
|
15.7
|
1.0
|
CZ
|
A:ARG254
|
4.2
|
23.5
|
0.3
|
CG
|
A:HIS230
|
4.2
|
20.6
|
1.0
|
NE2
|
A:HIS55
|
4.2
|
10.8
|
1.0
|
NE2
|
A:HIS201
|
4.3
|
23.7
|
1.0
|
CD2
|
A:HIS201
|
4.3
|
18.1
|
1.0
|
CA
|
A:HIS201
|
4.4
|
15.8
|
1.0
|
OD2
|
A:ASP301
|
4.5
|
15.4
|
1.0
|
C2
|
A:CAC2403
|
4.5
|
20.5
|
0.7
|
C1
|
A:CAC2403
|
4.5
|
26.3
|
0.7
|
CD1
|
A:TRP131
|
4.6
|
14.8
|
1.0
|
CE
|
A:KCX169
|
4.6
|
17.7
|
1.0
|
NE
|
A:ARG254
|
4.7
|
20.1
|
0.3
|
|
Zinc binding site 3 out
of 4 in 4xd5
Go back to
Zinc Binding Sites List in 4xd5
Zinc binding site 3 out
of 4 in the Phosphotriesterase Variant R2
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn402
b:14.9
occ:0.95
|
O1
|
G:CAC401
|
1.9
|
17.9
|
0.8
|
NE2
|
G:HIS57
|
2.1
|
12.5
|
1.0
|
OQ2
|
G:KCX169
|
2.1
|
16.1
|
1.0
|
NE2
|
G:HIS55
|
2.1
|
19.6
|
1.0
|
OD1
|
G:ASP301
|
2.2
|
15.8
|
1.0
|
CD2
|
G:HIS55
|
3.0
|
18.2
|
1.0
|
CE1
|
G:HIS57
|
3.0
|
15.3
|
1.0
|
CD2
|
G:HIS57
|
3.1
|
14.6
|
1.0
|
CG
|
G:ASP301
|
3.1
|
18.4
|
1.0
|
CX
|
G:KCX169
|
3.1
|
19.8
|
1.0
|
CE1
|
G:HIS55
|
3.2
|
16.1
|
1.0
|
AS
|
G:CAC401
|
3.3
|
26.3
|
0.8
|
OD2
|
G:ASP301
|
3.4
|
23.6
|
1.0
|
OQ1
|
G:KCX169
|
3.7
|
17.1
|
1.0
|
ZN
|
G:ZN403
|
3.8
|
18.0
|
0.9
|
C2
|
G:CAC401
|
3.9
|
19.7
|
0.8
|
CG2
|
G:VAL101
|
4.1
|
12.1
|
1.0
|
CE1
|
G:HIS230
|
4.1
|
19.8
|
1.0
|
NZ
|
G:KCX169
|
4.1
|
15.8
|
1.0
|
ND1
|
G:HIS57
|
4.2
|
12.3
|
1.0
|
CG
|
G:HIS55
|
4.2
|
15.1
|
1.0
|
CG
|
G:HIS57
|
4.2
|
16.1
|
1.0
|
ND1
|
G:HIS55
|
4.2
|
18.0
|
1.0
|
O2
|
G:CAC401
|
4.2
|
22.3
|
0.8
|
NE2
|
G:HIS230
|
4.3
|
18.7
|
1.0
|
CB
|
G:ASP301
|
4.4
|
13.7
|
1.0
|
C1
|
G:CAC401
|
4.8
|
26.7
|
0.8
|
CA
|
G:ASP301
|
4.9
|
14.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4xd5
Go back to
Zinc Binding Sites List in 4xd5
Zinc binding site 4 out
of 4 in the Phosphotriesterase Variant R2
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant R2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn403
b:18.0
occ:0.87
|
OQ1
|
G:KCX169
|
2.0
|
17.1
|
1.0
|
ND1
|
G:HIS201
|
2.1
|
15.1
|
1.0
|
NE2
|
G:HIS230
|
2.1
|
18.7
|
1.0
|
O2
|
G:CAC401
|
2.2
|
22.3
|
0.8
|
O1
|
G:CAC401
|
2.8
|
17.9
|
0.8
|
CX
|
G:KCX169
|
2.9
|
19.8
|
1.0
|
CD2
|
G:HIS230
|
3.0
|
21.6
|
1.0
|
CE1
|
G:HIS201
|
3.0
|
25.4
|
1.0
|
AS
|
G:CAC401
|
3.1
|
26.3
|
0.8
|
CG
|
G:HIS201
|
3.2
|
15.6
|
1.0
|
OQ2
|
G:KCX169
|
3.2
|
16.1
|
1.0
|
CE1
|
G:HIS230
|
3.2
|
19.8
|
1.0
|
NH2
|
G:ARG254
|
3.4
|
25.9
|
0.3
|
CB
|
G:HIS201
|
3.5
|
11.8
|
1.0
|
ZN
|
G:ZN402
|
3.8
|
14.9
|
0.9
|
NE1
|
G:TRP131
|
3.9
|
18.6
|
1.0
|
NZ
|
G:KCX169
|
4.1
|
15.8
|
1.0
|
NE2
|
G:HIS201
|
4.2
|
21.2
|
1.0
|
CG
|
G:HIS230
|
4.2
|
18.5
|
1.0
|
CD2
|
G:HIS201
|
4.2
|
22.3
|
1.0
|
ND1
|
G:HIS230
|
4.3
|
17.3
|
1.0
|
CE1
|
G:HIS55
|
4.3
|
16.1
|
1.0
|
NE2
|
G:HIS55
|
4.3
|
19.6
|
1.0
|
C1
|
G:CAC401
|
4.4
|
26.7
|
0.8
|
CZ
|
G:ARG254
|
4.4
|
25.9
|
0.3
|
CA
|
G:HIS201
|
4.4
|
17.0
|
1.0
|
C2
|
G:CAC401
|
4.6
|
19.7
|
0.8
|
CD1
|
G:TRP131
|
4.6
|
16.7
|
1.0
|
CE
|
G:KCX169
|
4.6
|
17.7
|
1.0
|
OD2
|
G:ASP301
|
4.7
|
23.6
|
1.0
|
NE
|
G:ARG254
|
4.7
|
22.3
|
0.3
|
|
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
|