Zinc in PDB 5ud2: Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap, PDB code: 5ud2
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)
|
35.79 /
1.78
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.407,
63.089,
64.789,
82.51,
75.96,
74.39
|
|
R / Rfree (%)
|
19.3 /
21.6
|
Other elements in 5ud2:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap
(pdb code 5ud2). 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 Dhap, PDB code: 5ud2:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5ud2
Go back to
Zinc Binding Sites List in 5ud2
Zinc binding site 1 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:37.2
occ:0.70
|
HE1
|
A:HIS83
|
1.8
|
30.7
|
0.3
|
|
O
|
A:HOH512
|
2.1
|
34.6
|
1.0
|
|
O
|
A:HOH598
|
2.4
|
27.3
|
1.0
|
|
NE2
|
A:HIS83
|
2.5
|
25.7
|
0.7
|
|
ND1
|
A:HIS210
|
2.6
|
15.1
|
0.7
|
|
CE1
|
A:HIS83
|
2.7
|
25.6
|
0.3
|
|
OE2
|
A:GLU134
|
2.7
|
27.2
|
1.0
|
|
OE1
|
A:GLU134
|
2.8
|
27.0
|
1.0
|
|
CD
|
A:GLU134
|
3.1
|
25.8
|
1.0
|
|
HE1
|
A:HIS83
|
3.2
|
30.1
|
0.7
|
|
CE1
|
A:HIS83
|
3.2
|
25.0
|
0.7
|
|
ND1
|
A:HIS210
|
3.4
|
17.2
|
0.3
|
|
CE1
|
A:HIS210
|
3.4
|
15.6
|
0.7
|
|
NE2
|
A:HIS83
|
3.4
|
26.0
|
0.3
|
|
HE1
|
A:HIS210
|
3.4
|
18.7
|
0.7
|
|
CD2
|
A:HIS83
|
3.6
|
25.6
|
0.7
|
|
CG
|
A:HIS210
|
3.7
|
16.1
|
0.7
|
|
HB3
|
A:HIS210
|
3.7
|
20.3
|
0.7
|
|
ND1
|
A:HIS83
|
3.7
|
25.4
|
0.3
|
|
HB3
|
A:HIS210
|
3.7
|
20.2
|
0.3
|
|
ZN
|
A:ZN403
|
3.8
|
24.2
|
0.3
|
|
CG
|
A:HIS210
|
3.8
|
16.7
|
0.3
|
|
HD2
|
A:HIS83
|
3.9
|
30.8
|
0.7
|
|
HD1
|
A:HIS83
|
3.9
|
30.5
|
0.3
|
|
CE1
|
A:HIS210
|
3.9
|
16.6
|
0.3
|
|
HE1
|
A:MET102
|
4.0
|
23.2
|
1.0
|
|
OD2
|
A:ASP104
|
4.0
|
30.2
|
1.0
|
|
HB2
|
A:HIS210
|
4.0
|
20.2
|
0.3
|
|
HB2
|
A:HIS210
|
4.0
|
20.3
|
0.7
|
|
CB
|
A:HIS210
|
4.1
|
16.9
|
0.7
|
|
CB
|
A:HIS210
|
4.1
|
16.9
|
0.3
|
|
HE1
|
A:HIS210
|
4.2
|
19.9
|
0.3
|
|
ND1
|
A:HIS83
|
4.4
|
24.3
|
0.7
|
|
CD2
|
A:HIS210
|
4.4
|
17.1
|
0.3
|
|
NE2
|
A:HIS210
|
4.5
|
16.7
|
0.3
|
|
CG
|
A:GLU134
|
4.6
|
20.3
|
1.0
|
|
O
|
A:HOH510
|
4.6
|
37.0
|
1.0
|
|
NE2
|
A:HIS210
|
4.6
|
17.4
|
0.7
|
|
CG
|
A:HIS83
|
4.7
|
24.1
|
0.7
|
|
CD2
|
A:HIS83
|
4.7
|
25.2
|
0.3
|
|
CD2
|
A:HIS210
|
4.8
|
16.9
|
0.7
|
|
O
|
A:HOH597
|
4.8
|
22.3
|
1.0
|
|
CG
|
A:ASP104
|
4.8
|
29.0
|
1.0
|
|
HG3
|
A:GLU134
|
4.8
|
24.4
|
1.0
|
|
CG
|
A:HIS83
|
4.8
|
24.2
|
0.3
|
|
CE
|
A:MET102
|
4.9
|
19.3
|
1.0
|
|
HB2
|
A:GLU134
|
5.0
|
19.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5ud2
Go back to
Zinc Binding Sites List in 5ud2
Zinc binding site 2 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:24.2
occ:0.30
|
HE1
|
A:HIS83
|
1.7
|
30.1
|
0.7
|
|
O
|
A:HOH598
|
2.1
|
27.3
|
1.0
|
|
NE2
|
A:HIS83
|
2.1
|
26.0
|
0.3
|
|
O
|
A:HOH501
|
2.2
|
31.5
|
1.0
|
|
ND1
|
A:HIS210
|
2.3
|
17.2
|
0.3
|
|
CE1
|
A:HIS83
|
2.4
|
25.0
|
0.7
|
|
O2
|
A:13P404
|
2.5
|
31.5
|
1.0
|
|
O3
|
A:13P404
|
2.7
|
28.3
|
1.0
|
|
HB3
|
A:HIS210
|
2.8
|
20.3
|
0.7
|
|
HB3
|
A:HIS210
|
2.9
|
20.2
|
0.3
|
|
CE1
|
A:HIS83
|
3.1
|
25.6
|
0.3
|
|
NE2
|
A:HIS83
|
3.1
|
25.7
|
0.7
|
|
CD2
|
A:HIS83
|
3.1
|
25.2
|
0.3
|
|
HE1
|
A:HIS83
|
3.2
|
30.7
|
0.3
|
|
CE1
|
A:HIS210
|
3.2
|
16.6
|
0.3
|
|
CG
|
A:HIS210
|
3.2
|
16.7
|
0.3
|
|
ND1
|
A:HIS83
|
3.3
|
24.3
|
0.7
|
|
C2
|
A:13P404
|
3.3
|
31.4
|
1.0
|
|
HD2
|
A:HIS83
|
3.3
|
30.3
|
0.3
|
|
HE1
|
A:HIS210
|
3.4
|
19.9
|
0.3
|
|
HO3
|
A:13P404
|
3.4
|
34.0
|
1.0
|
|
C3
|
A:13P404
|
3.5
|
29.7
|
1.0
|
|
HD1
|
A:HIS83
|
3.5
|
29.2
|
0.7
|
|
CG
|
A:HIS210
|
3.5
|
16.1
|
0.7
|
|
CB
|
A:HIS210
|
3.5
|
16.9
|
0.3
|
|
HD22
|
A:ASN253
|
3.5
|
13.4
|
1.0
|
|
CB
|
A:HIS210
|
3.5
|
16.9
|
0.7
|
|
ND1
|
A:HIS210
|
3.6
|
15.1
|
0.7
|
|
H
|
A:GLY211
|
3.6
|
26.8
|
1.0
|
|
ZN
|
A:ZN402
|
3.8
|
37.2
|
0.7
|
|
H31
|
A:13P404
|
3.8
|
35.6
|
1.0
|
|
HA
|
A:HIS210
|
4.0
|
21.2
|
0.7
|
|
HA
|
A:HIS210
|
4.1
|
20.8
|
0.3
|
|
CD2
|
A:HIS210
|
4.1
|
16.9
|
0.7
|
|
ND1
|
A:HIS83
|
4.2
|
25.4
|
0.3
|
|
CD2
|
A:HIS83
|
4.2
|
25.6
|
0.7
|
|
CG
|
A:HIS83
|
4.2
|
24.2
|
0.3
|
|
CE1
|
A:HIS210
|
4.2
|
15.6
|
0.7
|
|
N
|
A:GLY211
|
4.3
|
22.4
|
1.0
|
|
HB2
|
A:HIS210
|
4.3
|
20.2
|
0.3
|
|
HB2
|
A:HIS210
|
4.3
|
20.3
|
0.7
|
|
CG
|
A:HIS83
|
4.3
|
24.1
|
0.7
|
|
CA
|
A:HIS210
|
4.3
|
17.7
|
0.7
|
|
CA
|
A:HIS210
|
4.3
|
17.3
|
0.3
|
|
ND2
|
A:ASN253
|
4.3
|
11.1
|
1.0
|
|
NE2
|
A:HIS210
|
4.4
|
16.7
|
0.3
|
|
CD2
|
A:HIS210
|
4.4
|
17.1
|
0.3
|
|
H32
|
A:13P404
|
4.5
|
35.6
|
1.0
|
|
OD1
|
A:ASP82
|
4.5
|
19.4
|
1.0
|
|
NE2
|
A:HIS210
|
4.5
|
17.4
|
0.7
|
|
HD2
|
A:HIS210
|
4.6
|
20.2
|
0.7
|
|
C1
|
A:13P404
|
4.6
|
31.3
|
1.0
|
|
HB3
|
A:ASN253
|
4.6
|
11.8
|
1.0
|
|
CB
|
A:GLN180
|
4.7
|
99.8
|
1.0
|
|
HD21
|
A:ASN253
|
4.7
|
13.4
|
1.0
|
|
HE1
|
A:HIS210
|
4.7
|
18.7
|
0.7
|
|
HB2
|
A:ASN253
|
4.7
|
11.8
|
1.0
|
|
C
|
A:HIS210
|
4.8
|
19.4
|
0.3
|
|
C
|
A:HIS210
|
4.8
|
19.3
|
0.7
|
|
H12
|
A:13P404
|
4.9
|
37.6
|
1.0
|
|
O
|
A:HOH590
|
4.9
|
31.1
|
1.0
|
|
HD1
|
A:HIS83
|
5.0
|
30.5
|
0.3
|
|
HD2
|
A:HIS83
|
5.0
|
30.8
|
0.7
|
|
OD2
|
A:ASP82
|
5.0
|
20.2
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5ud2
Go back to
Zinc Binding Sites List in 5ud2
Zinc binding site 3 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:32.3
occ:0.50
|
HE1
|
B:HIS83
|
1.6
|
26.1
|
0.5
|
|
O
|
B:HOH536
|
2.1
|
27.2
|
1.0
|
|
NE2
|
B:HIS83
|
2.5
|
21.8
|
0.5
|
|
CE1
|
B:HIS83
|
2.5
|
21.7
|
0.5
|
|
ND1
|
B:HIS210
|
2.6
|
17.3
|
0.5
|
|
OE1
|
B:GLU134
|
2.7
|
26.3
|
1.0
|
|
OE2
|
B:GLU134
|
2.9
|
26.2
|
1.0
|
|
CD
|
B:GLU134
|
3.2
|
24.8
|
1.0
|
|
HE1
|
B:HIS83
|
3.2
|
21.2
|
0.5
|
|
CE1
|
B:HIS83
|
3.2
|
17.7
|
0.5
|
|
NE2
|
B:HIS83
|
3.2
|
21.9
|
0.5
|
|
ND1
|
B:HIS210
|
3.2
|
17.9
|
0.5
|
|
CE1
|
B:HIS210
|
3.4
|
18.4
|
0.5
|
|
HB3
|
B:HIS210
|
3.5
|
21.6
|
0.5
|
|
HE1
|
B:HIS210
|
3.5
|
22.1
|
0.5
|
|
HB3
|
B:HIS210
|
3.5
|
21.6
|
0.5
|
|
ZN
|
B:ZN403
|
3.6
|
25.0
|
0.5
|
|
CG
|
B:HIS210
|
3.6
|
17.9
|
0.5
|
|
CD2
|
B:HIS83
|
3.6
|
20.9
|
0.5
|
|
CG
|
B:HIS210
|
3.6
|
17.8
|
0.5
|
|
ND1
|
B:HIS83
|
3.6
|
21.2
|
0.5
|
|
HB2
|
B:HIS210
|
3.8
|
21.6
|
0.5
|
|
HB2
|
B:HIS210
|
3.8
|
21.6
|
0.5
|
|
CE1
|
B:HIS210
|
3.8
|
17.3
|
0.5
|
|
HD1
|
B:HIS83
|
3.9
|
25.4
|
0.5
|
|
CB
|
B:HIS210
|
3.9
|
18.0
|
0.5
|
|
HD2
|
B:HIS83
|
3.9
|
25.1
|
0.5
|
|
CB
|
B:HIS210
|
3.9
|
18.0
|
0.5
|
|
O
|
B:HOH506
|
4.0
|
23.1
|
1.0
|
|
HE1
|
B:MET102
|
4.1
|
22.9
|
1.0
|
|
HE1
|
B:HIS210
|
4.1
|
20.7
|
0.5
|
|
OD2
|
B:ASP104
|
4.3
|
21.9
|
1.0
|
|
O
|
B:HOH548
|
4.3
|
32.7
|
1.0
|
|
CD2
|
B:HIS210
|
4.4
|
17.6
|
0.5
|
|
ND1
|
B:HIS83
|
4.4
|
20.8
|
0.5
|
|
CD2
|
B:HIS83
|
4.5
|
20.9
|
0.5
|
|
NE2
|
B:HIS210
|
4.5
|
18.3
|
0.5
|
|
NE2
|
B:HIS210
|
4.6
|
18.3
|
0.5
|
|
CG
|
B:HIS83
|
4.6
|
19.7
|
0.5
|
|
O
|
B:HOH525
|
4.6
|
21.1
|
1.0
|
|
CG
|
B:GLU134
|
4.7
|
19.2
|
1.0
|
|
CG
|
B:HIS83
|
4.7
|
20.1
|
0.5
|
|
CD2
|
B:HIS210
|
4.7
|
18.2
|
0.5
|
|
CG
|
B:ASP104
|
4.9
|
20.6
|
1.0
|
|
CE
|
B:MET102
|
4.9
|
19.1
|
1.0
|
|
HE3
|
B:MET102
|
5.0
|
22.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5ud2
Go back to
Zinc Binding Sites List in 5ud2
Zinc binding site 4 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase H180Q 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 4 of Class II Fructose-1,6-Bisphosphate Aldolase H180Q Variant of Helicobacter Pylori with Dhap within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:25.0
occ:0.50
|
HE1
|
B:HIS83
|
1.6
|
21.2
|
0.5
|
|
NE2
|
B:HIS83
|
2.0
|
21.9
|
0.5
|
|
CE1
|
B:HIS83
|
2.2
|
17.7
|
0.5
|
|
O
|
B:HOH548
|
2.3
|
32.7
|
1.0
|
|
ND1
|
B:HIS210
|
2.4
|
17.9
|
0.5
|
|
O3
|
B:13P404
|
2.5
|
29.8
|
1.0
|
|
O2
|
B:13P404
|
2.5
|
31.2
|
1.0
|
|
HB3
|
B:HIS210
|
2.8
|
21.6
|
0.5
|
|
HB3
|
B:HIS210
|
2.9
|
21.6
|
0.5
|
|
NE2
|
B:HIS83
|
2.9
|
21.8
|
0.5
|
|
CD2
|
B:HIS83
|
3.0
|
20.9
|
0.5
|
|
CE1
|
B:HIS83
|
3.0
|
21.7
|
0.5
|
|
HO3
|
B:13P404
|
3.1
|
35.7
|
1.0
|
|
HD2
|
B:HIS83
|
3.1
|
25.1
|
0.5
|
|
ND1
|
B:HIS83
|
3.2
|
20.8
|
0.5
|
|
C2
|
B:13P404
|
3.3
|
31.4
|
1.0
|
|
C3
|
B:13P404
|
3.3
|
30.7
|
1.0
|
|
HE1
|
B:HIS83
|
3.3
|
26.1
|
0.5
|
|
CG
|
B:HIS210
|
3.3
|
17.8
|
0.5
|
|
CE1
|
B:HIS210
|
3.4
|
17.3
|
0.5
|
|
HD1
|
B:HIS83
|
3.5
|
25.0
|
0.5
|
|
H32
|
B:13P404
|
3.5
|
36.9
|
1.0
|
|
HE1
|
B:HIS210
|
3.5
|
20.7
|
0.5
|
|
CB
|
B:HIS210
|
3.5
|
18.0
|
0.5
|
|
CG
|
B:HIS210
|
3.5
|
17.9
|
0.5
|
|
ND1
|
B:HIS210
|
3.6
|
17.3
|
0.5
|
|
ZN
|
B:ZN402
|
3.6
|
32.3
|
0.5
|
|
HD22
|
B:ASN253
|
3.6
|
15.1
|
1.0
|
|
CB
|
B:HIS210
|
3.6
|
18.0
|
0.5
|
|
H
|
B:GLY211
|
3.7
|
24.6
|
1.0
|
|
CD2
|
B:HIS83
|
4.0
|
20.9
|
0.5
|
|
CG
|
B:HIS83
|
4.1
|
20.1
|
0.5
|
|
ND1
|
B:HIS83
|
4.1
|
21.2
|
0.5
|
|
HA
|
B:HIS210
|
4.1
|
21.2
|
0.5
|
|
HA
|
B:HIS210
|
4.2
|
21.3
|
0.5
|
|
CG
|
B:HIS83
|
4.2
|
19.7
|
0.5
|
|
CE1
|
B:HIS210
|
4.3
|
18.4
|
0.5
|
|
CD2
|
B:HIS210
|
4.3
|
18.2
|
0.5
|
|
HB2
|
B:HIS210
|
4.3
|
21.6
|
0.5
|
|
HB2
|
B:HIS210
|
4.3
|
21.6
|
0.5
|
|
H31
|
B:13P404
|
4.3
|
36.9
|
1.0
|
|
ND2
|
B:ASN253
|
4.4
|
12.6
|
1.0
|
|
N
|
B:GLY211
|
4.4
|
20.5
|
1.0
|
|
CA
|
B:HIS210
|
4.4
|
17.7
|
0.5
|
|
CA
|
B:HIS210
|
4.4
|
17.7
|
0.5
|
|
OD1
|
B:ASP82
|
4.4
|
14.2
|
1.0
|
|
NE2
|
B:HIS210
|
4.5
|
18.3
|
0.5
|
|
CD2
|
B:HIS210
|
4.5
|
17.6
|
0.5
|
|
O
|
B:HOH558
|
4.6
|
32.6
|
1.0
|
|
NE2
|
B:HIS210
|
4.6
|
18.3
|
0.5
|
|
C1
|
B:13P404
|
4.7
|
31.6
|
1.0
|
|
HB3
|
B:ASN253
|
4.7
|
14.4
|
1.0
|
|
HE1
|
B:HIS210
|
4.7
|
22.1
|
0.5
|
|
HD2
|
B:HIS210
|
4.7
|
21.8
|
0.5
|
|
HD21
|
B:ASN253
|
4.8
|
15.1
|
1.0
|
|
HB2
|
B:ASN253
|
4.8
|
14.4
|
1.0
|
|
HD2
|
B:HIS83
|
4.8
|
25.1
|
0.5
|
|
C
|
B:HIS210
|
4.9
|
18.7
|
0.5
|
|
C
|
B:HIS210
|
4.9
|
18.7
|
0.5
|
|
HD1
|
B:HIS83
|
4.9
|
25.4
|
0.5
|
|
CB
|
B:GLN180
|
5.0
|
80.4
|
1.0
|
|
OD2
|
B:ASP82
|
5.0
|
13.6
|
1.0
|
|
O1
|
B:13P404
|
5.0
|
29.7
|
1.0
|
|
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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