Zinc in PDB 4xaf: Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
Protein crystallography data
The structure of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes, PDB code: 4xaf
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)
|
35.71 /
1.66
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.687,
85.733,
88.380,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.9 /
22
|
Other elements in 4xaf:
The structure of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
(pdb code 4xaf). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes, PDB code: 4xaf:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 4xaf
Go back to
Zinc Binding Sites List in 4xaf
Zinc binding site 1 out
of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2401
b:19.5
occ:0.60
|
O1
|
A:CAC2403
|
2.0
|
34.4
|
0.7
|
NE2
|
A:HIS57
|
2.1
|
18.9
|
1.0
|
OD1
|
A:ASP301
|
2.1
|
21.9
|
1.0
|
OQ2
|
A:KCX169
|
2.3
|
32.1
|
1.0
|
NE2
|
A:HIS55
|
2.3
|
21.3
|
1.0
|
CE1
|
A:HIS57
|
3.0
|
19.4
|
1.0
|
CG
|
A:ASP301
|
3.0
|
23.0
|
1.0
|
CD2
|
A:HIS55
|
3.1
|
19.9
|
1.0
|
CD2
|
A:HIS57
|
3.1
|
14.1
|
1.0
|
CX
|
A:KCX169
|
3.2
|
42.7
|
1.0
|
OD2
|
A:ASP301
|
3.3
|
27.6
|
1.0
|
AS
|
A:CAC2403
|
3.4
|
56.5
|
0.7
|
CE1
|
A:HIS55
|
3.4
|
18.2
|
1.0
|
OQ1
|
A:KCX169
|
3.7
|
33.8
|
1.0
|
ZN
|
A:ZN2402
|
3.9
|
21.9
|
0.3
|
C2
|
A:CAC2403
|
4.0
|
35.3
|
0.7
|
O2
|
A:CAC2403
|
4.1
|
35.4
|
0.7
|
CG2
|
A:VAL101
|
4.1
|
16.1
|
1.0
|
ND1
|
A:HIS57
|
4.1
|
18.6
|
1.0
|
NZ
|
A:KCX169
|
4.2
|
31.5
|
1.0
|
CG
|
A:HIS57
|
4.2
|
14.5
|
1.0
|
CE1
|
A:HIS230
|
4.3
|
35.2
|
1.0
|
CG
|
A:HIS55
|
4.3
|
19.9
|
1.0
|
CB
|
A:ASP301
|
4.4
|
20.1
|
1.0
|
ND1
|
A:HIS55
|
4.4
|
23.6
|
1.0
|
O
|
A:HOH2643
|
4.6
|
42.2
|
1.0
|
NE2
|
A:HIS230
|
4.6
|
29.5
|
1.0
|
CA
|
A:ASP301
|
4.8
|
18.6
|
1.0
|
C1
|
A:CAC2403
|
5.0
|
48.7
|
0.7
|
|
Zinc binding site 2 out
of 4 in 4xaf
Go back to
Zinc Binding Sites List in 4xaf
Zinc binding site 2 out
of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2402
b:21.9
occ:0.31
|
OQ1
|
A:KCX169
|
1.8
|
33.8
|
1.0
|
NE2
|
A:HIS230
|
2.1
|
29.5
|
1.0
|
ND1
|
A:HIS201
|
2.2
|
34.2
|
1.0
|
O2
|
A:CAC2403
|
2.3
|
35.4
|
0.7
|
CX
|
A:KCX169
|
2.9
|
42.7
|
1.0
|
CE1
|
A:HIS230
|
3.0
|
35.2
|
1.0
|
O1
|
A:CAC2403
|
3.1
|
34.4
|
0.7
|
CG
|
A:HIS201
|
3.1
|
41.7
|
1.0
|
CE1
|
A:HIS201
|
3.1
|
50.2
|
1.0
|
CD2
|
A:HIS230
|
3.2
|
46.8
|
1.0
|
OQ2
|
A:KCX169
|
3.3
|
32.1
|
1.0
|
NH2
|
A:ARG254
|
3.3
|
43.3
|
0.4
|
CB
|
A:HIS201
|
3.4
|
35.5
|
1.0
|
AS
|
A:CAC2403
|
3.4
|
56.5
|
0.7
|
ZN
|
A:ZN2401
|
3.9
|
19.5
|
0.6
|
NE1
|
A:TRP131
|
3.9
|
30.6
|
1.0
|
NZ
|
A:KCX169
|
4.1
|
31.5
|
1.0
|
ND1
|
A:HIS230
|
4.2
|
46.2
|
1.0
|
NE2
|
A:HIS201
|
4.2
|
41.5
|
1.0
|
CD2
|
A:HIS201
|
4.2
|
44.0
|
1.0
|
CZ
|
A:ARG254
|
4.3
|
44.4
|
0.4
|
CG
|
A:HIS230
|
4.3
|
58.0
|
1.0
|
O
|
A:HOH2621
|
4.3
|
40.8
|
1.0
|
NE2
|
A:HIS55
|
4.4
|
21.3
|
1.0
|
CE1
|
A:HIS55
|
4.5
|
18.2
|
1.0
|
CD1
|
A:TRP131
|
4.5
|
21.9
|
1.0
|
OD2
|
A:ASP301
|
4.5
|
27.6
|
1.0
|
CA
|
A:HIS201
|
4.6
|
28.2
|
1.0
|
C1
|
A:CAC2403
|
4.7
|
48.7
|
0.7
|
NE
|
A:ARG254
|
4.7
|
38.9
|
0.4
|
CE
|
A:KCX169
|
4.7
|
22.8
|
1.0
|
C2
|
A:CAC2403
|
4.9
|
35.3
|
0.7
|
|
Zinc binding site 3 out
of 4 in 4xaf
Go back to
Zinc Binding Sites List in 4xaf
Zinc binding site 3 out
of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn402
b:18.9
occ:0.67
|
O1
|
G:CAC401
|
1.9
|
31.2
|
0.7
|
NE2
|
G:HIS57
|
2.1
|
15.7
|
1.0
|
OQ2
|
G:KCX169
|
2.2
|
30.4
|
1.0
|
OD1
|
G:ASP301
|
2.2
|
21.4
|
1.0
|
NE2
|
G:HIS55
|
2.2
|
21.8
|
1.0
|
CE1
|
G:HIS57
|
3.1
|
22.9
|
1.0
|
CG
|
G:ASP301
|
3.1
|
22.2
|
1.0
|
CD2
|
G:HIS55
|
3.1
|
21.6
|
1.0
|
CD2
|
G:HIS57
|
3.1
|
21.8
|
1.0
|
CX
|
G:KCX169
|
3.2
|
39.6
|
1.0
|
CE1
|
G:HIS55
|
3.2
|
19.9
|
1.0
|
AS
|
G:CAC401
|
3.4
|
39.1
|
0.7
|
OD2
|
G:ASP301
|
3.4
|
22.1
|
1.0
|
OQ1
|
G:KCX169
|
3.7
|
31.0
|
1.0
|
ZN
|
G:ZN403
|
3.8
|
20.5
|
0.4
|
CE1
|
G:HIS230
|
4.0
|
24.3
|
1.0
|
C2
|
G:CAC401
|
4.1
|
30.0
|
0.7
|
O2
|
G:CAC401
|
4.1
|
28.3
|
0.7
|
CG2
|
G:VAL101
|
4.2
|
18.0
|
1.0
|
ND1
|
G:HIS57
|
4.2
|
18.4
|
1.0
|
NZ
|
G:KCX169
|
4.2
|
32.8
|
1.0
|
NE2
|
G:HIS230
|
4.2
|
27.4
|
1.0
|
CG
|
G:HIS57
|
4.2
|
20.1
|
1.0
|
CG
|
G:HIS55
|
4.3
|
20.0
|
1.0
|
ND1
|
G:HIS55
|
4.3
|
20.8
|
1.0
|
CB
|
G:ASP301
|
4.4
|
15.0
|
1.0
|
C1
|
G:CAC401
|
4.9
|
41.9
|
0.7
|
CA
|
G:ASP301
|
4.9
|
14.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 4xaf
Go back to
Zinc Binding Sites List in 4xaf
Zinc binding site 4 out
of 4 in the Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cycles of Destabilization and Repair Underlie Evolutionary Transitions in Enzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn403
b:20.5
occ:0.44
|
OQ1
|
G:KCX169
|
2.0
|
31.0
|
1.0
|
NE2
|
G:HIS230
|
2.1
|
27.4
|
1.0
|
ND1
|
G:HIS201
|
2.1
|
30.8
|
1.0
|
O2
|
G:CAC401
|
2.2
|
28.3
|
0.7
|
O1
|
G:CAC401
|
2.9
|
31.2
|
0.7
|
CD2
|
G:HIS230
|
2.9
|
27.9
|
1.0
|
CX
|
G:KCX169
|
3.0
|
39.6
|
1.0
|
CE1
|
G:HIS201
|
3.0
|
34.1
|
1.0
|
CG
|
G:HIS201
|
3.1
|
28.4
|
1.0
|
CE1
|
G:HIS230
|
3.2
|
24.3
|
1.0
|
AS
|
G:CAC401
|
3.2
|
39.1
|
0.7
|
OQ2
|
G:KCX169
|
3.2
|
30.4
|
1.0
|
NH2
|
G:ARG254
|
3.3
|
28.1
|
0.4
|
CB
|
G:HIS201
|
3.5
|
27.1
|
1.0
|
ZN
|
G:ZN402
|
3.8
|
18.9
|
0.7
|
NE2
|
G:HIS201
|
4.1
|
46.3
|
1.0
|
NE1
|
G:TRP131
|
4.1
|
24.7
|
1.0
|
CG
|
G:HIS230
|
4.1
|
23.8
|
1.0
|
CZ
|
G:ARG254
|
4.2
|
25.6
|
0.4
|
NZ
|
G:KCX169
|
4.2
|
32.8
|
1.0
|
CD2
|
G:HIS201
|
4.2
|
41.6
|
1.0
|
ND1
|
G:HIS230
|
4.2
|
26.4
|
1.0
|
CE1
|
G:HIS55
|
4.3
|
19.9
|
1.0
|
NE2
|
G:HIS55
|
4.3
|
21.8
|
1.0
|
C1
|
G:CAC401
|
4.4
|
41.9
|
0.7
|
NE
|
G:ARG254
|
4.6
|
27.1
|
0.4
|
OD2
|
G:ASP301
|
4.6
|
22.1
|
1.0
|
CA
|
G:HIS201
|
4.6
|
24.6
|
1.0
|
CE
|
G:KCX169
|
4.7
|
26.4
|
1.0
|
CD1
|
G:TRP131
|
4.7
|
20.8
|
1.0
|
C2
|
G:CAC401
|
4.8
|
30.0
|
0.7
|
|
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 10:21:51 2024
|