Zinc in PDB 5uck: Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products, PDB code: 5uck
was solved by
B.Jacques,
J.Sygusch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.19 /
1.78
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.384,
62.843,
64.754,
82.23,
75.97,
74.40
|
R / Rfree (%)
|
19.1 /
23.2
|
Other elements in 5uck:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
(pdb code 5uck). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products, PDB code: 5uck:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5uck
Go back to
Zinc Binding Sites List in 5uck
Zinc binding site 1 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:55.6
occ:0.70
|
HE1
|
A:HIS83
|
1.8
|
37.5
|
0.3
|
O
|
A:HOH513
|
2.4
|
27.1
|
1.0
|
NE2
|
A:HIS83
|
2.6
|
31.6
|
0.7
|
ND1
|
A:HIS210
|
2.6
|
13.7
|
0.7
|
CE1
|
A:HIS83
|
2.6
|
31.3
|
0.3
|
OE2
|
A:GLU134
|
2.8
|
43.7
|
1.0
|
OE1
|
A:GLU134
|
2.9
|
42.0
|
1.0
|
NE2
|
A:HIS83
|
3.1
|
31.9
|
0.3
|
CD
|
A:GLU134
|
3.2
|
39.6
|
1.0
|
CE1
|
A:HIS210
|
3.4
|
13.2
|
0.7
|
CE1
|
A:HIS83
|
3.4
|
32.5
|
0.7
|
HE1
|
A:HIS210
|
3.4
|
15.8
|
0.7
|
HE1
|
A:HIS83
|
3.4
|
39.0
|
0.7
|
NE2
|
A:HIS180
|
3.5
|
79.0
|
1.0
|
ND1
|
A:HIS210
|
3.5
|
14.2
|
0.3
|
CG
|
A:HIS210
|
3.6
|
15.0
|
0.7
|
CD2
|
A:HIS83
|
3.7
|
31.1
|
0.7
|
HB3
|
A:HIS210
|
3.7
|
20.7
|
0.3
|
HB3
|
A:HIS210
|
3.7
|
20.7
|
0.7
|
ZN
|
A:ZN403
|
3.8
|
38.2
|
0.3
|
HB2
|
A:HIS210
|
3.8
|
20.7
|
0.3
|
CG
|
A:HIS210
|
3.8
|
15.2
|
0.3
|
ND1
|
A:HIS83
|
3.8
|
30.6
|
0.3
|
HB2
|
A:HIS210
|
3.8
|
20.7
|
0.7
|
HD2
|
A:HIS83
|
3.9
|
37.2
|
0.7
|
HE1
|
A:MET102
|
3.9
|
35.5
|
1.0
|
CE1
|
A:HIS180
|
4.0
|
84.6
|
1.0
|
CB
|
A:HIS210
|
4.0
|
17.3
|
0.7
|
CB
|
A:HIS210
|
4.0
|
17.3
|
0.3
|
HD1
|
A:HIS83
|
4.1
|
36.7
|
0.3
|
CE1
|
A:HIS210
|
4.1
|
13.5
|
0.3
|
O
|
A:HOH505
|
4.2
|
26.5
|
1.0
|
O
|
A:HOH509
|
4.2
|
28.3
|
1.0
|
O
|
A:HOH629
|
4.3
|
30.3
|
1.0
|
OD2
|
A:ASP104
|
4.3
|
27.7
|
1.0
|
CD2
|
A:HIS180
|
4.3
|
85.8
|
1.0
|
CD2
|
A:HIS83
|
4.4
|
31.0
|
0.3
|
HE1
|
A:HIS210
|
4.5
|
16.2
|
0.3
|
CD2
|
A:HIS210
|
4.5
|
13.5
|
0.3
|
NE2
|
A:HIS210
|
4.5
|
13.2
|
0.7
|
ND1
|
A:HIS83
|
4.6
|
30.8
|
0.7
|
CD2
|
A:HIS210
|
4.7
|
12.9
|
0.7
|
CG
|
A:GLU134
|
4.7
|
29.8
|
1.0
|
NE2
|
A:HIS210
|
4.7
|
12.6
|
0.3
|
CG
|
A:HIS83
|
4.8
|
29.9
|
0.7
|
CG
|
A:HIS83
|
4.8
|
30.2
|
0.3
|
O
|
A:HOH503
|
4.9
|
40.0
|
1.0
|
CE
|
A:MET102
|
4.9
|
29.6
|
1.0
|
ND1
|
A:HIS180
|
4.9
|
85.6
|
1.0
|
HG3
|
A:GLU134
|
5.0
|
35.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5uck
Go back to
Zinc Binding Sites List in 5uck
Zinc binding site 2 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:38.2
occ:0.30
|
HE1
|
A:HIS83
|
1.3
|
39.0
|
0.7
|
NE2
|
A:HIS180
|
2.0
|
79.0
|
1.0
|
CE1
|
A:HIS83
|
2.0
|
32.5
|
0.7
|
NE2
|
A:HIS83
|
2.1
|
31.9
|
0.3
|
ND1
|
A:HIS210
|
2.3
|
14.2
|
0.3
|
O3
|
A:13P404
|
2.3
|
32.3
|
0.7
|
O1
|
A:G3H405
|
2.7
|
20.2
|
0.3
|
HB3
|
A:HIS210
|
2.7
|
20.7
|
0.7
|
O2
|
A:13P404
|
2.7
|
43.1
|
0.7
|
HB3
|
A:HIS210
|
2.7
|
20.7
|
0.3
|
HD2
|
A:HIS83
|
2.8
|
37.2
|
0.3
|
CD2
|
A:HIS83
|
2.8
|
31.0
|
0.3
|
HO3
|
A:13P404
|
2.9
|
38.7
|
0.7
|
NE2
|
A:HIS83
|
2.9
|
31.6
|
0.7
|
CD2
|
A:HIS180
|
2.9
|
85.8
|
1.0
|
ND1
|
A:HIS83
|
3.0
|
30.8
|
0.7
|
CE1
|
A:HIS180
|
3.0
|
84.6
|
1.0
|
HD1
|
A:HIS83
|
3.2
|
36.9
|
0.7
|
H11
|
A:G3H405
|
3.2
|
24.9
|
0.3
|
HD22
|
A:ASN253
|
3.2
|
24.6
|
1.0
|
CG
|
A:HIS210
|
3.2
|
15.2
|
0.3
|
CE1
|
A:HIS83
|
3.3
|
31.3
|
0.3
|
CG
|
A:HIS210
|
3.3
|
15.0
|
0.7
|
CE1
|
A:HIS210
|
3.3
|
13.5
|
0.3
|
CB
|
A:HIS210
|
3.4
|
17.3
|
0.3
|
CB
|
A:HIS210
|
3.4
|
17.3
|
0.7
|
ND1
|
A:HIS210
|
3.5
|
13.7
|
0.7
|
O1
|
A:G3H405
|
3.5
|
20.2
|
0.3
|
HE1
|
A:HIS210
|
3.5
|
16.2
|
0.3
|
C3
|
A:13P404
|
3.5
|
36.1
|
0.7
|
C2
|
A:13P404
|
3.5
|
40.4
|
0.7
|
HE1
|
A:HIS83
|
3.6
|
37.5
|
0.3
|
C1
|
A:G3H405
|
3.7
|
20.8
|
0.3
|
ZN
|
A:ZN402
|
3.8
|
55.6
|
0.7
|
C1
|
A:G3H405
|
3.8
|
20.3
|
0.3
|
CD2
|
A:HIS210
|
3.8
|
12.9
|
0.7
|
H
|
A:GLY211
|
3.9
|
29.1
|
1.0
|
ND2
|
A:ASN253
|
4.0
|
20.5
|
1.0
|
ND1
|
A:HIS180
|
4.0
|
85.6
|
1.0
|
CD2
|
A:HIS83
|
4.0
|
31.1
|
0.7
|
CE1
|
A:HIS210
|
4.0
|
13.2
|
0.7
|
CG
|
A:HIS180
|
4.0
|
89.9
|
1.0
|
CG
|
A:HIS83
|
4.0
|
30.2
|
0.3
|
CG
|
A:HIS83
|
4.1
|
29.9
|
0.7
|
H11
|
A:G3H405
|
4.1
|
24.3
|
0.3
|
HA
|
A:HIS210
|
4.1
|
23.8
|
0.7
|
HB2
|
A:HIS210
|
4.1
|
20.7
|
0.3
|
H32
|
A:13P404
|
4.1
|
43.3
|
0.7
|
HB2
|
A:HIS210
|
4.1
|
20.7
|
0.7
|
HA
|
A:HIS210
|
4.1
|
23.9
|
0.3
|
OD1
|
A:ASP82
|
4.2
|
24.2
|
1.0
|
HD2
|
A:HIS210
|
4.2
|
15.4
|
0.7
|
NE2
|
A:HIS210
|
4.2
|
13.2
|
0.7
|
H31
|
A:13P404
|
4.2
|
43.3
|
0.7
|
ND1
|
A:HIS83
|
4.2
|
30.6
|
0.3
|
HD21
|
A:ASN253
|
4.2
|
24.6
|
1.0
|
CA
|
A:HIS210
|
4.4
|
19.8
|
0.7
|
CA
|
A:HIS210
|
4.4
|
20.0
|
0.3
|
CD2
|
A:HIS210
|
4.4
|
13.5
|
0.3
|
NE2
|
A:HIS210
|
4.4
|
12.6
|
0.3
|
HB3
|
A:ASN253
|
4.5
|
14.5
|
1.0
|
N
|
A:GLY211
|
4.6
|
24.3
|
1.0
|
HE1
|
A:HIS210
|
4.6
|
15.8
|
0.7
|
HB2
|
A:ASN253
|
4.8
|
14.5
|
1.0
|
HE2
|
A:HIS210
|
4.8
|
15.8
|
0.7
|
HD2
|
A:HIS83
|
4.8
|
37.2
|
0.7
|
CG
|
A:ASN253
|
4.9
|
16.1
|
1.0
|
C1
|
A:13P404
|
5.0
|
39.8
|
0.7
|
OD2
|
A:ASP82
|
5.0
|
27.3
|
1.0
|
C
|
A:HIS210
|
5.0
|
23.1
|
0.3
|
C
|
A:HIS210
|
5.0
|
23.2
|
0.7
|
CB
|
A:ASN253
|
5.0
|
12.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5uck
Go back to
Zinc Binding Sites List in 5uck
Zinc binding site 3 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:48.4
occ:0.60
|
HE1
|
B:HIS83
|
2.1
|
34.8
|
0.4
|
OE2
|
B:GLU134
|
2.4
|
46.5
|
1.0
|
O
|
B:HOH530
|
2.5
|
28.9
|
1.0
|
ND1
|
B:HIS210
|
2.7
|
22.5
|
0.6
|
NE2
|
B:HIS83
|
2.8
|
29.9
|
0.6
|
CE1
|
B:HIS83
|
2.8
|
29.1
|
0.4
|
OE1
|
B:GLU134
|
2.8
|
46.3
|
1.0
|
CE1
|
B:HIS180
|
2.8
|
68.6
|
1.0
|
CD
|
B:GLU134
|
2.9
|
42.2
|
1.0
|
NE2
|
B:HIS180
|
3.2
|
65.0
|
1.0
|
NE2
|
B:HIS83
|
3.2
|
30.5
|
0.4
|
HE1
|
B:HIS83
|
3.3
|
36.8
|
0.6
|
CE1
|
B:HIS83
|
3.4
|
30.7
|
0.6
|
ND1
|
B:HIS210
|
3.5
|
24.9
|
0.4
|
HB3
|
B:HIS210
|
3.6
|
26.4
|
0.4
|
HB3
|
B:HIS210
|
3.6
|
26.5
|
0.6
|
CE1
|
B:HIS210
|
3.6
|
23.8
|
0.6
|
CG
|
B:HIS210
|
3.6
|
23.7
|
0.4
|
CG
|
B:HIS210
|
3.7
|
23.8
|
0.6
|
HB2
|
B:HIS210
|
3.7
|
26.5
|
0.6
|
HB2
|
B:HIS210
|
3.7
|
26.4
|
0.4
|
ZN
|
B:ZN403
|
3.7
|
32.1
|
0.4
|
HE1
|
B:HIS210
|
3.7
|
28.5
|
0.6
|
CB
|
B:HIS210
|
3.8
|
22.1
|
0.4
|
CB
|
B:HIS210
|
3.9
|
22.1
|
0.6
|
CD2
|
B:HIS83
|
4.0
|
29.3
|
0.6
|
HE1
|
B:MET102
|
4.0
|
34.7
|
1.0
|
CE1
|
B:HIS210
|
4.1
|
23.6
|
0.4
|
ND1
|
B:HIS180
|
4.1
|
68.9
|
1.0
|
ND1
|
B:HIS83
|
4.1
|
28.6
|
0.4
|
O
|
B:HOH507
|
4.2
|
23.2
|
1.0
|
HD2
|
B:HIS83
|
4.3
|
35.1
|
0.6
|
CD2
|
B:HIS210
|
4.3
|
24.0
|
0.4
|
CG
|
B:GLU134
|
4.4
|
30.7
|
1.0
|
HD1
|
B:HIS83
|
4.5
|
34.3
|
0.4
|
HE1
|
B:HIS210
|
4.5
|
28.3
|
0.4
|
CD2
|
B:HIS180
|
4.5
|
68.7
|
1.0
|
NE2
|
B:HIS210
|
4.5
|
24.3
|
0.4
|
CD2
|
B:HIS83
|
4.5
|
28.8
|
0.4
|
ND1
|
B:HIS83
|
4.7
|
28.9
|
0.6
|
HG3
|
B:GLU134
|
4.7
|
36.8
|
1.0
|
OD2
|
B:ASP104
|
4.7
|
27.3
|
1.0
|
NE2
|
B:HIS210
|
4.8
|
23.8
|
0.6
|
CD2
|
B:HIS210
|
4.8
|
23.2
|
0.6
|
HD2
|
B:HIS210
|
4.8
|
28.7
|
0.4
|
HG2
|
B:GLU134
|
4.9
|
36.8
|
1.0
|
CE
|
B:MET102
|
4.9
|
29.0
|
1.0
|
HB2
|
B:GLU134
|
5.0
|
25.3
|
1.0
|
CG
|
B:HIS180
|
5.0
|
69.5
|
1.0
|
CG
|
B:HIS83
|
5.0
|
28.0
|
0.6
|
CG
|
B:HIS83
|
5.0
|
28.0
|
0.4
|
|
Zinc binding site 4 out
of 4 in 5uck
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Zinc Binding Sites List in 5uck
Zinc binding site 4 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products
Mono view
Stereo pair view
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A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase of Helicobacter Pylori with Cleavage Products within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:32.1
occ:0.40
|
HE1
|
B:HIS83
|
1.2
|
36.8
|
0.6
|
HO3
|
B:13P404
|
1.8
|
36.0
|
0.7
|
CE1
|
B:HIS83
|
2.0
|
30.7
|
0.6
|
NE2
|
B:HIS180
|
2.0
|
65.0
|
1.0
|
NE2
|
B:HIS83
|
2.1
|
30.5
|
0.4
|
ND1
|
B:HIS210
|
2.1
|
24.9
|
0.4
|
O3
|
B:13P404
|
2.5
|
30.1
|
0.7
|
CD2
|
B:HIS180
|
2.6
|
68.7
|
1.0
|
O2
|
B:13P404
|
2.7
|
37.7
|
0.7
|
HD2
|
B:HIS83
|
2.7
|
34.5
|
0.4
|
CD2
|
B:HIS83
|
2.7
|
28.8
|
0.4
|
ND1
|
B:HIS83
|
2.9
|
28.9
|
0.6
|
NE2
|
B:HIS83
|
2.9
|
29.9
|
0.6
|
HB3
|
B:HIS210
|
2.9
|
26.5
|
0.6
|
CE1
|
B:HIS210
|
3.0
|
23.6
|
0.4
|
HB3
|
B:HIS210
|
3.0
|
26.4
|
0.4
|
HD1
|
B:HIS83
|
3.0
|
34.6
|
0.6
|
HE1
|
B:HIS210
|
3.1
|
28.3
|
0.4
|
CE1
|
B:HIS180
|
3.1
|
68.6
|
1.0
|
H11
|
B:G3H405
|
3.1
|
22.4
|
0.3
|
CG
|
B:HIS210
|
3.2
|
23.7
|
0.4
|
CE1
|
B:HIS83
|
3.2
|
29.1
|
0.4
|
HD22
|
B:ASN253
|
3.3
|
23.2
|
1.0
|
O1
|
B:G3H405
|
3.4
|
18.5
|
0.3
|
O1
|
B:G3H405
|
3.4
|
18.2
|
0.3
|
C2
|
B:13P404
|
3.4
|
36.4
|
0.7
|
ND1
|
B:HIS210
|
3.4
|
22.5
|
0.6
|
C3
|
B:13P404
|
3.5
|
32.6
|
0.7
|
CG
|
B:HIS210
|
3.5
|
23.8
|
0.6
|
CB
|
B:HIS210
|
3.6
|
22.1
|
0.4
|
CB
|
B:HIS210
|
3.6
|
22.1
|
0.6
|
C1
|
B:G3H405
|
3.6
|
18.7
|
0.3
|
HE1
|
B:HIS83
|
3.6
|
34.8
|
0.4
|
ZN
|
B:ZN402
|
3.7
|
48.4
|
0.6
|
CG
|
B:HIS180
|
3.9
|
69.5
|
1.0
|
H32
|
B:13P404
|
3.9
|
39.1
|
0.7
|
CG
|
B:HIS83
|
4.0
|
28.0
|
0.4
|
CD2
|
B:HIS83
|
4.0
|
29.3
|
0.6
|
CG
|
B:HIS83
|
4.0
|
28.0
|
0.6
|
ND1
|
B:HIS180
|
4.1
|
68.9
|
1.0
|
CE1
|
B:HIS210
|
4.1
|
23.8
|
0.6
|
ND2
|
B:ASN253
|
4.1
|
19.3
|
1.0
|
H
|
B:GLY211
|
4.1
|
31.4
|
1.0
|
CD2
|
B:HIS210
|
4.1
|
23.2
|
0.6
|
NE2
|
B:HIS210
|
4.2
|
24.3
|
0.4
|
ND1
|
B:HIS83
|
4.2
|
28.6
|
0.4
|
OD1
|
B:ASP82
|
4.2
|
26.6
|
1.0
|
HB2
|
B:HIS210
|
4.3
|
26.5
|
0.6
|
CD2
|
B:HIS210
|
4.3
|
24.0
|
0.4
|
HA
|
B:HIS210
|
4.3
|
26.6
|
0.4
|
HA
|
B:HIS210
|
4.3
|
26.7
|
0.6
|
HB2
|
B:HIS210
|
4.3
|
26.4
|
0.4
|
HD21
|
B:ASN253
|
4.3
|
23.2
|
1.0
|
H31
|
B:13P404
|
4.4
|
39.1
|
0.7
|
NE2
|
B:HIS210
|
4.4
|
23.8
|
0.6
|
HE1
|
B:HIS210
|
4.5
|
28.5
|
0.6
|
CA
|
B:HIS210
|
4.5
|
22.2
|
0.4
|
CA
|
B:HIS210
|
4.6
|
22.3
|
0.6
|
C1
|
B:G3H405
|
4.6
|
19.0
|
0.3
|
HD2
|
B:HIS210
|
4.6
|
27.8
|
0.6
|
HO2
|
B:G3H405
|
4.7
|
23.5
|
0.3
|
HB3
|
B:ASN253
|
4.7
|
18.7
|
1.0
|
N
|
B:GLY211
|
4.8
|
26.2
|
1.0
|
OD2
|
B:ASP82
|
4.8
|
28.8
|
1.0
|
HD2
|
B:HIS83
|
4.8
|
35.1
|
0.6
|
C1
|
B:13P404
|
4.9
|
37.9
|
0.7
|
HE2
|
B:HIS210
|
4.9
|
29.1
|
0.4
|
CG
|
B:ASP82
|
4.9
|
25.8
|
1.0
|
O2
|
B:G3H405
|
5.0
|
19.6
|
0.3
|
HD1
|
B:HIS83
|
5.0
|
34.3
|
0.4
|
|
Reference:
B.Jacques,
M.Coincon,
J.Sygusch.
Active Site Remodeling During the Catalytic Cycle in Metal-Dependent Fructose-1,6-Bisphosphate Aldolases. J. Biol. Chem. V. 293 7737 2018.
ISSN: ESSN 1083-351X
PubMed: 29593097
DOI: 10.1074/JBC.RA117.001098
Page generated: Mon Oct 28 09:21:25 2024
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