Zinc in PDB 5ucz: Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucz
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)
|
29.91 /
1.78
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.474,
86.133,
91.196,
90.00,
100.28,
90.00
|
|
R / Rfree (%)
|
18.4 /
22.7
|
Other elements in 5ucz:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
(pdb code 5ucz). 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 E149A Variant of Helicobacter Pylori with Dhap, PDB code: 5ucz:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5ucz
Go back to
Zinc Binding Sites List in 5ucz
Zinc binding site 1 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:47.4
occ:0.50
|
HE1
|
A:HIS83
|
1.9
|
89.6
|
0.5
|
|
ZN
|
A:ZN403
|
2.1
|
51.6
|
0.5
|
|
ND1
|
A:HIS210
|
2.5
|
55.8
|
0.5
|
|
OE2
|
A:GLU134
|
2.5
|
55.1
|
1.0
|
|
NE2
|
A:HIS83
|
2.6
|
78.6
|
0.5
|
|
CE1
|
A:HIS83
|
2.6
|
74.6
|
0.5
|
|
OE1
|
A:GLU134
|
2.7
|
71.1
|
1.0
|
|
HE1
|
A:HIS83
|
2.8
|
87.6
|
0.5
|
|
CD
|
A:GLU134
|
2.9
|
52.9
|
1.0
|
|
CE1
|
A:HIS83
|
3.0
|
73.0
|
0.5
|
|
NE2
|
A:HIS83
|
3.0
|
76.7
|
0.5
|
|
HB3
|
A:HIS210
|
3.2
|
49.6
|
0.5
|
|
HB3
|
A:HIS210
|
3.2
|
49.7
|
0.5
|
|
ND1
|
A:HIS210
|
3.2
|
44.5
|
0.5
|
|
CG
|
A:HIS210
|
3.4
|
42.4
|
0.5
|
|
CG
|
A:HIS210
|
3.4
|
41.9
|
0.5
|
|
HB2
|
A:HIS210
|
3.4
|
49.6
|
0.5
|
|
HB2
|
A:HIS210
|
3.5
|
49.7
|
0.5
|
|
CE1
|
A:HIS210
|
3.5
|
53.5
|
0.5
|
|
CB
|
A:HIS210
|
3.6
|
41.4
|
0.5
|
|
CB
|
A:HIS210
|
3.6
|
41.4
|
0.5
|
|
HE1
|
A:HIS210
|
3.7
|
64.2
|
0.5
|
|
ND1
|
A:HIS83
|
3.8
|
70.5
|
0.5
|
|
CD2
|
A:HIS83
|
3.8
|
67.5
|
0.5
|
|
NE2
|
A:HIS180
|
3.8
|
73.3
|
1.0
|
|
CE1
|
A:HIS210
|
3.9
|
47.2
|
0.5
|
|
CD2
|
A:HIS210
|
4.1
|
43.6
|
0.5
|
|
HE1
|
A:MET102
|
4.2
|
65.6
|
1.0
|
|
HD1
|
A:HIS83
|
4.2
|
84.5
|
0.5
|
|
HD2
|
A:HIS83
|
4.3
|
81.0
|
0.5
|
|
O
|
A:HOH501
|
4.3
|
37.2
|
1.0
|
|
ND1
|
A:HIS83
|
4.3
|
71.2
|
0.5
|
|
CD2
|
A:HIS180
|
4.3
|
74.7
|
1.0
|
|
HE1
|
A:HIS210
|
4.3
|
56.6
|
0.5
|
|
CD2
|
A:HIS83
|
4.4
|
67.6
|
0.5
|
|
NE2
|
A:HIS210
|
4.4
|
41.2
|
0.5
|
|
CG
|
A:GLU134
|
4.4
|
34.7
|
1.0
|
|
OD2
|
A:ASP104
|
4.5
|
45.6
|
1.0
|
|
CD2
|
A:HIS210
|
4.6
|
48.2
|
0.5
|
|
NE2
|
A:HIS210
|
4.6
|
40.7
|
0.5
|
|
CE1
|
A:HIS180
|
4.7
|
76.5
|
1.0
|
|
HG3
|
A:GLU134
|
4.7
|
41.7
|
1.0
|
|
HD2
|
A:HIS210
|
4.7
|
52.3
|
0.5
|
|
CG
|
A:HIS83
|
4.7
|
63.5
|
0.5
|
|
CG
|
A:HIS83
|
4.8
|
63.2
|
0.5
|
|
HB2
|
A:GLU134
|
4.9
|
36.9
|
1.0
|
|
HD1
|
A:HIS83
|
4.9
|
85.5
|
0.5
|
|
HE3
|
A:MET102
|
4.9
|
65.6
|
1.0
|
|
HG2
|
A:GLU134
|
4.9
|
41.7
|
1.0
|
|
CE
|
A:MET102
|
5.0
|
54.6
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5ucz
Go back to
Zinc Binding Sites List in 5ucz
Zinc binding site 2 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:51.6
occ:0.50
|
HE1
|
A:HIS83
|
1.3
|
87.6
|
0.5
|
|
NE2
|
A:HIS83
|
1.9
|
76.7
|
0.5
|
|
NE2
|
A:HIS180
|
1.9
|
73.3
|
1.0
|
|
CE1
|
A:HIS83
|
1.9
|
73.0
|
0.5
|
|
ZN
|
A:ZN402
|
2.1
|
47.4
|
0.5
|
|
HE1
|
A:HIS83
|
2.4
|
89.6
|
0.5
|
|
ND1
|
A:HIS210
|
2.4
|
44.5
|
0.5
|
|
NE2
|
A:HIS83
|
2.4
|
78.6
|
0.5
|
|
CE1
|
A:HIS83
|
2.4
|
74.6
|
0.5
|
|
HB3
|
A:HIS210
|
2.6
|
49.6
|
0.5
|
|
HB3
|
A:HIS210
|
2.6
|
49.7
|
0.5
|
|
ND1
|
A:HIS210
|
2.6
|
55.8
|
0.5
|
|
CE1
|
A:HIS180
|
2.7
|
76.5
|
1.0
|
|
CD2
|
A:HIS180
|
2.8
|
74.7
|
1.0
|
|
CG
|
A:HIS210
|
3.1
|
42.4
|
0.5
|
|
ND1
|
A:HIS83
|
3.2
|
71.2
|
0.5
|
|
CD2
|
A:HIS83
|
3.2
|
67.6
|
0.5
|
|
CG
|
A:HIS210
|
3.2
|
41.9
|
0.5
|
|
CB
|
A:HIS210
|
3.3
|
41.4
|
0.5
|
|
CB
|
A:HIS210
|
3.3
|
41.4
|
0.5
|
|
CE1
|
A:HIS210
|
3.4
|
47.2
|
0.5
|
|
O3
|
A:13P404
|
3.4
|
34.7
|
0.3
|
|
O3
|
A:13P404
|
3.4
|
34.8
|
0.3
|
|
HD1
|
A:HIS83
|
3.6
|
85.5
|
0.5
|
|
CE1
|
A:HIS210
|
3.6
|
53.5
|
0.5
|
|
HD2
|
A:HIS83
|
3.6
|
81.1
|
0.5
|
|
ND1
|
A:HIS83
|
3.7
|
70.5
|
0.5
|
|
HE1
|
A:HIS210
|
3.7
|
56.6
|
0.5
|
|
HB2
|
A:HIS210
|
3.7
|
49.6
|
0.5
|
|
HB2
|
A:HIS210
|
3.7
|
49.7
|
0.5
|
|
CD2
|
A:HIS83
|
3.7
|
67.5
|
0.5
|
|
O2
|
A:13P404
|
3.8
|
34.6
|
0.3
|
|
ND1
|
A:HIS180
|
3.8
|
72.2
|
1.0
|
|
O2
|
A:13P404
|
3.8
|
34.6
|
0.3
|
|
HO3
|
A:13P404
|
3.8
|
41.8
|
0.3
|
|
HO3
|
A:13P404
|
3.8
|
41.7
|
0.3
|
|
CG
|
A:HIS180
|
3.8
|
70.8
|
1.0
|
|
HE1
|
A:HIS210
|
3.9
|
64.2
|
0.5
|
|
CG
|
A:HIS83
|
4.0
|
63.2
|
0.5
|
|
CG
|
A:HIS83
|
4.0
|
63.5
|
0.5
|
|
CD2
|
A:HIS210
|
4.2
|
43.6
|
0.5
|
|
CD2
|
A:HIS210
|
4.3
|
48.2
|
0.5
|
|
HD22
|
A:ASN253
|
4.3
|
40.1
|
1.0
|
|
NE2
|
A:HIS210
|
4.3
|
41.2
|
0.5
|
|
HD1
|
A:HIS83
|
4.3
|
84.5
|
0.5
|
|
C3
|
A:13P404
|
4.4
|
34.7
|
0.3
|
|
C2
|
A:13P404
|
4.4
|
34.5
|
0.3
|
|
H
|
A:GLY211
|
4.4
|
55.7
|
1.0
|
|
HD2
|
A:HIS83
|
4.4
|
81.0
|
0.5
|
|
OE1
|
A:GLU134
|
4.4
|
71.1
|
1.0
|
|
NE2
|
A:HIS210
|
4.4
|
40.7
|
0.5
|
|
C3
|
A:13P404
|
4.5
|
34.7
|
0.3
|
|
C2
|
A:13P404
|
4.5
|
34.6
|
0.3
|
|
CA
|
A:HIS210
|
4.5
|
30.8
|
0.5
|
|
CA
|
A:HIS210
|
4.5
|
30.8
|
0.5
|
|
OE2
|
A:GLU134
|
4.5
|
55.1
|
1.0
|
|
HA
|
A:HIS210
|
4.6
|
37.0
|
0.5
|
|
HA
|
A:HIS210
|
4.6
|
37.0
|
0.5
|
|
H32
|
A:13P404
|
4.6
|
41.6
|
0.3
|
|
H32
|
A:13P404
|
4.7
|
41.7
|
0.3
|
|
N
|
A:GLY211
|
4.8
|
46.4
|
1.0
|
|
CD
|
A:GLU134
|
4.9
|
52.9
|
1.0
|
|
ND2
|
A:ASN253
|
5.0
|
33.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5ucz
Go back to
Zinc Binding Sites List in 5ucz
Zinc binding site 3 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:43.4
occ:0.50
|
ZN
|
B:ZN403
|
1.2
|
45.6
|
0.5
|
|
O
|
B:HOH503
|
1.9
|
26.2
|
1.0
|
|
NE2
|
B:HIS83
|
2.0
|
32.5
|
1.0
|
|
NE2
|
B:HIS180
|
2.1
|
46.8
|
1.0
|
|
ND1
|
B:HIS210
|
2.4
|
26.4
|
1.0
|
|
CE1
|
B:HIS83
|
2.7
|
39.4
|
1.0
|
|
HE1
|
B:HIS83
|
2.7
|
47.2
|
1.0
|
|
CE1
|
B:HIS180
|
2.8
|
55.0
|
1.0
|
|
HB3
|
B:HIS210
|
2.8
|
34.9
|
1.0
|
|
HE1
|
B:HIS180
|
2.8
|
66.0
|
1.0
|
|
CD2
|
B:HIS83
|
3.2
|
23.8
|
1.0
|
|
CG
|
B:HIS210
|
3.2
|
19.8
|
1.0
|
|
CD2
|
B:HIS180
|
3.2
|
50.1
|
1.0
|
|
CE1
|
B:HIS210
|
3.4
|
24.2
|
1.0
|
|
CB
|
B:HIS210
|
3.4
|
29.1
|
1.0
|
|
O
|
B:HOH642
|
3.5
|
43.5
|
1.0
|
|
HD2
|
B:HIS180
|
3.5
|
60.1
|
1.0
|
|
HD2
|
B:HIS83
|
3.5
|
28.6
|
1.0
|
|
HE1
|
B:HIS210
|
3.6
|
29.0
|
1.0
|
|
O3
|
B:13P404
|
3.7
|
29.8
|
0.4
|
|
HB2
|
B:HIS210
|
3.8
|
34.9
|
1.0
|
|
O3
|
B:13P404
|
3.8
|
29.9
|
0.4
|
|
ND1
|
B:HIS83
|
3.9
|
38.6
|
1.0
|
|
ND1
|
B:HIS180
|
4.0
|
57.8
|
1.0
|
|
HO3
|
B:13P404
|
4.0
|
35.7
|
0.4
|
|
OE2
|
B:GLU134
|
4.0
|
41.1
|
1.0
|
|
O2
|
B:13P404
|
4.1
|
29.4
|
0.4
|
|
CG
|
B:HIS83
|
4.2
|
41.2
|
1.0
|
|
CG
|
B:HIS180
|
4.2
|
53.0
|
1.0
|
|
O2
|
B:13P404
|
4.2
|
29.9
|
0.4
|
|
HO3
|
B:13P404
|
4.3
|
35.9
|
0.4
|
|
CD2
|
B:HIS210
|
4.3
|
30.7
|
1.0
|
|
NE2
|
B:HIS210
|
4.4
|
22.9
|
1.0
|
|
HE1
|
B:MET102
|
4.4
|
44.9
|
1.0
|
|
HD22
|
B:ASN253
|
4.6
|
30.7
|
1.0
|
|
HD1
|
B:HIS83
|
4.6
|
46.3
|
1.0
|
|
HD1
|
B:HIS180
|
4.7
|
69.3
|
1.0
|
|
H
|
B:GLY211
|
4.7
|
26.4
|
1.0
|
|
CA
|
B:HIS210
|
4.7
|
29.1
|
1.0
|
|
OE1
|
B:GLU134
|
4.8
|
53.6
|
1.0
|
|
C3
|
B:13P404
|
4.8
|
29.6
|
0.4
|
|
CD
|
B:GLU134
|
4.8
|
38.8
|
1.0
|
|
HA
|
B:HIS210
|
4.8
|
34.9
|
1.0
|
|
C2
|
B:13P404
|
4.8
|
29.3
|
0.4
|
|
C2
|
B:13P404
|
4.8
|
29.7
|
0.4
|
|
C3
|
B:13P404
|
4.9
|
29.9
|
0.4
|
|
Zinc binding site 4 out
of 4 in 5ucz
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Zinc Binding Sites List in 5ucz
Zinc binding site 4 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase E149A Variant of Helicobacter Pylori with Dhap
 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 E149A Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:45.6
occ:0.50
|
ZN
|
B:ZN402
|
1.2
|
43.4
|
0.5
|
|
NE2
|
B:HIS180
|
1.9
|
46.8
|
1.0
|
|
NE2
|
B:HIS83
|
2.1
|
32.5
|
1.0
|
|
ND1
|
B:HIS210
|
2.1
|
26.4
|
1.0
|
|
HE1
|
B:HIS180
|
2.2
|
66.0
|
1.0
|
|
CE1
|
B:HIS180
|
2.3
|
55.0
|
1.0
|
|
O3
|
B:13P404
|
2.5
|
29.8
|
0.4
|
|
O3
|
B:13P404
|
2.6
|
29.9
|
0.4
|
|
HB3
|
B:HIS210
|
2.8
|
34.9
|
1.0
|
|
CD2
|
B:HIS83
|
2.8
|
23.8
|
1.0
|
|
HO3
|
B:13P404
|
2.9
|
35.7
|
0.4
|
|
HD2
|
B:HIS83
|
2.9
|
28.6
|
1.0
|
|
CE1
|
B:HIS210
|
3.0
|
24.2
|
1.0
|
|
O
|
B:HOH503
|
3.1
|
26.2
|
1.0
|
|
HO3
|
B:13P404
|
3.1
|
35.9
|
0.4
|
|
CG
|
B:HIS210
|
3.1
|
19.8
|
1.0
|
|
O2
|
B:13P404
|
3.2
|
29.4
|
0.4
|
|
CE1
|
B:HIS83
|
3.2
|
39.4
|
1.0
|
|
HE1
|
B:HIS210
|
3.2
|
29.0
|
1.0
|
|
CD2
|
B:HIS180
|
3.3
|
50.1
|
1.0
|
|
O2
|
B:13P404
|
3.3
|
29.9
|
0.4
|
|
CB
|
B:HIS210
|
3.4
|
29.1
|
1.0
|
|
HE1
|
B:HIS83
|
3.5
|
47.2
|
1.0
|
|
HD22
|
B:ASN253
|
3.5
|
30.7
|
1.0
|
|
ND1
|
B:HIS180
|
3.6
|
57.8
|
1.0
|
|
C3
|
B:13P404
|
3.6
|
29.6
|
0.4
|
|
C3
|
B:13P404
|
3.7
|
29.9
|
0.4
|
|
HD2
|
B:HIS180
|
3.8
|
60.1
|
1.0
|
|
C2
|
B:13P404
|
3.8
|
29.3
|
0.4
|
|
C2
|
B:13P404
|
3.8
|
29.7
|
0.4
|
|
H32
|
B:13P404
|
4.0
|
35.5
|
0.4
|
|
HB2
|
B:HIS210
|
4.1
|
34.9
|
1.0
|
|
H32
|
B:13P404
|
4.1
|
35.8
|
0.4
|
|
CG
|
B:HIS83
|
4.1
|
41.2
|
1.0
|
|
CG
|
B:HIS180
|
4.1
|
53.0
|
1.0
|
|
NE2
|
B:HIS210
|
4.2
|
22.9
|
1.0
|
|
ND1
|
B:HIS83
|
4.2
|
38.6
|
1.0
|
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CD2
|
B:HIS210
|
4.2
|
30.7
|
1.0
|
|
H
|
B:GLY211
|
4.2
|
26.4
|
1.0
|
|
HD1
|
B:HIS180
|
4.3
|
69.3
|
1.0
|
|
ND2
|
B:ASN253
|
4.3
|
25.6
|
1.0
|
|
HA
|
B:HIS210
|
4.4
|
34.9
|
1.0
|
|
H31
|
B:13P404
|
4.5
|
35.5
|
0.4
|
|
OD1
|
B:ASP82
|
4.5
|
20.7
|
1.0
|
|
HD21
|
B:ASN253
|
4.5
|
30.7
|
1.0
|
|
CA
|
B:HIS210
|
4.5
|
29.1
|
1.0
|
|
O
|
B:HOH642
|
4.6
|
43.5
|
1.0
|
|
H31
|
B:13P404
|
4.6
|
35.8
|
0.4
|
|
HE1
|
B:MET102
|
4.8
|
44.9
|
1.0
|
|
H12
|
B:13P404
|
4.8
|
34.9
|
0.4
|
|
N
|
B:GLY211
|
4.9
|
22.0
|
1.0
|
|
HE2
|
B:HIS210
|
4.9
|
27.5
|
1.0
|
|
C1
|
B:13P404
|
5.0
|
29.1
|
0.4
|
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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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