Zinc in PDB 5ucp: Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products, PDB code: 5ucp
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)
|
29.21 /
1.44
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.476,
64.633,
62.845,
82.15,
74.39,
75.78
|
|
R / Rfree (%)
|
16.2 /
19.6
|
Other elements in 5ucp:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and 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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
(pdb code 5ucp). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products, PDB code: 5ucp:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 1 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and 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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:29.8
occ:0.40
|
HE1
|
A:HIS83
|
1.8
|
24.0
|
0.2
|
|
HE1
|
A:HIS83
|
1.9
|
15.1
|
0.3
|
|
ZN
|
A:ZN403
|
2.0
|
20.5
|
0.3
|
|
O
|
A:HOH517
|
2.3
|
29.8
|
1.0
|
|
ND1
|
A:HIS210
|
2.4
|
17.1
|
0.4
|
|
OE2
|
A:GLU134
|
2.4
|
34.4
|
1.0
|
|
NE2
|
A:HIS83
|
2.5
|
20.0
|
0.4
|
|
CE1
|
A:HIS83
|
2.6
|
20.0
|
0.2
|
|
CE1
|
A:HIS83
|
2.7
|
12.6
|
0.3
|
|
OE1
|
A:GLU134
|
2.8
|
43.9
|
1.0
|
|
ND1
|
A:HIS210
|
2.9
|
33.8
|
0.3
|
|
CE1
|
A:HIS180
|
2.9
|
51.8
|
1.0
|
|
CD
|
A:GLU134
|
3.0
|
34.3
|
1.0
|
|
NE2
|
A:HIS83
|
3.1
|
22.4
|
0.2
|
|
HE1
|
A:HIS83
|
3.1
|
33.5
|
0.4
|
|
CE1
|
A:HIS83
|
3.2
|
27.9
|
0.4
|
|
CE1
|
A:HIS210
|
3.2
|
12.5
|
0.4
|
|
NE2
|
A:HIS83
|
3.2
|
25.3
|
0.3
|
|
HE1
|
A:HIS210
|
3.3
|
14.9
|
0.4
|
|
ND1
|
A:HIS210
|
3.3
|
12.6
|
0.2
|
|
NE2
|
A:HIS180
|
3.4
|
50.8
|
1.0
|
|
CG
|
A:HIS210
|
3.4
|
24.3
|
0.4
|
|
HB3
|
A:HIS210
|
3.5
|
22.5
|
0.3
|
|
HB3
|
A:HIS210
|
3.5
|
22.9
|
0.2
|
|
HB3
|
A:HIS210
|
3.5
|
15.7
|
0.4
|
|
CG
|
A:HIS210
|
3.6
|
12.9
|
0.2
|
|
CG
|
A:HIS210
|
3.6
|
12.8
|
0.3
|
|
HB2
|
A:HIS210
|
3.7
|
22.5
|
0.3
|
|
ZN
|
A:ZN404
|
3.7
|
21.5
|
0.2
|
|
CD2
|
A:HIS83
|
3.7
|
18.6
|
0.4
|
|
HB2
|
A:HIS210
|
3.7
|
22.9
|
0.2
|
|
CE1
|
A:HIS210
|
3.7
|
12.3
|
0.3
|
|
HB2
|
A:HIS210
|
3.8
|
15.7
|
0.4
|
|
CB
|
A:HIS210
|
3.8
|
18.7
|
0.3
|
|
CB
|
A:HIS210
|
3.8
|
19.0
|
0.2
|
|
CB
|
A:HIS210
|
3.8
|
13.2
|
0.4
|
|
ND1
|
A:HIS83
|
3.8
|
21.5
|
0.2
|
|
CE1
|
A:HIS210
|
3.9
|
18.5
|
0.2
|
|
ND1
|
A:HIS83
|
3.9
|
27.2
|
0.3
|
|
HE1
|
A:HIS210
|
3.9
|
14.6
|
0.3
|
|
HD2
|
A:HIS83
|
4.0
|
22.4
|
0.4
|
|
HE1
|
A:MET102
|
4.0
|
18.1
|
1.0
|
|
ND1
|
A:HIS180
|
4.2
|
0.0
|
1.0
|
|
HD1
|
A:HIS83
|
4.2
|
25.8
|
0.2
|
|
HD1
|
A:HIS83
|
4.2
|
32.7
|
0.3
|
|
O
|
A:HOH501
|
4.2
|
17.4
|
1.0
|
|
HE1
|
A:HIS210
|
4.3
|
22.2
|
0.2
|
|
CD2
|
A:HIS210
|
4.3
|
12.5
|
0.2
|
|
NE2
|
A:HIS210
|
4.3
|
15.2
|
0.4
|
|
ND1
|
A:HIS83
|
4.4
|
16.3
|
0.4
|
|
CD2
|
A:HIS83
|
4.4
|
17.9
|
0.2
|
|
NE2
|
A:HIS210
|
4.4
|
17.5
|
0.2
|
|
CD2
|
A:HIS210
|
4.4
|
17.5
|
0.4
|
|
CG
|
A:GLU134
|
4.5
|
18.1
|
1.0
|
|
O
|
A:HOH521
|
4.5
|
36.2
|
1.0
|
|
OD2
|
A:ASP104
|
4.6
|
20.8
|
1.0
|
|
CD2
|
A:HIS83
|
4.6
|
9.5
|
0.3
|
|
CD2
|
A:HIS210
|
4.6
|
14.1
|
0.3
|
|
NE2
|
A:HIS210
|
4.6
|
12.2
|
0.3
|
|
CG
|
A:HIS83
|
4.7
|
16.8
|
0.4
|
|
CD2
|
A:HIS180
|
4.8
|
79.8
|
1.0
|
|
HG3
|
A:GLU134
|
4.8
|
21.8
|
1.0
|
|
CG
|
A:HIS83
|
4.8
|
7.8
|
0.2
|
|
HD2
|
A:HIS210
|
4.9
|
14.9
|
0.2
|
|
CG
|
A:HIS83
|
4.9
|
11.4
|
0.3
|
|
CE
|
A:MET102
|
4.9
|
15.1
|
1.0
|
|
HB2
|
A:GLU134
|
4.9
|
18.8
|
1.0
|
|
HG2
|
A:GLU134
|
4.9
|
21.8
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 2 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and 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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn403
b:20.5
occ:0.30
|
HE1
|
A:HIS83
|
1.5
|
33.5
|
0.4
|
|
NE2
|
A:HIS83
|
1.7
|
22.4
|
0.2
|
|
ZN
|
A:ZN404
|
1.7
|
21.5
|
0.2
|
|
NE2
|
A:HIS83
|
1.8
|
25.3
|
0.3
|
|
CE1
|
A:HIS83
|
1.8
|
27.9
|
0.4
|
|
NE2
|
A:HIS180
|
2.0
|
50.8
|
1.0
|
|
NE2
|
A:HIS83
|
2.0
|
20.0
|
0.4
|
|
ZN
|
A:ZN402
|
2.0
|
29.8
|
0.4
|
|
HE1
|
A:HIS83
|
2.1
|
15.1
|
0.3
|
|
HE1
|
A:HIS83
|
2.1
|
24.0
|
0.2
|
|
ND1
|
A:HIS210
|
2.2
|
33.8
|
0.3
|
|
CE1
|
A:HIS83
|
2.2
|
20.0
|
0.2
|
|
CE1
|
A:HIS83
|
2.2
|
12.6
|
0.3
|
|
ND1
|
A:HIS210
|
2.3
|
12.6
|
0.2
|
|
CE1
|
A:HIS180
|
2.3
|
51.8
|
1.0
|
|
ND1
|
A:HIS210
|
2.8
|
17.1
|
0.4
|
|
HB3
|
A:HIS210
|
2.9
|
22.5
|
0.3
|
|
HB3
|
A:HIS210
|
2.9
|
22.9
|
0.2
|
|
HB3
|
A:HIS210
|
2.9
|
15.7
|
0.4
|
|
CD2
|
A:HIS83
|
3.0
|
17.9
|
0.2
|
|
ND1
|
A:HIS83
|
3.1
|
16.3
|
0.4
|
|
CG
|
A:HIS210
|
3.1
|
12.9
|
0.2
|
|
CE1
|
A:HIS210
|
3.1
|
18.5
|
0.2
|
|
CD2
|
A:HIS83
|
3.1
|
9.5
|
0.3
|
|
HO3
|
A:P6F405
|
3.1
|
30.6
|
0.7
|
|
CE1
|
A:HIS210
|
3.1
|
12.3
|
0.3
|
|
CG
|
A:HIS210
|
3.1
|
12.8
|
0.3
|
|
CG
|
A:HIS210
|
3.2
|
24.3
|
0.4
|
|
CD2
|
A:HIS83
|
3.3
|
18.6
|
0.4
|
|
CD2
|
A:HIS180
|
3.3
|
79.8
|
1.0
|
|
HE1
|
A:HIS210
|
3.3
|
14.6
|
0.3
|
|
HE1
|
A:HIS210
|
3.3
|
22.2
|
0.2
|
|
ND1
|
A:HIS83
|
3.4
|
21.5
|
0.2
|
|
CE1
|
A:HIS210
|
3.4
|
12.5
|
0.4
|
|
CB
|
A:HIS210
|
3.4
|
18.7
|
0.3
|
|
ND1
|
A:HIS83
|
3.5
|
27.2
|
0.3
|
|
CB
|
A:HIS210
|
3.5
|
19.0
|
0.2
|
|
HD2
|
A:HIS83
|
3.5
|
21.6
|
0.2
|
|
CB
|
A:HIS210
|
3.5
|
13.2
|
0.4
|
|
ND1
|
A:HIS180
|
3.6
|
0.0
|
1.0
|
|
HD1
|
A:HIS83
|
3.6
|
19.6
|
0.4
|
|
HD2
|
A:HIS83
|
3.6
|
11.4
|
0.3
|
|
O
|
A:HOH517
|
3.7
|
29.8
|
1.0
|
|
HE1
|
A:HIS210
|
3.8
|
14.9
|
0.4
|
|
CG
|
A:HIS83
|
3.8
|
16.8
|
0.4
|
|
HB2
|
A:HIS210
|
3.8
|
22.5
|
0.3
|
|
CG
|
A:HIS83
|
3.8
|
7.8
|
0.2
|
|
HB2
|
A:HIS210
|
3.8
|
22.9
|
0.2
|
|
CG
|
A:HIS83
|
3.9
|
11.4
|
0.3
|
|
HB2
|
A:HIS210
|
3.9
|
15.7
|
0.4
|
|
HD2
|
A:HIS83
|
3.9
|
22.4
|
0.4
|
|
CD2
|
A:HIS210
|
4.0
|
17.5
|
0.4
|
|
O3
|
A:P6F405
|
4.1
|
25.5
|
0.7
|
|
CG
|
A:HIS180
|
4.1
|
85.9
|
1.0
|
|
NE2
|
A:HIS210
|
4.1
|
15.2
|
0.4
|
|
O2
|
A:P6F405
|
4.1
|
25.4
|
0.7
|
|
NE2
|
A:HIS210
|
4.1
|
17.5
|
0.2
|
|
O4
|
A:P6F405
|
4.1
|
30.1
|
0.7
|
|
HD1
|
A:HIS83
|
4.1
|
25.8
|
0.2
|
|
HD1
|
A:HIS83
|
4.1
|
32.7
|
0.3
|
|
CD2
|
A:HIS210
|
4.1
|
12.5
|
0.2
|
|
OE2
|
A:GLU134
|
4.2
|
34.4
|
1.0
|
|
NE2
|
A:HIS210
|
4.2
|
12.2
|
0.3
|
|
CD2
|
A:HIS210
|
4.3
|
14.1
|
0.3
|
|
OE1
|
A:GLU134
|
4.4
|
43.9
|
1.0
|
|
HO4
|
A:P6F405
|
4.5
|
36.1
|
0.7
|
|
HE1
|
A:MET102
|
4.5
|
18.1
|
1.0
|
|
HD22
|
A:ASN253
|
4.6
|
19.4
|
1.0
|
|
HD2
|
A:HIS210
|
4.6
|
21.1
|
0.4
|
|
CD
|
A:GLU134
|
4.7
|
34.3
|
1.0
|
|
HE2
|
A:HIS210
|
4.8
|
18.2
|
0.4
|
|
HA
|
A:HIS210
|
4.8
|
17.3
|
0.4
|
|
CA
|
A:HIS210
|
4.8
|
13.8
|
0.3
|
|
H
|
A:GLY211
|
4.8
|
24.9
|
1.0
|
|
CA
|
A:HIS210
|
4.8
|
15.7
|
0.2
|
|
CA
|
A:HIS210
|
4.8
|
14.4
|
0.4
|
|
HA
|
A:HIS210
|
4.8
|
18.9
|
0.2
|
|
HA
|
A:HIS210
|
4.8
|
16.6
|
0.3
|
|
HE2
|
A:HIS210
|
4.8
|
21.1
|
0.2
|
|
C2
|
A:P6F405
|
4.9
|
25.9
|
0.7
|
|
C3
|
A:P6F405
|
4.9
|
26.4
|
0.7
|
|
C4
|
A:P6F405
|
4.9
|
28.1
|
0.7
|
|
HD2
|
A:HIS210
|
4.9
|
14.9
|
0.2
|
|
H4
|
A:P6F405
|
4.9
|
33.8
|
0.7
|
|
Zinc binding site 3 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 3 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and 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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn404
b:21.5
occ:0.20
|
HE1
|
A:HIS83
|
1.3
|
33.5
|
0.4
|
|
HO3
|
A:P6F405
|
1.4
|
30.6
|
0.7
|
|
ZN
|
A:ZN403
|
1.7
|
20.5
|
0.3
|
|
NE2
|
A:HIS180
|
2.0
|
50.8
|
1.0
|
|
NE2
|
A:HIS83
|
2.0
|
25.3
|
0.3
|
|
NE2
|
A:HIS83
|
2.0
|
22.4
|
0.2
|
|
CE1
|
A:HIS83
|
2.0
|
27.9
|
0.4
|
|
ND1
|
A:HIS210
|
2.2
|
12.6
|
0.2
|
|
O3
|
A:P6F405
|
2.4
|
25.5
|
0.7
|
|
ND1
|
A:HIS210
|
2.5
|
33.8
|
0.3
|
|
CD2
|
A:HIS83
|
2.7
|
17.9
|
0.2
|
|
HD2
|
A:HIS83
|
2.7
|
21.6
|
0.2
|
|
O2
|
A:P6F405
|
2.7
|
25.4
|
0.7
|
|
CD2
|
A:HIS83
|
2.8
|
9.5
|
0.3
|
|
CD2
|
A:HIS180
|
2.8
|
79.8
|
1.0
|
|
HD2
|
A:HIS83
|
2.8
|
11.4
|
0.3
|
|
ND1
|
A:HIS83
|
2.9
|
16.3
|
0.4
|
|
O4
|
A:P6F405
|
2.9
|
30.1
|
0.7
|
|
HD1
|
A:HIS83
|
3.0
|
19.6
|
0.4
|
|
NE2
|
A:HIS83
|
3.0
|
20.0
|
0.4
|
|
HB3
|
A:HIS210
|
3.0
|
22.5
|
0.3
|
|
CE1
|
A:HIS210
|
3.1
|
18.5
|
0.2
|
|
HB3
|
A:HIS210
|
3.1
|
15.7
|
0.4
|
|
CE1
|
A:HIS180
|
3.1
|
51.8
|
1.0
|
|
HB3
|
A:HIS210
|
3.1
|
22.9
|
0.2
|
|
CE1
|
A:HIS83
|
3.1
|
12.6
|
0.3
|
|
HE1
|
A:HIS210
|
3.1
|
22.2
|
0.2
|
|
C3
|
A:P6F405
|
3.2
|
26.4
|
0.7
|
|
CE1
|
A:HIS83
|
3.2
|
20.0
|
0.2
|
|
HO4
|
A:P6F405
|
3.2
|
36.1
|
0.7
|
|
HD22
|
A:ASN253
|
3.2
|
19.4
|
1.0
|
|
C2
|
A:P6F405
|
3.3
|
25.9
|
0.7
|
|
CG
|
A:HIS210
|
3.3
|
12.9
|
0.2
|
|
CE1
|
A:HIS210
|
3.3
|
12.3
|
0.3
|
|
CG
|
A:HIS210
|
3.3
|
12.8
|
0.3
|
|
C4
|
A:P6F405
|
3.4
|
28.1
|
0.7
|
|
HE1
|
A:HIS83
|
3.5
|
15.1
|
0.3
|
|
HE1
|
A:HIS210
|
3.5
|
14.6
|
0.3
|
|
CG
|
A:HIS210
|
3.5
|
24.3
|
0.4
|
|
HE1
|
A:HIS83
|
3.6
|
24.0
|
0.2
|
|
H4
|
A:P6F405
|
3.6
|
33.8
|
0.7
|
|
CB
|
A:HIS210
|
3.7
|
18.7
|
0.3
|
|
ZN
|
A:ZN402
|
3.7
|
29.8
|
0.4
|
|
CB
|
A:HIS210
|
3.7
|
19.0
|
0.2
|
|
ND1
|
A:HIS210
|
3.7
|
17.1
|
0.4
|
|
CB
|
A:HIS210
|
3.8
|
13.2
|
0.4
|
|
CD2
|
A:HIS210
|
4.0
|
17.5
|
0.4
|
|
CG
|
A:HIS83
|
4.0
|
7.8
|
0.2
|
|
ND2
|
A:ASN253
|
4.0
|
16.2
|
1.0
|
|
CG
|
A:HIS180
|
4.0
|
85.9
|
1.0
|
|
CG
|
A:HIS83
|
4.0
|
16.8
|
0.4
|
|
CG
|
A:HIS83
|
4.0
|
11.4
|
0.3
|
|
OD1
|
A:ASP82
|
4.0
|
16.7
|
1.0
|
|
H
|
A:GLY211
|
4.0
|
24.9
|
1.0
|
|
CD2
|
A:HIS83
|
4.1
|
18.6
|
0.4
|
|
ND1
|
A:HIS180
|
4.1
|
0.0
|
1.0
|
|
ND1
|
A:HIS83
|
4.1
|
27.2
|
0.3
|
|
ND1
|
A:HIS83
|
4.2
|
21.5
|
0.2
|
|
CE1
|
A:HIS210
|
4.2
|
12.5
|
0.4
|
|
H3
|
A:P6F405
|
4.2
|
31.7
|
0.7
|
|
NE2
|
A:HIS210
|
4.2
|
17.5
|
0.2
|
|
HD21
|
A:ASN253
|
4.2
|
19.4
|
1.0
|
|
HA
|
A:HIS210
|
4.2
|
17.3
|
0.4
|
|
HA
|
A:HIS210
|
4.3
|
18.9
|
0.2
|
|
HA
|
A:HIS210
|
4.3
|
16.6
|
0.3
|
|
NE2
|
A:HIS210
|
4.3
|
15.2
|
0.4
|
|
NE2
|
A:HIS210
|
4.3
|
12.2
|
0.3
|
|
HD2
|
A:HIS210
|
4.3
|
21.1
|
0.4
|
|
CD2
|
A:HIS210
|
4.4
|
14.1
|
0.3
|
|
CD2
|
A:HIS210
|
4.4
|
12.5
|
0.2
|
|
HB2
|
A:HIS210
|
4.4
|
22.5
|
0.3
|
|
HB2
|
A:HIS210
|
4.4
|
22.9
|
0.2
|
|
HB2
|
A:HIS210
|
4.5
|
15.7
|
0.4
|
|
CA
|
A:HIS210
|
4.6
|
13.8
|
0.3
|
|
CA
|
A:HIS210
|
4.6
|
15.7
|
0.2
|
|
CA
|
A:HIS210
|
4.6
|
14.4
|
0.4
|
|
HB3
|
A:ASN253
|
4.6
|
17.8
|
1.0
|
|
N
|
A:GLY211
|
4.7
|
20.7
|
1.0
|
|
O
|
A:HOH609
|
4.7
|
25.9
|
0.4
|
|
OD2
|
A:ASP82
|
4.7
|
25.1
|
1.0
|
|
HE1
|
A:HIS210
|
4.7
|
14.9
|
0.4
|
|
C1
|
A:P6F405
|
4.7
|
26.4
|
0.7
|
|
CG
|
A:ASP82
|
4.8
|
19.8
|
1.0
|
|
HE2
|
A:HIS210
|
4.9
|
18.2
|
0.4
|
|
HB2
|
A:ASN253
|
4.9
|
17.8
|
1.0
|
|
HD2
|
A:HIS83
|
4.9
|
22.4
|
0.4
|
|
C5
|
A:P6F405
|
4.9
|
27.8
|
0.7
|
|
HD1
|
A:HIS83
|
5.0
|
32.7
|
0.3
|
|
HD1
|
A:HIS83
|
5.0
|
25.8
|
0.2
|
|
HE2
|
A:HIS210
|
5.0
|
21.1
|
0.2
|
|
CG
|
A:ASN253
|
5.0
|
10.7
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 4 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
 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 E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:25.4
occ:0.40
|
HE1
|
B:HIS83
|
1.7
|
22.6
|
0.2
|
|
HD1
|
B:HIS210
|
1.8
|
13.1
|
0.4
|
|
HE1
|
B:HIS83
|
1.9
|
19.1
|
0.3
|
|
HD1
|
B:HIS210
|
1.9
|
26.0
|
0.3
|
|
ZN
|
B:ZN403
|
2.0
|
29.6
|
0.3
|
|
O
|
B:HOH563
|
2.2
|
23.6
|
1.0
|
|
OE2
|
B:GLU134
|
2.4
|
43.8
|
1.0
|
|
ND1
|
B:HIS210
|
2.4
|
10.9
|
0.4
|
|
NE2
|
B:HIS83
|
2.4
|
17.0
|
0.4
|
|
CE1
|
B:HIS83
|
2.5
|
18.8
|
0.2
|
|
OE1
|
B:GLU134
|
2.6
|
31.1
|
1.0
|
|
ND1
|
B:HIS210
|
2.6
|
21.7
|
0.3
|
|
CE1
|
B:HIS83
|
2.7
|
15.9
|
0.3
|
|
CD
|
B:GLU134
|
2.8
|
43.6
|
1.0
|
|
CE1
|
B:HIS210
|
3.1
|
10.8
|
0.4
|
|
NE2
|
B:HIS83
|
3.1
|
31.7
|
0.2
|
|
CE1
|
B:HIS180
|
3.1
|
75.9
|
1.0
|
|
HE1
|
B:HIS210
|
3.1
|
13.0
|
0.4
|
|
HE1
|
B:HIS83
|
3.2
|
35.1
|
0.4
|
|
CE1
|
B:HIS83
|
3.2
|
29.2
|
0.4
|
|
NE2
|
B:HIS83
|
3.2
|
28.5
|
0.3
|
|
HD1
|
B:HIS210
|
3.2
|
15.0
|
0.2
|
|
ND1
|
B:HIS210
|
3.3
|
12.4
|
0.2
|
|
CG
|
B:HIS210
|
3.4
|
19.1
|
0.4
|
|
NE2
|
B:HIS180
|
3.4
|
77.8
|
1.0
|
|
CE1
|
B:HIS210
|
3.5
|
11.7
|
0.3
|
|
HB3
|
B:HIS210
|
3.5
|
19.2
|
0.2
|
|
CD2
|
B:HIS83
|
3.6
|
17.1
|
0.4
|
|
HB3
|
B:HIS210
|
3.6
|
10.3
|
0.3
|
|
HB3
|
B:HIS210
|
3.6
|
36.3
|
0.4
|
|
CG
|
B:HIS210
|
3.6
|
10.3
|
0.3
|
|
HE1
|
B:HIS210
|
3.6
|
14.1
|
0.3
|
|
CG
|
B:HIS210
|
3.6
|
11.2
|
0.2
|
|
ZN
|
B:ZN404
|
3.6
|
23.9
|
0.2
|
|
ND1
|
B:HIS83
|
3.7
|
22.7
|
0.2
|
|
HB2
|
B:HIS210
|
3.7
|
19.2
|
0.2
|
|
HB2
|
B:HIS210
|
3.8
|
10.3
|
0.3
|
|
HD2
|
B:HIS83
|
3.8
|
20.5
|
0.4
|
|
ND1
|
B:HIS83
|
3.8
|
25.6
|
0.3
|
|
CB
|
B:HIS210
|
3.9
|
16.0
|
0.2
|
|
CB
|
B:HIS210
|
3.9
|
30.2
|
0.4
|
|
CB
|
B:HIS210
|
3.9
|
8.7
|
0.3
|
|
HB2
|
B:HIS210
|
3.9
|
36.3
|
0.4
|
|
CE1
|
B:HIS210
|
3.9
|
30.2
|
0.2
|
|
HE1
|
B:MET102
|
3.9
|
16.5
|
1.0
|
|
HD1
|
B:HIS83
|
4.1
|
27.2
|
0.2
|
|
O
|
B:HOH502
|
4.1
|
21.8
|
1.0
|
|
HD1
|
B:HIS83
|
4.1
|
30.8
|
0.3
|
|
NE2
|
B:HIS210
|
4.1
|
12.9
|
0.4
|
|
HE1
|
B:HIS210
|
4.3
|
36.3
|
0.2
|
|
CD2
|
B:HIS210
|
4.3
|
8.5
|
0.2
|
|
O
|
B:HOH529
|
4.3
|
30.3
|
1.0
|
|
CD2
|
B:HIS210
|
4.3
|
10.0
|
0.4
|
|
ND1
|
B:HIS180
|
4.3
|
0.7
|
1.0
|
|
CG
|
B:GLU134
|
4.3
|
17.2
|
1.0
|
|
ND1
|
B:HIS83
|
4.4
|
16.4
|
0.4
|
|
CD2
|
B:HIS83
|
4.4
|
20.4
|
0.2
|
|
OD2
|
B:ASP104
|
4.4
|
27.3
|
1.0
|
|
NE2
|
B:HIS210
|
4.4
|
26.2
|
0.2
|
|
CD2
|
B:HIS83
|
4.5
|
23.9
|
0.3
|
|
NE2
|
B:HIS210
|
4.6
|
8.2
|
0.3
|
|
CG
|
B:HIS83
|
4.6
|
19.5
|
0.4
|
|
HG3
|
B:GLU134
|
4.6
|
20.7
|
1.0
|
|
CD2
|
B:HIS210
|
4.6
|
20.3
|
0.3
|
|
CG
|
B:HIS83
|
4.7
|
16.6
|
0.2
|
|
CD2
|
B:HIS180
|
4.7
|
89.5
|
1.0
|
|
HG2
|
B:GLU134
|
4.8
|
20.7
|
1.0
|
|
HB2
|
B:GLU134
|
4.8
|
21.3
|
1.0
|
|
CE
|
B:MET102
|
4.8
|
13.7
|
1.0
|
|
CG
|
B:HIS83
|
4.8
|
10.5
|
0.3
|
|
HD2
|
B:HIS210
|
4.8
|
10.3
|
0.2
|
|
HE2
|
B:HIS210
|
4.8
|
15.5
|
0.4
|
|
HE3
|
B:MET102
|
4.9
|
16.5
|
1.0
|
|
CG
|
B:ASP104
|
5.0
|
24.2
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 5 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn403
b:29.6
occ:0.30
|
HD1
|
B:HIS210
|
1.4
|
26.0
|
0.3
|
|
HE1
|
B:HIS83
|
1.6
|
35.1
|
0.4
|
|
ZN
|
B:ZN404
|
1.7
|
23.9
|
0.2
|
|
NE2
|
B:HIS83
|
1.8
|
31.7
|
0.2
|
|
HD1
|
B:HIS210
|
1.8
|
15.0
|
0.2
|
|
NE2
|
B:HIS83
|
1.9
|
28.5
|
0.3
|
|
CE1
|
B:HIS83
|
1.9
|
29.2
|
0.4
|
|
NE2
|
B:HIS180
|
1.9
|
77.8
|
1.0
|
|
NE2
|
B:HIS83
|
2.0
|
17.0
|
0.4
|
|
ZN
|
B:ZN402
|
2.0
|
25.4
|
0.4
|
|
HE1
|
B:HIS83
|
2.0
|
19.1
|
0.3
|
|
HE1
|
B:HIS83
|
2.1
|
22.6
|
0.2
|
|
CE1
|
B:HIS83
|
2.2
|
15.9
|
0.3
|
|
CE1
|
B:HIS83
|
2.2
|
18.8
|
0.2
|
|
ND1
|
B:HIS210
|
2.2
|
21.7
|
0.3
|
|
ND1
|
B:HIS210
|
2.4
|
12.4
|
0.2
|
|
CE1
|
B:HIS180
|
2.4
|
75.9
|
1.0
|
|
HD1
|
B:HIS210
|
2.8
|
13.1
|
0.4
|
|
HB3
|
B:HIS210
|
2.8
|
19.2
|
0.2
|
|
HB3
|
B:HIS210
|
2.8
|
10.3
|
0.3
|
|
ND1
|
B:HIS210
|
2.8
|
10.9
|
0.4
|
|
HB3
|
B:HIS210
|
2.9
|
36.3
|
0.4
|
|
CD2
|
B:HIS83
|
3.1
|
20.4
|
0.2
|
|
CG
|
B:HIS210
|
3.1
|
11.2
|
0.2
|
|
CG
|
B:HIS210
|
3.1
|
19.1
|
0.4
|
|
ND1
|
B:HIS83
|
3.2
|
16.4
|
0.4
|
|
CG
|
B:HIS210
|
3.2
|
10.3
|
0.3
|
|
CE1
|
B:HIS210
|
3.2
|
11.7
|
0.3
|
|
CD2
|
B:HIS180
|
3.2
|
89.5
|
1.0
|
|
CD2
|
B:HIS83
|
3.2
|
23.9
|
0.3
|
|
CE1
|
B:HIS210
|
3.2
|
30.2
|
0.2
|
|
CD2
|
B:HIS83
|
3.3
|
17.1
|
0.4
|
|
HE1
|
B:HIS210
|
3.4
|
14.1
|
0.3
|
|
CB
|
B:HIS210
|
3.4
|
16.0
|
0.2
|
|
CB
|
B:HIS210
|
3.4
|
8.7
|
0.3
|
|
ND1
|
B:HIS83
|
3.4
|
22.7
|
0.2
|
|
CE1
|
B:HIS210
|
3.4
|
10.8
|
0.4
|
|
ND1
|
B:HIS83
|
3.5
|
25.6
|
0.3
|
|
CB
|
B:HIS210
|
3.5
|
30.2
|
0.4
|
|
HE1
|
B:HIS210
|
3.5
|
36.3
|
0.2
|
|
HD2
|
B:HIS83
|
3.6
|
24.4
|
0.2
|
|
O
|
B:HOH563
|
3.6
|
23.6
|
1.0
|
|
ND1
|
B:HIS180
|
3.7
|
0.7
|
1.0
|
|
HD1
|
B:HIS83
|
3.7
|
19.7
|
0.4
|
|
HD2
|
B:HIS83
|
3.7
|
28.8
|
0.3
|
|
HB2
|
B:HIS210
|
3.8
|
19.2
|
0.2
|
|
HB2
|
B:HIS210
|
3.8
|
10.3
|
0.3
|
|
HE1
|
B:HIS210
|
3.8
|
13.0
|
0.4
|
|
CG
|
B:HIS83
|
3.8
|
19.5
|
0.4
|
|
O1
|
B:G3H406
|
3.8
|
29.6
|
0.4
|
|
CD2
|
B:HIS210
|
3.8
|
10.0
|
0.4
|
|
O2
|
B:13P405
|
3.9
|
29.1
|
0.8
|
|
CG
|
B:HIS83
|
3.9
|
16.6
|
0.2
|
|
O3
|
B:13P405
|
3.9
|
28.0
|
0.8
|
|
HB2
|
B:HIS210
|
3.9
|
36.3
|
0.4
|
|
HD2
|
B:HIS83
|
4.0
|
20.5
|
0.4
|
|
CG
|
B:HIS83
|
4.0
|
10.5
|
0.3
|
|
NE2
|
B:HIS210
|
4.0
|
12.9
|
0.4
|
|
CG
|
B:HIS180
|
4.0
|
0.3
|
1.0
|
|
HD1
|
B:HIS83
|
4.1
|
30.8
|
0.3
|
|
HD1
|
B:HIS83
|
4.1
|
27.2
|
0.2
|
|
CD2
|
B:HIS210
|
4.2
|
8.5
|
0.2
|
|
NE2
|
B:HIS210
|
4.2
|
26.2
|
0.2
|
|
OE1
|
B:GLU134
|
4.2
|
31.1
|
1.0
|
|
OE2
|
B:GLU134
|
4.2
|
43.8
|
1.0
|
|
H11
|
B:G3H406
|
4.3
|
35.2
|
0.3
|
|
NE2
|
B:HIS210
|
4.3
|
8.2
|
0.3
|
|
CD2
|
B:HIS210
|
4.3
|
20.3
|
0.3
|
|
HO3
|
B:13P405
|
4.4
|
33.6
|
0.8
|
|
HD2
|
B:HIS210
|
4.5
|
12.0
|
0.4
|
|
HD22
|
B:ASN253
|
4.5
|
18.9
|
1.0
|
|
HE2
|
B:HIS210
|
4.6
|
15.5
|
0.4
|
|
CD
|
B:GLU134
|
4.6
|
43.6
|
1.0
|
|
H
|
B:GLY211
|
4.7
|
22.8
|
1.0
|
|
HE1
|
B:MET102
|
4.7
|
16.5
|
1.0
|
|
HA
|
B:HIS210
|
4.7
|
13.8
|
0.4
|
|
CA
|
B:HIS210
|
4.7
|
11.5
|
0.4
|
|
CA
|
B:HIS210
|
4.7
|
10.5
|
0.2
|
|
CA
|
B:HIS210
|
4.7
|
10.5
|
0.3
|
|
C1
|
B:G3H406
|
4.8
|
28.6
|
0.4
|
|
HA
|
B:HIS210
|
4.8
|
12.7
|
0.2
|
|
HA
|
B:HIS210
|
4.8
|
12.7
|
0.3
|
|
H11
|
B:G3H406
|
4.8
|
34.4
|
0.4
|
|
C2
|
B:13P405
|
4.9
|
29.2
|
0.8
|
|
HE2
|
B:HIS210
|
5.0
|
31.5
|
0.2
|
|
HD2
|
B:HIS210
|
5.0
|
10.3
|
0.2
|
|
Zinc binding site 6 out
of 6 in 5ucp
Go back to
Zinc Binding Sites List in 5ucp
Zinc binding site 6 out
of 6 in the Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Class II Fructose-1,6-Bisphosphate Aldolase E142A Variant of Helicobacter Pylori with Fbp and Cleavage Products within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn404
b:23.9
occ:0.20
|
HE1
|
B:HIS83
|
1.3
|
35.1
|
0.4
|
|
HD1
|
B:HIS210
|
1.5
|
15.0
|
0.2
|
|
ZN
|
B:ZN403
|
1.7
|
29.6
|
0.3
|
|
NE2
|
B:HIS180
|
2.0
|
77.8
|
1.0
|
|
NE2
|
B:HIS83
|
2.0
|
28.5
|
0.3
|
|
NE2
|
B:HIS83
|
2.0
|
31.7
|
0.2
|
|
CE1
|
B:HIS83
|
2.1
|
29.2
|
0.4
|
|
O3
|
B:13P405
|
2.3
|
28.0
|
0.8
|
|
ND1
|
B:HIS210
|
2.3
|
12.4
|
0.2
|
|
HD1
|
B:HIS210
|
2.4
|
26.0
|
0.3
|
|
O2
|
B:13P405
|
2.5
|
29.1
|
0.8
|
|
O1
|
B:G3H406
|
2.5
|
29.6
|
0.4
|
|
CD2
|
B:HIS180
|
2.7
|
89.5
|
1.0
|
|
ND1
|
B:HIS210
|
2.8
|
21.7
|
0.3
|
|
CD2
|
B:HIS83
|
2.8
|
20.4
|
0.2
|
|
HD2
|
B:HIS83
|
2.9
|
24.4
|
0.2
|
|
CD2
|
B:HIS83
|
2.9
|
23.9
|
0.3
|
|
HO3
|
B:13P405
|
2.9
|
33.6
|
0.8
|
|
ND1
|
B:HIS83
|
2.9
|
16.4
|
0.4
|
|
H11
|
B:G3H406
|
2.9
|
35.2
|
0.3
|
|
HB3
|
B:HIS210
|
3.0
|
10.3
|
0.3
|
|
HD2
|
B:HIS83
|
3.0
|
28.8
|
0.3
|
|
HB3
|
B:HIS210
|
3.0
|
19.2
|
0.2
|
|
NE2
|
B:HIS83
|
3.0
|
17.0
|
0.4
|
|
HB3
|
B:HIS210
|
3.1
|
36.3
|
0.4
|
|
HD1
|
B:HIS83
|
3.1
|
19.7
|
0.4
|
|
CE1
|
B:HIS83
|
3.1
|
15.9
|
0.3
|
|
CE1
|
B:HIS180
|
3.1
|
75.9
|
1.0
|
|
CE1
|
B:HIS83
|
3.2
|
18.8
|
0.2
|
|
CE1
|
B:HIS210
|
3.2
|
30.2
|
0.2
|
|
HD22
|
B:ASN253
|
3.3
|
18.9
|
1.0
|
|
C2
|
B:13P405
|
3.3
|
29.2
|
0.8
|
|
CG
|
B:HIS210
|
3.3
|
11.2
|
0.2
|
|
CG
|
B:HIS210
|
3.4
|
10.3
|
0.3
|
|
HE1
|
B:HIS83
|
3.4
|
19.1
|
0.3
|
|
HE1
|
B:HIS210
|
3.4
|
36.3
|
0.2
|
|
C3
|
B:13P405
|
3.4
|
27.9
|
0.8
|
|
HE1
|
B:HIS83
|
3.5
|
22.6
|
0.2
|
|
CG
|
B:HIS210
|
3.5
|
19.1
|
0.4
|
|
CE1
|
B:HIS210
|
3.5
|
11.7
|
0.3
|
|
C1
|
B:G3H406
|
3.6
|
28.6
|
0.4
|
|
CB
|
B:HIS210
|
3.6
|
16.0
|
0.2
|
|
CB
|
B:HIS210
|
3.6
|
8.7
|
0.3
|
|
ZN
|
B:ZN402
|
3.6
|
25.4
|
0.4
|
|
CB
|
B:HIS210
|
3.7
|
30.2
|
0.4
|
|
ND1
|
B:HIS210
|
3.8
|
10.9
|
0.4
|
|
HE1
|
B:HIS210
|
3.8
|
14.1
|
0.3
|
|
CD2
|
B:HIS210
|
3.8
|
10.0
|
0.4
|
|
C1
|
B:G3H406
|
3.8
|
29.3
|
0.3
|
|
H
|
B:GLY211
|
3.9
|
22.8
|
1.0
|
|
H11
|
B:G3H406
|
3.9
|
34.4
|
0.4
|
|
CG
|
B:HIS180
|
3.9
|
0.3
|
1.0
|
|
H31
|
B:13P405
|
4.0
|
33.5
|
0.8
|
|
HD1
|
B:HIS210
|
4.0
|
13.1
|
0.4
|
|
CG
|
B:HIS83
|
4.0
|
16.6
|
0.2
|
|
ND2
|
B:ASN253
|
4.0
|
15.7
|
1.0
|
|
CG
|
B:HIS83
|
4.0
|
19.5
|
0.4
|
|
CG
|
B:HIS83
|
4.1
|
10.5
|
0.3
|
|
CD2
|
B:HIS83
|
4.1
|
17.1
|
0.4
|
|
ND1
|
B:HIS180
|
4.1
|
0.7
|
1.0
|
|
ND1
|
B:HIS83
|
4.1
|
25.6
|
0.3
|
|
O1
|
B:G3H406
|
4.1
|
29.4
|
0.3
|
|
HD2
|
B:HIS210
|
4.1
|
12.0
|
0.4
|
|
ND1
|
B:HIS83
|
4.2
|
22.7
|
0.2
|
|
HA
|
B:HIS210
|
4.2
|
13.8
|
0.4
|
|
OD1
|
B:ASP82
|
4.2
|
17.3
|
1.0
|
|
H32
|
B:13P405
|
4.2
|
33.5
|
0.8
|
|
CE1
|
B:HIS210
|
4.2
|
10.8
|
0.4
|
|
HA
|
B:HIS210
|
4.2
|
12.7
|
0.2
|
|
HA
|
B:HIS210
|
4.2
|
12.7
|
0.3
|
|
NE2
|
B:HIS210
|
4.3
|
12.9
|
0.4
|
|
CD2
|
B:HIS210
|
4.3
|
20.3
|
0.3
|
|
HD21
|
B:ASN253
|
4.3
|
18.9
|
1.0
|
|
HB2
|
B:HIS210
|
4.3
|
19.2
|
0.2
|
|
HB2
|
B:HIS210
|
4.3
|
10.3
|
0.3
|
|
NE2
|
B:HIS210
|
4.3
|
8.2
|
0.3
|
|
NE2
|
B:HIS210
|
4.4
|
26.2
|
0.2
|
|
CD2
|
B:HIS210
|
4.4
|
8.5
|
0.2
|
|
HB2
|
B:HIS210
|
4.5
|
36.3
|
0.4
|
|
CA
|
B:HIS210
|
4.5
|
10.5
|
0.2
|
|
CA
|
B:HIS210
|
4.5
|
10.5
|
0.3
|
|
CA
|
B:HIS210
|
4.5
|
11.5
|
0.4
|
|
N
|
B:GLY211
|
4.5
|
19.0
|
1.0
|
|
HB3
|
B:ASN253
|
4.6
|
11.3
|
1.0
|
|
C1
|
B:13P405
|
4.7
|
29.6
|
0.8
|
|
HE1
|
B:HIS210
|
4.8
|
13.0
|
0.4
|
|
HE2
|
B:HIS210
|
4.8
|
15.5
|
0.4
|
|
HB2
|
B:ASN253
|
4.8
|
11.3
|
1.0
|
|
OD2
|
B:ASP82
|
4.9
|
25.8
|
1.0
|
|
C2
|
B:G3H406
|
4.9
|
27.0
|
0.4
|
|
HD2
|
B:HIS83
|
4.9
|
20.5
|
0.4
|
|
HD1
|
B:HIS83
|
4.9
|
30.8
|
0.3
|
|
CG
|
B:ASP82
|
5.0
|
22.5
|
1.0
|
|
HD1
|
B:HIS83
|
5.0
|
27.2
|
0.2
|
|
O2
|
B:G3H406
|
5.0
|
27.3
|
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
|
