Zinc in PDB 5ud3: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp, PDB code: 5ud3
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)
|
37.07 /
1.44
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.480,
64.904,
62.706,
82.10,
74.17,
75.83
|
|
R / Rfree (%)
|
13.5 /
16.4
|
Other elements in 5ud3:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
(pdb code 5ud3). 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 H180Q Variant of Helicobacter Pylori with Fbp, PDB code: 5ud3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5ud3
Go back to
Zinc Binding Sites List in 5ud3
Zinc binding site 1 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
 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 H180Q Variant of Helicobacter Pylori with Fbp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:47.8
occ:0.59
|
O
|
A:HOH573
|
1.2
|
30.1
|
0.4
|
|
HE1
|
A:HIS83
|
1.9
|
22.2
|
0.1
|
|
O
|
A:HOH511
|
1.9
|
20.4
|
0.6
|
|
ZN
|
A:ZN403
|
2.0
|
66.7
|
0.4
|
|
OE1
|
A:GLU134
|
2.5
|
24.0
|
0.6
|
|
OE2
|
A:GLU134
|
2.5
|
18.9
|
0.4
|
|
OE2
|
A:GLU134
|
2.6
|
19.1
|
0.6
|
|
NE2
|
A:HIS83
|
2.6
|
17.6
|
0.4
|
|
CE1
|
A:HIS83
|
2.7
|
18.5
|
0.1
|
|
OE1
|
A:GLU134
|
2.7
|
20.7
|
0.4
|
|
NE2
|
A:HIS83
|
2.7
|
17.6
|
0.5
|
|
ND1
|
A:HIS210
|
2.7
|
15.6
|
1.0
|
|
CD
|
A:GLU134
|
2.8
|
19.9
|
0.4
|
|
CD
|
A:GLU134
|
2.8
|
20.9
|
0.6
|
|
HE1
|
A:HIS83
|
3.2
|
20.9
|
0.5
|
|
NE2
|
A:HIS83
|
3.2
|
18.5
|
0.1
|
|
CE1
|
A:HIS83
|
3.3
|
17.4
|
0.5
|
|
HE1
|
A:HIS210
|
3.4
|
19.5
|
1.0
|
|
CE1
|
A:HIS210
|
3.4
|
16.2
|
1.0
|
|
CE1
|
A:HIS83
|
3.5
|
17.4
|
0.4
|
|
O
|
A:HOH736
|
3.5
|
29.4
|
1.0
|
|
HE1
|
A:HIS83
|
3.5
|
20.9
|
0.4
|
|
NE2
|
A:GLN180
|
3.6
|
36.6
|
1.0
|
|
CD2
|
A:HIS83
|
3.7
|
17.8
|
0.4
|
|
CG
|
A:HIS210
|
3.8
|
14.9
|
1.0
|
|
O
|
A:HOH649
|
3.9
|
60.3
|
1.0
|
|
ND1
|
A:HIS83
|
3.9
|
18.4
|
0.1
|
|
CD2
|
A:HIS83
|
3.9
|
17.8
|
0.5
|
|
HB3
|
A:HIS210
|
3.9
|
18.6
|
1.0
|
|
HD2
|
A:HIS83
|
3.9
|
21.4
|
0.4
|
|
O
|
A:HOH504
|
4.0
|
30.4
|
0.5
|
|
HB2
|
A:HIS210
|
4.1
|
18.6
|
1.0
|
|
OD2
|
A:ASP104
|
4.1
|
21.2
|
1.0
|
|
CB
|
A:HIS210
|
4.2
|
15.5
|
1.0
|
|
HD1
|
A:HIS83
|
4.2
|
22.1
|
0.1
|
|
CG
|
A:GLU134
|
4.2
|
18.5
|
0.4
|
|
HE3
|
A:MET102
|
4.2
|
25.5
|
1.0
|
|
HD2
|
A:HIS83
|
4.2
|
21.4
|
0.5
|
|
HG3
|
A:GLU134
|
4.2
|
22.1
|
0.4
|
|
O
|
A:HOH603
|
4.3
|
29.5
|
1.0
|
|
CG
|
A:GLU134
|
4.4
|
18.6
|
0.6
|
|
O
|
A:HOH631
|
4.4
|
38.1
|
1.0
|
|
O
|
A:HOH569
|
4.5
|
27.8
|
1.0
|
|
O
|
A:HOH737
|
4.5
|
36.1
|
1.0
|
|
CD2
|
A:HIS83
|
4.5
|
18.1
|
0.1
|
|
ND1
|
A:HIS83
|
4.5
|
16.6
|
0.5
|
|
NE2
|
A:HIS210
|
4.6
|
15.8
|
1.0
|
|
CD
|
A:GLN180
|
4.6
|
35.7
|
1.0
|
|
ND1
|
A:HIS83
|
4.7
|
16.5
|
0.4
|
|
HG3
|
A:GLU134
|
4.7
|
22.3
|
0.6
|
|
HG2
|
A:GLU134
|
4.7
|
22.1
|
0.4
|
|
CD2
|
A:HIS210
|
4.8
|
15.1
|
1.0
|
|
CG
|
A:ASP104
|
4.8
|
20.1
|
1.0
|
|
HG2
|
A:GLU134
|
4.8
|
22.3
|
0.6
|
|
CG
|
A:HIS83
|
4.8
|
16.7
|
0.4
|
|
HB2
|
A:GLU134
|
4.8
|
19.4
|
0.6
|
|
OE1
|
A:GLN180
|
4.8
|
36.7
|
1.0
|
|
CG
|
A:HIS83
|
4.8
|
17.7
|
0.1
|
|
CG
|
A:HIS83
|
4.9
|
16.8
|
0.5
|
|
HB2
|
A:GLU134
|
4.9
|
19.8
|
0.4
|
|
Zinc binding site 2 out
of 4 in 5ud3
Go back to
Zinc Binding Sites List in 5ud3
Zinc binding site 2 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
 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 H180Q Variant of Helicobacter Pylori with Fbp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:66.7
occ:0.41
|
O
|
A:HOH511
|
0.1
|
20.4
|
0.6
|
|
HE1
|
A:HIS83
|
1.9
|
22.2
|
0.1
|
|
ZN
|
A:ZN402
|
2.0
|
47.8
|
0.6
|
|
O
|
A:HOH736
|
2.3
|
29.4
|
1.0
|
|
OD2
|
A:ASP104
|
2.4
|
21.2
|
1.0
|
|
OE1
|
A:GLU134
|
2.4
|
20.7
|
0.4
|
|
O
|
A:HOH649
|
2.5
|
60.3
|
1.0
|
|
OE2
|
A:GLU134
|
2.6
|
19.1
|
0.6
|
|
CE1
|
A:HIS83
|
2.7
|
18.5
|
0.1
|
|
NE2
|
A:HIS83
|
2.7
|
17.6
|
0.5
|
|
OE2
|
A:GLU134
|
2.7
|
18.9
|
0.4
|
|
O
|
A:HOH573
|
2.7
|
30.1
|
0.4
|
|
NE2
|
A:HIS83
|
2.9
|
17.6
|
0.4
|
|
HD2
|
A:HIS83
|
2.9
|
21.4
|
0.4
|
|
CD
|
A:GLU134
|
2.9
|
19.9
|
0.4
|
|
HD2
|
A:HIS83
|
3.1
|
21.4
|
0.5
|
|
CD2
|
A:HIS83
|
3.2
|
17.8
|
0.4
|
|
HD1
|
A:HIS83
|
3.2
|
22.1
|
0.1
|
|
CD2
|
A:HIS83
|
3.3
|
17.8
|
0.5
|
|
CG
|
A:ASP104
|
3.3
|
20.1
|
1.0
|
|
ND1
|
A:HIS83
|
3.3
|
18.4
|
0.1
|
|
CD
|
A:GLU134
|
3.3
|
20.9
|
0.6
|
|
OE1
|
A:GLU134
|
3.4
|
24.0
|
0.6
|
|
NE2
|
A:HIS83
|
3.8
|
18.5
|
0.1
|
|
OD1
|
A:ASP104
|
3.8
|
20.0
|
1.0
|
|
CE1
|
A:HIS83
|
3.9
|
17.4
|
0.5
|
|
CE1
|
A:HIS83
|
4.1
|
17.4
|
0.4
|
|
O
|
A:HOH534
|
4.2
|
46.0
|
1.0
|
|
HE1
|
A:HIS83
|
4.2
|
20.9
|
0.5
|
|
HB2
|
A:ASP104
|
4.3
|
21.3
|
1.0
|
|
HE3
|
A:MET102
|
4.3
|
25.5
|
1.0
|
|
O
|
A:HOH681
|
4.3
|
40.4
|
1.0
|
|
O
|
A:HOH719
|
4.3
|
32.1
|
1.0
|
|
CB
|
A:ASP104
|
4.4
|
17.7
|
1.0
|
|
OG
|
A:SER106
|
4.4
|
21.1
|
1.0
|
|
CG
|
A:GLU134
|
4.5
|
18.5
|
0.4
|
|
NE2
|
A:GLN180
|
4.5
|
36.6
|
1.0
|
|
HE1
|
A:HIS210
|
4.5
|
19.5
|
1.0
|
|
ND1
|
A:HIS210
|
4.5
|
15.6
|
1.0
|
|
CG
|
A:HIS83
|
4.6
|
16.8
|
0.5
|
|
CG
|
A:HIS83
|
4.6
|
16.7
|
0.4
|
|
HE1
|
A:HIS83
|
4.6
|
20.9
|
0.4
|
|
CG
|
A:HIS83
|
4.6
|
17.7
|
0.1
|
|
O
|
A:HOH569
|
4.6
|
27.8
|
1.0
|
|
CG
|
A:GLU134
|
4.7
|
18.6
|
0.6
|
|
HG
|
A:SER106
|
4.7
|
25.3
|
1.0
|
|
HB3
|
A:ASP104
|
4.7
|
21.3
|
1.0
|
|
HG2
|
A:GLU134
|
4.8
|
22.1
|
0.4
|
|
CD2
|
A:HIS83
|
4.8
|
18.1
|
0.1
|
|
ND1
|
A:HIS83
|
4.8
|
16.6
|
0.5
|
|
CE1
|
A:HIS210
|
4.9
|
16.2
|
1.0
|
|
HG2
|
A:GLU134
|
4.9
|
22.3
|
0.6
|
|
HG3
|
A:GLU134
|
4.9
|
22.1
|
0.4
|
|
ND1
|
A:HIS83
|
5.0
|
16.5
|
0.4
|
|
Zinc binding site 3 out
of 4 in 5ud3
Go back to
Zinc Binding Sites List in 5ud3
Zinc binding site 3 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
 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 H180Q Variant of Helicobacter Pylori with Fbp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:48.1
occ:0.50
|
O
|
B:HOH666
|
1.1
|
30.1
|
0.5
|
|
O
|
B:HOH516
|
1.9
|
20.4
|
0.5
|
|
HE1
|
B:HIS83
|
1.9
|
20.6
|
0.1
|
|
ZN
|
B:ZN403
|
2.0
|
52.8
|
0.5
|
|
OE1
|
B:GLU134
|
2.4
|
21.2
|
0.5
|
|
OE2
|
B:GLU134
|
2.5
|
19.2
|
0.5
|
|
OE2
|
B:GLU134
|
2.5
|
17.9
|
0.5
|
|
OE1
|
B:GLU134
|
2.6
|
17.8
|
0.5
|
|
ND1
|
B:HIS210
|
2.6
|
16.3
|
1.0
|
|
NE2
|
B:HIS83
|
2.7
|
16.4
|
0.4
|
|
CE1
|
B:HIS83
|
2.7
|
17.2
|
0.1
|
|
NE2
|
B:HIS83
|
2.7
|
17.4
|
0.5
|
|
CD
|
B:GLU134
|
2.8
|
19.7
|
0.5
|
|
CD
|
B:GLU134
|
2.8
|
18.1
|
0.5
|
|
HE1
|
B:HIS83
|
3.2
|
20.7
|
0.5
|
|
NE2
|
B:HIS83
|
3.2
|
17.1
|
0.1
|
|
CE1
|
B:HIS83
|
3.3
|
17.2
|
0.5
|
|
HE1
|
B:HIS210
|
3.3
|
20.5
|
1.0
|
|
CE1
|
B:HIS210
|
3.3
|
17.1
|
1.0
|
|
HE1
|
B:HIS83
|
3.4
|
19.1
|
0.4
|
|
CE1
|
B:HIS83
|
3.4
|
16.0
|
0.4
|
|
O
|
B:HOH720
|
3.5
|
30.6
|
1.0
|
|
O
|
B:HOH733
|
3.6
|
50.1
|
1.0
|
|
NE2
|
B:GLN180
|
3.6
|
33.0
|
1.0
|
|
CG
|
B:HIS210
|
3.7
|
14.9
|
1.0
|
|
CD2
|
B:HIS83
|
3.8
|
15.7
|
0.4
|
|
HB3
|
B:HIS210
|
3.9
|
17.4
|
1.0
|
|
ND1
|
B:HIS83
|
3.9
|
16.6
|
0.1
|
|
CD2
|
B:HIS83
|
3.9
|
16.6
|
0.5
|
|
O
|
B:HOH507
|
4.0
|
27.6
|
0.5
|
|
HB2
|
B:HIS210
|
4.0
|
17.4
|
1.0
|
|
HD2
|
B:HIS83
|
4.0
|
18.9
|
0.4
|
|
CB
|
B:HIS210
|
4.1
|
14.5
|
1.0
|
|
CG
|
B:GLU134
|
4.1
|
16.7
|
0.5
|
|
HE2
|
B:MET102
|
4.1
|
25.5
|
1.0
|
|
HG3
|
B:GLU134
|
4.2
|
20.0
|
0.5
|
|
OD2
|
B:ASP104
|
4.2
|
19.8
|
1.0
|
|
HD1
|
B:HIS83
|
4.2
|
20.0
|
0.1
|
|
HD2
|
B:HIS83
|
4.3
|
20.0
|
0.5
|
|
O
|
B:HOH515
|
4.3
|
27.1
|
1.0
|
|
CG
|
B:GLU134
|
4.3
|
17.2
|
0.5
|
|
O
|
B:HOH526
|
4.5
|
28.6
|
1.0
|
|
O
|
B:HOH752
|
4.5
|
46.6
|
1.0
|
|
NE2
|
B:HIS210
|
4.5
|
15.8
|
1.0
|
|
O
|
B:HOH579
|
4.5
|
37.2
|
1.0
|
|
CD2
|
B:HIS83
|
4.5
|
16.5
|
0.1
|
|
ND1
|
B:HIS83
|
4.6
|
16.1
|
0.5
|
|
ND1
|
B:HIS83
|
4.6
|
14.9
|
0.4
|
|
HG3
|
B:GLU134
|
4.6
|
20.7
|
0.5
|
|
HG2
|
B:GLU134
|
4.7
|
20.7
|
0.5
|
|
HG2
|
B:GLU134
|
4.7
|
20.0
|
0.5
|
|
CD
|
B:GLN180
|
4.7
|
32.0
|
1.0
|
|
CD2
|
B:HIS210
|
4.7
|
16.0
|
1.0
|
|
HB2
|
B:GLU134
|
4.8
|
18.4
|
0.5
|
|
CG
|
B:ASP104
|
4.8
|
18.7
|
1.0
|
|
CG
|
B:HIS83
|
4.8
|
15.1
|
0.4
|
|
HB2
|
B:GLU134
|
4.9
|
18.4
|
0.5
|
|
CG
|
B:HIS83
|
4.9
|
16.2
|
0.1
|
|
CG
|
B:HIS83
|
4.9
|
16.2
|
0.5
|
|
OE1
|
B:GLN180
|
4.9
|
33.0
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5ud3
Go back to
Zinc Binding Sites List in 5ud3
Zinc binding site 4 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Fbp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:52.8
occ:0.50
|
O
|
B:HOH516
|
0.1
|
20.4
|
0.5
|
|
HE1
|
B:HIS83
|
1.8
|
20.6
|
0.1
|
|
ZN
|
B:ZN402
|
2.0
|
48.1
|
0.5
|
|
O
|
B:HOH720
|
2.3
|
30.6
|
1.0
|
|
O
|
B:HOH733
|
2.4
|
50.1
|
1.0
|
|
OD2
|
B:ASP104
|
2.5
|
19.8
|
1.0
|
|
OE1
|
B:GLU134
|
2.5
|
17.8
|
0.5
|
|
CE1
|
B:HIS83
|
2.6
|
17.2
|
0.1
|
|
OE2
|
B:GLU134
|
2.6
|
17.9
|
0.5
|
|
NE2
|
B:HIS83
|
2.6
|
17.4
|
0.5
|
|
OE2
|
B:GLU134
|
2.6
|
19.2
|
0.5
|
|
O
|
B:HOH666
|
2.7
|
30.1
|
0.5
|
|
NE2
|
B:HIS83
|
2.7
|
16.4
|
0.4
|
|
HD2
|
B:HIS83
|
2.9
|
18.9
|
0.4
|
|
CD
|
B:GLU134
|
2.9
|
18.1
|
0.5
|
|
HD2
|
B:HIS83
|
3.1
|
20.0
|
0.5
|
|
CD2
|
B:HIS83
|
3.2
|
15.7
|
0.4
|
|
HD1
|
B:HIS83
|
3.2
|
20.0
|
0.1
|
|
CD2
|
B:HIS83
|
3.2
|
16.6
|
0.5
|
|
ND1
|
B:HIS83
|
3.3
|
16.6
|
0.1
|
|
CG
|
B:ASP104
|
3.3
|
18.7
|
1.0
|
|
CD
|
B:GLU134
|
3.4
|
19.7
|
0.5
|
|
OE1
|
B:GLU134
|
3.5
|
21.2
|
0.5
|
|
NE2
|
B:HIS83
|
3.7
|
17.1
|
0.1
|
|
CE1
|
B:HIS83
|
3.8
|
17.2
|
0.5
|
|
OD1
|
B:ASP104
|
3.8
|
17.9
|
1.0
|
|
CE1
|
B:HIS83
|
4.0
|
16.0
|
0.4
|
|
HE1
|
B:HIS83
|
4.2
|
20.7
|
0.5
|
|
HG
|
B:SER106
|
4.2
|
23.7
|
1.0
|
|
HE2
|
B:MET102
|
4.3
|
25.5
|
1.0
|
|
HB2
|
B:ASP104
|
4.3
|
20.9
|
1.0
|
|
O
|
B:HOH628
|
4.3
|
38.8
|
1.0
|
|
HE1
|
B:HIS83
|
4.4
|
19.1
|
0.4
|
|
CB
|
B:ASP104
|
4.4
|
17.5
|
1.0
|
|
HE1
|
B:HIS210
|
4.4
|
20.5
|
1.0
|
|
O
|
B:HOH638
|
4.4
|
45.4
|
1.0
|
|
ND1
|
B:HIS210
|
4.4
|
16.3
|
1.0
|
|
NE2
|
B:GLN180
|
4.5
|
33.0
|
1.0
|
|
O
|
B:HOH681
|
4.5
|
30.2
|
1.0
|
|
CG
|
B:GLU134
|
4.5
|
16.7
|
0.5
|
|
CG
|
B:HIS83
|
4.5
|
15.1
|
0.4
|
|
OG
|
B:SER106
|
4.5
|
19.8
|
1.0
|
|
CG
|
B:HIS83
|
4.5
|
16.2
|
0.5
|
|
CG
|
B:HIS83
|
4.6
|
16.2
|
0.1
|
|
O
|
B:HOH526
|
4.7
|
28.6
|
1.0
|
|
CG
|
B:GLU134
|
4.7
|
17.2
|
0.5
|
|
CD2
|
B:HIS83
|
4.7
|
16.5
|
0.1
|
|
ND1
|
B:HIS83
|
4.8
|
16.1
|
0.5
|
|
HB3
|
B:ASP104
|
4.8
|
20.9
|
1.0
|
|
CE1
|
B:HIS210
|
4.8
|
17.1
|
1.0
|
|
HG2
|
B:GLU134
|
4.8
|
20.7
|
0.5
|
|
HG2
|
B:GLU134
|
4.8
|
20.0
|
0.5
|
|
ND1
|
B:HIS83
|
4.9
|
14.9
|
0.4
|
|
HG3
|
B:GLU134
|
4.9
|
20.0
|
0.5
|
|
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 09:23:37 2024
|
