Zinc in PDB 3n9r: Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor, PDB code: 3n9r
was solved by
M.Coincon,
S.Sygusch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
41.53 /
1.80
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.400,
104.400,
111.900,
98.50,
90.00,
90.00
|
|
R / Rfree (%)
|
15.8 /
20.3
|
Other elements in 3n9r:
The structure of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
(pdb code 3n9r). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor, PDB code: 3n9r:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 1 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn308
b:15.8
occ:1.00
|
O01
|
A:TD3311
|
2.0
|
30.1
|
1.0
|
|
NE2
|
A:HIS180
|
2.1
|
16.2
|
1.0
|
|
ND1
|
A:HIS210
|
2.1
|
11.1
|
1.0
|
|
NE2
|
A:HIS83
|
2.1
|
11.8
|
1.0
|
|
O13
|
A:TD3311
|
2.4
|
13.6
|
1.0
|
|
N02
|
A:TD3311
|
2.9
|
31.9
|
1.0
|
|
HB3
|
A:HIS210
|
2.9
|
13.3
|
1.0
|
|
CE1
|
A:HIS210
|
3.0
|
14.2
|
1.0
|
|
C12
|
A:TD3311
|
3.0
|
18.0
|
1.0
|
|
CE1
|
A:HIS180
|
3.0
|
27.7
|
1.0
|
|
CD2
|
A:HIS180
|
3.0
|
14.8
|
1.0
|
|
CE1
|
A:HIS83
|
3.1
|
13.8
|
1.0
|
|
HE1
|
A:HIS210
|
3.1
|
17.0
|
1.0
|
|
CD2
|
A:HIS83
|
3.1
|
14.3
|
1.0
|
|
CG
|
A:HIS210
|
3.1
|
15.4
|
1.0
|
|
HE1
|
A:HIS180
|
3.2
|
33.2
|
1.0
|
|
HE1
|
A:HIS83
|
3.2
|
16.5
|
1.0
|
|
HD2
|
A:HIS180
|
3.2
|
17.7
|
1.0
|
|
HD2
|
A:HIS83
|
3.3
|
17.2
|
1.0
|
|
HD22
|
A:ASN253
|
3.3
|
16.9
|
1.0
|
|
CB
|
A:HIS210
|
3.5
|
11.1
|
1.0
|
|
H
|
A:GLY211
|
4.0
|
12.1
|
1.0
|
|
ND1
|
A:HIS180
|
4.1
|
21.9
|
1.0
|
|
ND2
|
A:ASN253
|
4.1
|
14.1
|
1.0
|
|
NE2
|
A:HIS210
|
4.1
|
11.8
|
1.0
|
|
CG
|
A:HIS180
|
4.1
|
16.0
|
1.0
|
|
HA
|
A:HIS210
|
4.2
|
11.1
|
1.0
|
|
ND1
|
A:HIS83
|
4.2
|
14.5
|
1.0
|
|
CD2
|
A:HIS210
|
4.2
|
9.4
|
1.0
|
|
C03
|
A:TD3311
|
4.2
|
29.3
|
1.0
|
|
HB2
|
A:HIS210
|
4.2
|
13.3
|
1.0
|
|
CG
|
A:HIS83
|
4.3
|
14.3
|
1.0
|
|
O
|
A:HOH807
|
4.3
|
41.1
|
1.0
|
|
OD1
|
A:ASP82
|
4.3
|
20.5
|
1.0
|
|
HD21
|
A:LEU138
|
4.3
|
41.0
|
1.0
|
|
HD21
|
A:ASN253
|
4.4
|
16.9
|
1.0
|
|
CA
|
A:HIS210
|
4.4
|
9.3
|
1.0
|
|
C14
|
A:TD3311
|
4.5
|
15.2
|
1.0
|
|
HD22
|
A:LEU138
|
4.5
|
41.0
|
1.0
|
|
N
|
A:GLY211
|
4.6
|
10.1
|
1.0
|
|
HB3
|
A:ASN253
|
4.7
|
12.9
|
1.0
|
|
HD23
|
A:LEU138
|
4.7
|
41.0
|
1.0
|
|
CD2
|
A:LEU138
|
4.7
|
34.2
|
1.0
|
|
HB2
|
A:ASN253
|
4.8
|
12.9
|
1.0
|
|
OD2
|
A:ASP82
|
4.8
|
24.7
|
1.0
|
|
HD1
|
A:HIS180
|
4.9
|
26.3
|
1.0
|
|
C04
|
A:TD3311
|
4.9
|
31.1
|
1.0
|
|
HE2
|
A:HIS210
|
4.9
|
14.1
|
1.0
|
|
HD1
|
A:HIS83
|
5.0
|
17.4
|
1.0
|
|
O15
|
A:TD3311
|
5.0
|
19.3
|
1.0
|
|
CG
|
A:ASP82
|
5.0
|
22.9
|
1.0
|
|
C
|
A:HIS210
|
5.0
|
13.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 2 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn308
b:14.5
occ:1.00
|
O01
|
B:TD3311
|
2.0
|
35.1
|
1.0
|
|
ND1
|
B:HIS210
|
2.0
|
13.0
|
1.0
|
|
NE2
|
B:HIS180
|
2.1
|
12.9
|
1.0
|
|
NE2
|
B:HIS83
|
2.1
|
13.0
|
1.0
|
|
O13
|
B:TD3311
|
2.4
|
15.9
|
1.0
|
|
N02
|
B:TD3311
|
2.9
|
33.9
|
1.0
|
|
HB3
|
B:HIS210
|
2.9
|
14.9
|
1.0
|
|
CE1
|
B:HIS210
|
2.9
|
15.8
|
1.0
|
|
C12
|
B:TD3311
|
3.0
|
17.9
|
1.0
|
|
CE1
|
B:HIS180
|
3.0
|
23.2
|
1.0
|
|
CD2
|
B:HIS180
|
3.0
|
16.0
|
1.0
|
|
HE1
|
B:HIS210
|
3.1
|
18.9
|
1.0
|
|
CG
|
B:HIS210
|
3.1
|
14.1
|
1.0
|
|
CD2
|
B:HIS83
|
3.1
|
13.2
|
1.0
|
|
CE1
|
B:HIS83
|
3.1
|
16.0
|
1.0
|
|
HD2
|
B:HIS180
|
3.2
|
19.2
|
1.0
|
|
HE1
|
B:HIS180
|
3.2
|
27.9
|
1.0
|
|
HD2
|
B:HIS83
|
3.3
|
15.9
|
1.0
|
|
HE1
|
B:HIS83
|
3.3
|
19.2
|
1.0
|
|
HD22
|
B:ASN253
|
3.3
|
16.9
|
1.0
|
|
CB
|
B:HIS210
|
3.5
|
12.4
|
1.0
|
|
H
|
B:GLY211
|
3.9
|
14.0
|
1.0
|
|
O
|
B:HOH1770
|
4.1
|
31.6
|
1.0
|
|
NE2
|
B:HIS210
|
4.1
|
11.9
|
1.0
|
|
ND2
|
B:ASN253
|
4.1
|
14.1
|
1.0
|
|
ND1
|
B:HIS180
|
4.1
|
20.6
|
1.0
|
|
CG
|
B:HIS180
|
4.1
|
17.0
|
1.0
|
|
HA
|
B:HIS210
|
4.2
|
13.3
|
1.0
|
|
CD2
|
B:HIS210
|
4.2
|
13.4
|
1.0
|
|
HB2
|
B:HIS210
|
4.2
|
14.9
|
1.0
|
|
ND1
|
B:HIS83
|
4.2
|
15.7
|
1.0
|
|
CG
|
B:HIS83
|
4.3
|
11.4
|
1.0
|
|
C03
|
B:TD3311
|
4.3
|
38.1
|
1.0
|
|
O
|
B:HOH641
|
4.3
|
45.3
|
1.0
|
|
HD21
|
B:LEU138
|
4.3
|
39.8
|
1.0
|
|
OD1
|
B:ASP82
|
4.4
|
23.5
|
1.0
|
|
HD22
|
B:LEU138
|
4.4
|
39.8
|
1.0
|
|
CA
|
B:HIS210
|
4.4
|
11.1
|
1.0
|
|
HD21
|
B:ASN253
|
4.4
|
16.9
|
1.0
|
|
C14
|
B:TD3311
|
4.5
|
18.0
|
1.0
|
|
N
|
B:GLY211
|
4.6
|
11.7
|
1.0
|
|
HB3
|
B:ASN253
|
4.6
|
15.1
|
1.0
|
|
HD23
|
B:LEU138
|
4.7
|
39.8
|
1.0
|
|
CD2
|
B:LEU138
|
4.7
|
33.2
|
1.0
|
|
HB2
|
B:ASN253
|
4.8
|
15.1
|
1.0
|
|
OD2
|
B:ASP82
|
4.8
|
29.2
|
1.0
|
|
HE2
|
B:HIS210
|
4.8
|
14.2
|
1.0
|
|
HD1
|
B:HIS180
|
4.9
|
24.6
|
1.0
|
|
C04
|
B:TD3311
|
4.9
|
38.7
|
1.0
|
|
O
|
B:HOH1459
|
4.9
|
49.9
|
1.0
|
|
C
|
B:HIS210
|
5.0
|
11.3
|
1.0
|
|
CG
|
B:ASP82
|
5.0
|
24.6
|
1.0
|
|
Zinc binding site 3 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 3 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Zn308
b:17.2
occ:1.00
|
NE2
|
K:HIS180
|
2.0
|
14.6
|
1.0
|
|
O01
|
K:TD3311
|
2.1
|
33.0
|
1.0
|
|
ND1
|
K:HIS210
|
2.1
|
13.9
|
1.0
|
|
NE2
|
K:HIS83
|
2.1
|
13.7
|
1.0
|
|
O13
|
K:TD3311
|
2.4
|
13.7
|
1.0
|
|
N02
|
K:TD3311
|
2.9
|
34.7
|
1.0
|
|
HB3
|
K:HIS210
|
3.0
|
12.2
|
1.0
|
|
CE1
|
K:HIS180
|
3.0
|
18.9
|
1.0
|
|
CE1
|
K:HIS210
|
3.0
|
17.0
|
1.0
|
|
C12
|
K:TD3311
|
3.0
|
20.6
|
1.0
|
|
CD2
|
K:HIS180
|
3.0
|
14.9
|
1.0
|
|
CD2
|
K:HIS83
|
3.1
|
16.0
|
1.0
|
|
HE1
|
K:HIS210
|
3.1
|
20.4
|
1.0
|
|
CE1
|
K:HIS83
|
3.1
|
16.6
|
1.0
|
|
HE1
|
K:HIS180
|
3.1
|
22.7
|
1.0
|
|
CG
|
K:HIS210
|
3.1
|
11.0
|
1.0
|
|
HD2
|
K:HIS83
|
3.2
|
19.2
|
1.0
|
|
HD2
|
K:HIS180
|
3.2
|
17.9
|
1.0
|
|
HE1
|
K:HIS83
|
3.3
|
19.9
|
1.0
|
|
HD22
|
K:ASN253
|
3.4
|
19.2
|
1.0
|
|
CB
|
K:HIS210
|
3.5
|
10.2
|
1.0
|
|
H
|
K:GLY211
|
3.9
|
14.7
|
1.0
|
|
ND1
|
K:HIS180
|
4.1
|
15.6
|
1.0
|
|
CG
|
K:HIS180
|
4.1
|
14.8
|
1.0
|
|
NE2
|
K:HIS210
|
4.1
|
12.1
|
1.0
|
|
ND2
|
K:ASN253
|
4.1
|
16.0
|
1.0
|
|
HA
|
K:HIS210
|
4.2
|
12.9
|
1.0
|
|
ND1
|
K:HIS83
|
4.2
|
15.1
|
1.0
|
|
CD2
|
K:HIS210
|
4.2
|
12.8
|
1.0
|
|
CG
|
K:HIS83
|
4.2
|
15.1
|
1.0
|
|
C03
|
K:TD3311
|
4.3
|
35.8
|
1.0
|
|
HB2
|
K:HIS210
|
4.3
|
12.2
|
1.0
|
|
HD21
|
K:LEU138
|
4.3
|
43.7
|
1.0
|
|
OD1
|
K:ASP82
|
4.3
|
21.5
|
1.0
|
|
HD22
|
K:LEU138
|
4.4
|
43.7
|
1.0
|
|
CA
|
K:HIS210
|
4.4
|
10.7
|
1.0
|
|
HD21
|
K:ASN253
|
4.5
|
19.2
|
1.0
|
|
C14
|
K:TD3311
|
4.5
|
19.8
|
1.0
|
|
N
|
K:GLY211
|
4.6
|
12.3
|
1.0
|
|
HB3
|
K:ASN253
|
4.6
|
15.3
|
1.0
|
|
CD2
|
K:LEU138
|
4.7
|
36.4
|
1.0
|
|
HD23
|
K:LEU138
|
4.7
|
43.7
|
1.0
|
|
HB2
|
K:ASN253
|
4.8
|
15.3
|
1.0
|
|
HD1
|
K:HIS180
|
4.8
|
18.7
|
1.0
|
|
OD2
|
K:ASP82
|
4.8
|
27.5
|
1.0
|
|
HE2
|
K:HIS210
|
4.9
|
14.5
|
1.0
|
|
C04
|
K:TD3311
|
4.9
|
31.2
|
1.0
|
|
O
|
K:HOH1068
|
4.9
|
46.4
|
1.0
|
|
Zinc binding site 4 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 4 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Zn308
b:13.5
occ:1.00
|
ND1
|
P:HIS210
|
2.1
|
11.5
|
1.0
|
|
NE2
|
P:HIS180
|
2.1
|
15.7
|
1.0
|
|
O01
|
P:TD3311
|
2.1
|
32.0
|
1.0
|
|
NE2
|
P:HIS83
|
2.1
|
12.5
|
1.0
|
|
O13
|
P:TD3311
|
2.4
|
15.2
|
1.0
|
|
N02
|
P:TD3311
|
3.0
|
29.4
|
1.0
|
|
CE1
|
P:HIS210
|
3.0
|
15.9
|
1.0
|
|
HB3
|
P:HIS210
|
3.0
|
9.5
|
1.0
|
|
CE1
|
P:HIS180
|
3.0
|
23.1
|
1.0
|
|
C12
|
P:TD3311
|
3.0
|
19.6
|
1.0
|
|
CD2
|
P:HIS180
|
3.1
|
15.3
|
1.0
|
|
HE1
|
P:HIS210
|
3.1
|
19.0
|
1.0
|
|
CD2
|
P:HIS83
|
3.1
|
13.4
|
1.0
|
|
CE1
|
P:HIS83
|
3.1
|
14.4
|
1.0
|
|
CG
|
P:HIS210
|
3.2
|
10.8
|
1.0
|
|
HE1
|
P:HIS180
|
3.2
|
27.7
|
1.0
|
|
HD2
|
P:HIS83
|
3.2
|
16.1
|
1.0
|
|
HD2
|
P:HIS180
|
3.3
|
18.3
|
1.0
|
|
HE1
|
P:HIS83
|
3.3
|
17.2
|
1.0
|
|
HD22
|
P:ASN253
|
3.3
|
19.4
|
1.0
|
|
CB
|
P:HIS210
|
3.6
|
7.9
|
1.0
|
|
H
|
P:GLY211
|
3.9
|
12.2
|
1.0
|
|
ND1
|
P:HIS180
|
4.1
|
19.7
|
1.0
|
|
ND2
|
P:ASN253
|
4.1
|
16.1
|
1.0
|
|
NE2
|
P:HIS210
|
4.1
|
12.7
|
1.0
|
|
CG
|
P:HIS180
|
4.1
|
16.6
|
1.0
|
|
HD11
|
P:LEU138
|
4.2
|
40.2
|
1.0
|
|
HA
|
P:HIS210
|
4.2
|
9.5
|
1.0
|
|
ND1
|
P:HIS83
|
4.2
|
14.1
|
1.0
|
|
CG
|
P:HIS83
|
4.2
|
12.2
|
1.0
|
|
CD2
|
P:HIS210
|
4.2
|
10.1
|
1.0
|
|
HB2
|
P:HIS210
|
4.3
|
9.5
|
1.0
|
|
C03
|
P:TD3311
|
4.3
|
29.0
|
1.0
|
|
OD1
|
P:ASP82
|
4.3
|
21.5
|
1.0
|
|
HD21
|
P:ASN253
|
4.4
|
19.4
|
1.0
|
|
CA
|
P:HIS210
|
4.4
|
8.0
|
1.0
|
|
HD12
|
P:LEU138
|
4.5
|
40.2
|
1.0
|
|
C14
|
P:TD3311
|
4.5
|
16.8
|
1.0
|
|
N
|
P:GLY211
|
4.6
|
10.2
|
1.0
|
|
HB3
|
P:ASN253
|
4.6
|
16.8
|
1.0
|
|
CD1
|
P:LEU138
|
4.8
|
33.6
|
1.0
|
|
OD2
|
P:ASP82
|
4.8
|
28.0
|
1.0
|
|
HB2
|
P:ASN253
|
4.8
|
16.8
|
1.0
|
|
HD1
|
P:HIS180
|
4.9
|
23.6
|
1.0
|
|
C04
|
P:TD3311
|
4.9
|
26.3
|
1.0
|
|
HE2
|
P:HIS210
|
4.9
|
15.2
|
1.0
|
|
CG
|
P:ASP82
|
5.0
|
24.1
|
1.0
|
|
C
|
P:HIS210
|
5.0
|
11.1
|
1.0
|
|
HD1
|
P:HIS83
|
5.0
|
16.9
|
1.0
|
|
Zinc binding site 5 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 5 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Zn308
b:27.4
occ:1.00
|
ND1
|
U:HIS210
|
2.0
|
28.2
|
1.0
|
|
NE2
|
U:HIS83
|
2.1
|
31.0
|
1.0
|
|
NE2
|
U:HIS180
|
2.1
|
33.2
|
1.0
|
|
O01
|
U:TD3311
|
2.2
|
44.8
|
1.0
|
|
O13
|
U:TD3311
|
2.4
|
35.5
|
1.0
|
|
N02
|
U:TD3311
|
2.9
|
45.9
|
1.0
|
|
CE1
|
U:HIS210
|
2.9
|
27.1
|
1.0
|
|
CE1
|
U:HIS180
|
2.9
|
40.9
|
1.0
|
|
HB3
|
U:HIS210
|
2.9
|
30.7
|
1.0
|
|
C12
|
U:TD3311
|
3.0
|
37.7
|
1.0
|
|
CE1
|
U:HIS83
|
3.0
|
34.2
|
1.0
|
|
HE1
|
U:HIS210
|
3.0
|
32.5
|
1.0
|
|
HE1
|
U:HIS180
|
3.1
|
49.0
|
1.0
|
|
HE1
|
U:HIS83
|
3.1
|
41.0
|
1.0
|
|
CG
|
U:HIS210
|
3.1
|
23.8
|
1.0
|
|
CD2
|
U:HIS180
|
3.1
|
30.4
|
1.0
|
|
CD2
|
U:HIS83
|
3.2
|
28.0
|
1.0
|
|
HD22
|
U:ASN253
|
3.3
|
29.4
|
1.0
|
|
HD2
|
U:HIS180
|
3.4
|
36.5
|
1.0
|
|
HD2
|
U:HIS83
|
3.4
|
33.6
|
1.0
|
|
CB
|
U:HIS210
|
3.5
|
25.6
|
1.0
|
|
HD11
|
U:LEU138
|
3.8
|
82.7
|
1.0
|
|
H
|
U:GLY211
|
3.9
|
24.9
|
1.0
|
|
ND1
|
U:HIS180
|
4.0
|
42.5
|
1.0
|
|
NE2
|
U:HIS210
|
4.1
|
24.0
|
1.0
|
|
ND2
|
U:ASN253
|
4.1
|
24.6
|
1.0
|
|
ND1
|
U:HIS83
|
4.1
|
32.1
|
1.0
|
|
C03
|
U:TD3311
|
4.1
|
41.4
|
1.0
|
|
CG
|
U:HIS180
|
4.2
|
35.6
|
1.0
|
|
CD2
|
U:HIS210
|
4.2
|
22.7
|
1.0
|
|
HA
|
U:HIS210
|
4.2
|
30.2
|
1.0
|
|
HB2
|
U:HIS210
|
4.2
|
30.7
|
1.0
|
|
HD13
|
U:LEU138
|
4.2
|
82.7
|
1.0
|
|
CG
|
U:HIS83
|
4.3
|
31.3
|
1.0
|
|
CD1
|
U:LEU138
|
4.3
|
68.9
|
1.0
|
|
OD1
|
U:ASP82
|
4.4
|
29.9
|
1.0
|
|
HD12
|
U:LEU138
|
4.4
|
82.7
|
1.0
|
|
HD21
|
U:ASN253
|
4.4
|
29.4
|
1.0
|
|
C14
|
U:TD3311
|
4.4
|
31.1
|
1.0
|
|
CA
|
U:HIS210
|
4.4
|
25.2
|
1.0
|
|
C04
|
U:TD3311
|
4.5
|
41.0
|
1.0
|
|
N
|
U:GLY211
|
4.6
|
20.8
|
1.0
|
|
C05
|
U:TD3311
|
4.6
|
38.3
|
1.0
|
|
HB3
|
U:ASN253
|
4.6
|
22.9
|
1.0
|
|
HB2
|
U:ASN253
|
4.7
|
22.9
|
1.0
|
|
HD1
|
U:HIS180
|
4.8
|
51.0
|
1.0
|
|
OD2
|
U:ASP82
|
4.8
|
41.6
|
1.0
|
|
HE2
|
U:HIS210
|
4.8
|
28.8
|
1.0
|
|
HD1
|
U:HIS83
|
4.9
|
38.5
|
1.0
|
|
O15
|
U:TD3311
|
5.0
|
24.2
|
1.0
|
|
CB
|
U:ASN253
|
5.0
|
19.1
|
1.0
|
|
HE1
|
U:MET102
|
5.0
|
38.2
|
1.0
|
|
Zinc binding site 6 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 6 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 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 From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Zn308
b:23.2
occ:1.00
|
NE2
|
Z:HIS180
|
2.0
|
28.0
|
1.0
|
|
ND1
|
Z:HIS210
|
2.1
|
22.2
|
1.0
|
|
NE2
|
Z:HIS83
|
2.2
|
24.7
|
1.0
|
|
O01
|
Z:TD3311
|
2.2
|
52.6
|
1.0
|
|
O13
|
Z:TD3311
|
2.3
|
24.4
|
1.0
|
|
CE1
|
Z:HIS180
|
2.7
|
35.2
|
1.0
|
|
HE1
|
Z:HIS180
|
2.7
|
42.2
|
1.0
|
|
HB3
|
Z:HIS210
|
2.9
|
24.2
|
1.0
|
|
CE1
|
Z:HIS210
|
3.0
|
22.3
|
1.0
|
|
C12
|
Z:TD3311
|
3.0
|
33.8
|
1.0
|
|
N02
|
Z:TD3311
|
3.0
|
45.5
|
1.0
|
|
HE1
|
Z:HIS210
|
3.1
|
26.7
|
1.0
|
|
CE1
|
Z:HIS83
|
3.1
|
23.6
|
1.0
|
|
CG
|
Z:HIS210
|
3.1
|
18.6
|
1.0
|
|
CD2
|
Z:HIS180
|
3.2
|
28.8
|
1.0
|
|
CD2
|
Z:HIS83
|
3.2
|
24.2
|
1.0
|
|
HE1
|
Z:HIS83
|
3.3
|
28.3
|
1.0
|
|
HD22
|
Z:ASN253
|
3.4
|
29.0
|
1.0
|
|
HD2
|
Z:HIS83
|
3.4
|
29.1
|
1.0
|
|
CB
|
Z:HIS210
|
3.5
|
20.2
|
1.0
|
|
HD2
|
Z:HIS180
|
3.6
|
34.5
|
1.0
|
|
ND1
|
Z:HIS180
|
3.9
|
42.4
|
1.0
|
|
H
|
Z:GLY211
|
3.9
|
25.0
|
1.0
|
|
ND2
|
Z:ASN253
|
4.1
|
24.2
|
1.0
|
|
NE2
|
Z:HIS210
|
4.1
|
25.4
|
1.0
|
|
HD22
|
Z:LEU138
|
4.1
|
57.4
|
1.0
|
|
CG
|
Z:HIS180
|
4.1
|
31.8
|
1.0
|
|
CD2
|
Z:HIS210
|
4.2
|
21.6
|
1.0
|
|
HB2
|
Z:HIS210
|
4.2
|
24.2
|
1.0
|
|
HA
|
Z:HIS210
|
4.2
|
27.4
|
1.0
|
|
OD1
|
Z:ASP82
|
4.2
|
29.3
|
1.0
|
|
ND1
|
Z:HIS83
|
4.3
|
23.2
|
1.0
|
|
CG
|
Z:HIS83
|
4.3
|
16.3
|
1.0
|
|
C03
|
Z:TD3311
|
4.3
|
41.7
|
1.0
|
|
HD21
|
Z:ASN253
|
4.4
|
29.0
|
1.0
|
|
C14
|
Z:TD3311
|
4.5
|
31.1
|
1.0
|
|
CA
|
Z:HIS210
|
4.5
|
22.9
|
1.0
|
|
HD21
|
Z:LEU138
|
4.5
|
57.4
|
1.0
|
|
HD1
|
Z:HIS180
|
4.6
|
50.8
|
1.0
|
|
HB3
|
Z:ASN253
|
4.6
|
22.3
|
1.0
|
|
N
|
Z:GLY211
|
4.6
|
20.8
|
1.0
|
|
OD2
|
Z:ASP82
|
4.7
|
31.3
|
1.0
|
|
CD2
|
Z:LEU138
|
4.7
|
47.9
|
1.0
|
|
HB2
|
Z:ASN253
|
4.7
|
22.3
|
1.0
|
|
C04
|
Z:TD3311
|
4.8
|
41.0
|
1.0
|
|
HE2
|
Z:HIS210
|
4.9
|
30.5
|
1.0
|
|
CG
|
Z:ASP82
|
4.9
|
25.6
|
1.0
|
|
HD23
|
Z:LEU138
|
4.9
|
57.4
|
1.0
|
|
O15
|
Z:TD3311
|
5.0
|
32.0
|
1.0
|
|
CG
|
Z:ASN253
|
5.0
|
27.4
|
1.0
|
|
CB
|
Z:ASN253
|
5.0
|
18.6
|
1.0
|
|
Zinc binding site 7 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 7 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
e:Zn308
b:26.2
occ:1.00
|
ND1
|
e:HIS210
|
2.0
|
23.8
|
1.0
|
|
NE2
|
e:HIS180
|
2.1
|
28.9
|
1.0
|
|
NE2
|
e:HIS83
|
2.1
|
30.5
|
1.0
|
|
O01
|
e:TD3311
|
2.3
|
43.8
|
1.0
|
|
O13
|
e:TD3311
|
2.5
|
36.0
|
1.0
|
|
HB3
|
e:HIS210
|
2.8
|
23.5
|
1.0
|
|
N02
|
e:TD3311
|
2.9
|
43.1
|
1.0
|
|
CE1
|
e:HIS180
|
2.9
|
42.5
|
1.0
|
|
C12
|
e:TD3311
|
2.9
|
34.1
|
1.0
|
|
CE1
|
e:HIS210
|
3.0
|
24.3
|
1.0
|
|
CE1
|
e:HIS83
|
3.0
|
32.3
|
1.0
|
|
CD2
|
e:HIS180
|
3.1
|
29.7
|
1.0
|
|
CG
|
e:HIS210
|
3.1
|
23.2
|
1.0
|
|
HE1
|
e:HIS180
|
3.1
|
51.0
|
1.0
|
|
HE1
|
e:HIS83
|
3.1
|
38.7
|
1.0
|
|
HE1
|
e:HIS210
|
3.1
|
29.1
|
1.0
|
|
CD2
|
e:HIS83
|
3.1
|
27.8
|
1.0
|
|
HD2
|
e:HIS180
|
3.3
|
35.6
|
1.0
|
|
HD22
|
e:ASN253
|
3.3
|
33.3
|
1.0
|
|
HD2
|
e:HIS83
|
3.4
|
33.4
|
1.0
|
|
CB
|
e:HIS210
|
3.4
|
19.6
|
1.0
|
|
H
|
e:GLY211
|
3.9
|
25.7
|
1.0
|
|
ND1
|
e:HIS180
|
4.0
|
42.6
|
1.0
|
|
C03
|
e:TD3311
|
4.1
|
41.0
|
1.0
|
|
ND2
|
e:ASN253
|
4.1
|
27.7
|
1.0
|
|
NE2
|
e:HIS210
|
4.1
|
23.6
|
1.0
|
|
CG
|
e:HIS180
|
4.1
|
30.8
|
1.0
|
|
HB2
|
e:HIS210
|
4.1
|
23.5
|
1.0
|
|
ND1
|
e:HIS83
|
4.2
|
31.3
|
1.0
|
|
HA
|
e:HIS210
|
4.2
|
27.1
|
1.0
|
|
HD22
|
e:LEU138
|
4.2
|
70.2
|
1.0
|
|
CD2
|
e:HIS210
|
4.2
|
24.7
|
1.0
|
|
CG
|
e:HIS83
|
4.3
|
30.8
|
1.0
|
|
OD1
|
e:ASP82
|
4.3
|
35.3
|
1.0
|
|
CA
|
e:HIS210
|
4.4
|
22.6
|
1.0
|
|
C14
|
e:TD3311
|
4.4
|
31.0
|
1.0
|
|
HD21
|
e:ASN253
|
4.4
|
33.3
|
1.0
|
|
C05
|
e:TD3311
|
4.5
|
42.6
|
1.0
|
|
C04
|
e:TD3311
|
4.5
|
41.7
|
1.0
|
|
HD21
|
e:LEU138
|
4.6
|
70.2
|
1.0
|
|
HB3
|
e:ASN253
|
4.6
|
21.4
|
1.0
|
|
N
|
e:GLY211
|
4.6
|
21.4
|
1.0
|
|
HB2
|
e:ASN253
|
4.7
|
21.4
|
1.0
|
|
OD2
|
e:ASP82
|
4.7
|
38.2
|
1.0
|
|
CD2
|
e:LEU138
|
4.7
|
58.5
|
1.0
|
|
HD1
|
e:HIS180
|
4.8
|
51.1
|
1.0
|
|
HE2
|
e:HIS210
|
4.9
|
28.3
|
1.0
|
|
HD23
|
e:LEU138
|
4.9
|
70.2
|
1.0
|
|
HD1
|
e:HIS83
|
4.9
|
37.5
|
1.0
|
|
O15
|
e:TD3311
|
4.9
|
27.8
|
1.0
|
|
CG
|
e:ASP82
|
5.0
|
37.0
|
1.0
|
|
CB
|
e:ASN253
|
5.0
|
17.9
|
1.0
|
|
C
|
e:HIS210
|
5.0
|
25.8
|
1.0
|
|
Zinc binding site 8 out
of 8 in 3n9r
Go back to
Zinc Binding Sites List in 3n9r
Zinc binding site 8 out
of 8 in the Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Class II Fructose-1,6-Bisphosphate Aldolase From Helicobacter Pylori in Complex with N-(4-Hydroxybutyl)-Phosphoglycolohydroxamic Acid, A Competitive Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
j:Zn308
b:24.5
occ:1.00
|
NE2
|
j:HIS180
|
2.0
|
26.5
|
1.0
|
|
ND1
|
j:HIS210
|
2.1
|
21.5
|
1.0
|
|
NE2
|
j:HIS83
|
2.2
|
24.0
|
1.0
|
|
O01
|
j:TD3311
|
2.2
|
52.6
|
1.0
|
|
O13
|
j:TD3311
|
2.3
|
25.4
|
1.0
|
|
CE1
|
j:HIS180
|
2.6
|
32.4
|
1.0
|
|
HE1
|
j:HIS180
|
2.6
|
38.8
|
1.0
|
|
CE1
|
j:HIS210
|
2.9
|
20.4
|
1.0
|
|
C12
|
j:TD3311
|
2.9
|
31.8
|
1.0
|
|
HB3
|
j:HIS210
|
2.9
|
24.9
|
1.0
|
|
N02
|
j:TD3311
|
3.0
|
43.8
|
1.0
|
|
HE1
|
j:HIS210
|
3.1
|
24.5
|
1.0
|
|
CD2
|
j:HIS83
|
3.1
|
22.2
|
1.0
|
|
CG
|
j:HIS210
|
3.1
|
18.7
|
1.0
|
|
CE1
|
j:HIS83
|
3.1
|
24.6
|
1.0
|
|
CD2
|
j:HIS180
|
3.2
|
30.5
|
1.0
|
|
HD2
|
j:HIS83
|
3.3
|
26.7
|
1.0
|
|
HE1
|
j:HIS83
|
3.3
|
29.5
|
1.0
|
|
HD22
|
j:ASN253
|
3.3
|
27.3
|
1.0
|
|
CB
|
j:HIS210
|
3.5
|
20.8
|
1.0
|
|
HD2
|
j:HIS180
|
3.6
|
36.6
|
1.0
|
|
ND1
|
j:HIS180
|
3.8
|
41.5
|
1.0
|
|
H
|
j:GLY211
|
3.9
|
26.4
|
1.0
|
|
ND2
|
j:ASN253
|
4.1
|
22.8
|
1.0
|
|
NE2
|
j:HIS210
|
4.1
|
19.7
|
1.0
|
|
CG
|
j:HIS180
|
4.1
|
33.5
|
1.0
|
|
HD22
|
j:LEU138
|
4.2
|
60.2
|
1.0
|
|
C03
|
j:TD3311
|
4.2
|
43.1
|
1.0
|
|
HA
|
j:HIS210
|
4.2
|
21.8
|
1.0
|
|
CD2
|
j:HIS210
|
4.2
|
21.9
|
1.0
|
|
OD1
|
j:ASP82
|
4.2
|
34.3
|
1.0
|
|
ND1
|
j:HIS83
|
4.2
|
22.3
|
1.0
|
|
HB2
|
j:HIS210
|
4.2
|
24.9
|
1.0
|
|
CG
|
j:HIS83
|
4.3
|
18.7
|
1.0
|
|
HD21
|
j:ASN253
|
4.4
|
27.3
|
1.0
|
|
C14
|
j:TD3311
|
4.4
|
32.5
|
1.0
|
|
CA
|
j:HIS210
|
4.5
|
18.2
|
1.0
|
|
C04
|
j:TD3311
|
4.5
|
44.0
|
1.0
|
|
HD1
|
j:HIS180
|
4.5
|
49.8
|
1.0
|
|
HD21
|
j:LEU138
|
4.5
|
60.2
|
1.0
|
|
HB3
|
j:ASN253
|
4.6
|
21.7
|
1.0
|
|
OD2
|
j:ASP82
|
4.6
|
30.6
|
1.0
|
|
N
|
j:GLY211
|
4.6
|
22.0
|
1.0
|
|
CD2
|
j:LEU138
|
4.7
|
50.2
|
1.0
|
|
HB2
|
j:ASN253
|
4.8
|
21.7
|
1.0
|
|
O
|
j:HOH1220
|
4.8
|
51.3
|
1.0
|
|
O
|
j:HOH350
|
4.8
|
43.1
|
1.0
|
|
CG
|
j:ASP82
|
4.8
|
26.1
|
1.0
|
|
HE2
|
j:HIS210
|
4.9
|
23.7
|
1.0
|
|
HD23
|
j:LEU138
|
4.9
|
60.2
|
1.0
|
|
O15
|
j:TD3311
|
4.9
|
37.5
|
1.0
|
|
Reference:
R.Daher,
M.Fonvielle,
P.M.Gest,
M.E.Guerin,
M.Jackson,
J.Sygusch,
M.Therisod.
Rational Design, Synthesis, and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-Phosphate Aldolases. J.Med.Chem. V. 53 7836 2010.
ISSN: ISSN 0022-2623
PubMed: 20929256
DOI: 10.1021/JM1009814
Page generated: Wed Aug 20 12:11:08 2025
|
