Sodium 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:
Sodium Binding Sites:
The binding sites of Sodium 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 Sodium atom.
In total 8 binding sites of Sodium 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 Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:27.8
occ:1.00
|
HE2
|
A:HIS80
|
2.2
|
19.9
|
1.0
|
|
HD21
|
A:ASN253
|
2.4
|
16.9
|
1.0
|
|
HZ1
|
A:LYS251
|
2.7
|
12.9
|
1.0
|
|
HZ2
|
A:LYS251
|
2.8
|
12.9
|
1.0
|
|
HE1
|
A:HIS210
|
2.9
|
17.0
|
1.0
|
|
OD1
|
A:ASP82
|
2.9
|
20.5
|
1.0
|
|
NE2
|
A:HIS80
|
3.0
|
16.6
|
1.0
|
|
HE2
|
A:HIS210
|
3.0
|
14.1
|
1.0
|
|
OE2
|
A:GLU132
|
3.1
|
17.8
|
1.0
|
|
NZ
|
A:LYS251
|
3.1
|
10.8
|
1.0
|
|
HA
|
A:ASP82
|
3.2
|
9.9
|
1.0
|
|
ND2
|
A:ASN253
|
3.2
|
14.1
|
1.0
|
|
OE1
|
A:GLU132
|
3.2
|
15.9
|
1.0
|
|
HB2
|
A:MET102
|
3.3
|
14.4
|
1.0
|
|
CE1
|
A:HIS210
|
3.3
|
14.2
|
1.0
|
|
NE2
|
A:HIS210
|
3.4
|
11.8
|
1.0
|
|
HZ3
|
A:LYS251
|
3.4
|
12.9
|
1.0
|
|
CD
|
A:GLU132
|
3.5
|
14.8
|
1.0
|
|
SD
|
A:MET102
|
3.5
|
14.5
|
1.0
|
|
HD22
|
A:ASN253
|
3.6
|
16.9
|
1.0
|
|
HD2
|
A:HIS80
|
3.6
|
15.5
|
1.0
|
|
OE1
|
A:GLN47
|
3.6
|
22.4
|
1.0
|
|
CD2
|
A:HIS80
|
3.7
|
13.0
|
1.0
|
|
H
|
A:HIS83
|
3.7
|
12.3
|
1.0
|
|
HB3
|
A:MET102
|
3.9
|
14.4
|
1.0
|
|
CB
|
A:MET102
|
3.9
|
12.0
|
1.0
|
|
CG
|
A:ASP82
|
3.9
|
22.9
|
1.0
|
|
CE1
|
A:HIS80
|
4.1
|
12.6
|
1.0
|
|
CA
|
A:ASP82
|
4.1
|
8.3
|
1.0
|
|
HG11
|
A:VAL208
|
4.1
|
13.4
|
1.0
|
|
CG
|
A:MET102
|
4.1
|
16.1
|
1.0
|
|
HG3
|
A:MET102
|
4.2
|
19.2
|
1.0
|
|
CG
|
A:ASN253
|
4.2
|
15.1
|
1.0
|
|
HE1
|
A:HIS80
|
4.3
|
15.1
|
1.0
|
|
OD1
|
A:ASN253
|
4.3
|
9.6
|
1.0
|
|
HE21
|
A:GLN47
|
4.4
|
22.9
|
1.0
|
|
CB
|
A:ASP82
|
4.4
|
14.2
|
1.0
|
|
N
|
A:HIS83
|
4.4
|
10.3
|
1.0
|
|
CE
|
A:LYS251
|
4.5
|
11.3
|
1.0
|
|
HB2
|
A:ASP82
|
4.5
|
17.0
|
1.0
|
|
ND1
|
A:HIS210
|
4.5
|
11.1
|
1.0
|
|
HE3
|
A:MET102
|
4.5
|
17.7
|
1.0
|
|
CD
|
A:GLN47
|
4.5
|
18.4
|
1.0
|
|
HE3
|
A:LYS251
|
4.5
|
13.6
|
1.0
|
|
CE
|
A:MET102
|
4.6
|
14.8
|
1.0
|
|
CD2
|
A:HIS210
|
4.6
|
9.4
|
1.0
|
|
HE1
|
A:MET102
|
4.8
|
17.7
|
1.0
|
|
NE2
|
A:GLN47
|
4.8
|
19.1
|
1.0
|
|
HB3
|
A:GLU132
|
4.8
|
11.5
|
1.0
|
|
CG
|
A:GLU132
|
4.8
|
9.3
|
1.0
|
|
C
|
A:ASP82
|
4.8
|
12.1
|
1.0
|
|
O
|
A:LEU81
|
4.9
|
12.2
|
1.0
|
|
CG
|
A:HIS80
|
4.9
|
14.4
|
1.0
|
|
OD2
|
A:ASP82
|
4.9
|
24.7
|
1.0
|
|
HE2
|
A:LYS251
|
4.9
|
13.6
|
1.0
|
|
CG1
|
A:VAL208
|
5.0
|
11.2
|
1.0
|
|
Sodium binding site 2 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:25.9
occ:1.00
|
HE2
|
B:HIS80
|
2.2
|
20.7
|
1.0
|
|
HD21
|
B:ASN253
|
2.4
|
16.9
|
1.0
|
|
HZ1
|
B:LYS251
|
2.7
|
16.7
|
1.0
|
|
OD1
|
B:ASP82
|
2.8
|
23.5
|
1.0
|
|
HE1
|
B:HIS210
|
2.8
|
18.9
|
1.0
|
|
HZ2
|
B:LYS251
|
2.9
|
16.7
|
1.0
|
|
HE2
|
B:HIS210
|
2.9
|
14.2
|
1.0
|
|
OE2
|
B:GLU132
|
3.0
|
19.1
|
1.0
|
|
NE2
|
B:HIS80
|
3.0
|
17.3
|
1.0
|
|
OE1
|
B:GLU132
|
3.2
|
17.7
|
1.0
|
|
NZ
|
B:LYS251
|
3.2
|
14.0
|
1.0
|
|
ND2
|
B:ASN253
|
3.2
|
14.1
|
1.0
|
|
HA
|
B:ASP82
|
3.2
|
12.3
|
1.0
|
|
CE1
|
B:HIS210
|
3.3
|
15.8
|
1.0
|
|
HB2
|
B:MET102
|
3.3
|
16.6
|
1.0
|
|
NE2
|
B:HIS210
|
3.3
|
11.9
|
1.0
|
|
CD
|
B:GLU132
|
3.4
|
17.0
|
1.0
|
|
SD
|
B:MET102
|
3.5
|
14.4
|
1.0
|
|
HZ3
|
B:LYS251
|
3.5
|
16.7
|
1.0
|
|
OE1
|
B:GLN47
|
3.6
|
24.9
|
1.0
|
|
HD22
|
B:ASN253
|
3.6
|
16.9
|
1.0
|
|
HD2
|
B:HIS80
|
3.6
|
16.2
|
1.0
|
|
H
|
B:HIS83
|
3.6
|
12.2
|
1.0
|
|
CD2
|
B:HIS80
|
3.7
|
13.6
|
1.0
|
|
CG
|
B:ASP82
|
3.9
|
24.6
|
1.0
|
|
HB3
|
B:MET102
|
3.9
|
16.6
|
1.0
|
|
CB
|
B:MET102
|
3.9
|
13.9
|
1.0
|
|
HG11
|
B:VAL208
|
4.0
|
17.8
|
1.0
|
|
CE1
|
B:HIS80
|
4.0
|
14.3
|
1.0
|
|
CA
|
B:ASP82
|
4.1
|
10.2
|
1.0
|
|
CG
|
B:MET102
|
4.2
|
17.5
|
1.0
|
|
CG
|
B:ASN253
|
4.2
|
15.1
|
1.0
|
|
HG3
|
B:MET102
|
4.2
|
20.9
|
1.0
|
|
HE1
|
B:HIS80
|
4.3
|
17.1
|
1.0
|
|
OD1
|
B:ASN253
|
4.4
|
12.3
|
1.0
|
|
N
|
B:HIS83
|
4.4
|
10.2
|
1.0
|
|
CB
|
B:ASP82
|
4.4
|
16.5
|
1.0
|
|
ND1
|
B:HIS210
|
4.4
|
13.0
|
1.0
|
|
HE3
|
B:LYS251
|
4.5
|
18.5
|
1.0
|
|
CE
|
B:LYS251
|
4.5
|
15.5
|
1.0
|
|
HB2
|
B:ASP82
|
4.5
|
19.7
|
1.0
|
|
CD2
|
B:HIS210
|
4.5
|
13.4
|
1.0
|
|
CD
|
B:GLN47
|
4.5
|
14.7
|
1.0
|
|
HE21
|
B:GLN47
|
4.5
|
22.6
|
1.0
|
|
HE3
|
B:MET102
|
4.6
|
23.3
|
1.0
|
|
CE
|
B:MET102
|
4.6
|
19.4
|
1.0
|
|
CG
|
B:GLU132
|
4.8
|
10.0
|
1.0
|
|
HB3
|
B:GLU132
|
4.8
|
10.4
|
1.0
|
|
HE1
|
B:MET102
|
4.8
|
23.3
|
1.0
|
|
C
|
B:ASP82
|
4.8
|
14.8
|
1.0
|
|
OD2
|
B:ASP82
|
4.9
|
29.2
|
1.0
|
|
O
|
B:LEU81
|
4.9
|
13.5
|
1.0
|
|
NE2
|
B:GLN47
|
4.9
|
18.8
|
1.0
|
|
CG1
|
B:VAL208
|
4.9
|
14.9
|
1.0
|
|
CG
|
B:HIS80
|
4.9
|
12.8
|
1.0
|
|
HG2
|
B:GLU132
|
5.0
|
11.9
|
1.0
|
|
HE2
|
B:LYS251
|
5.0
|
18.5
|
1.0
|
|
Sodium binding site 3 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:26.2
occ:1.00
|
HE2
|
K:HIS80
|
2.2
|
20.5
|
1.0
|
|
HD21
|
K:ASN253
|
2.3
|
19.2
|
1.0
|
|
HZ1
|
K:LYS251
|
2.7
|
19.3
|
1.0
|
|
HZ2
|
K:LYS251
|
2.8
|
19.3
|
1.0
|
|
HE1
|
K:HIS210
|
2.9
|
20.4
|
1.0
|
|
OD1
|
K:ASP82
|
2.9
|
21.5
|
1.0
|
|
HE2
|
K:HIS210
|
3.0
|
14.5
|
1.0
|
|
OE2
|
K:GLU132
|
3.0
|
20.9
|
1.0
|
|
NE2
|
K:HIS80
|
3.0
|
17.1
|
1.0
|
|
NZ
|
K:LYS251
|
3.1
|
16.1
|
1.0
|
|
ND2
|
K:ASN253
|
3.1
|
16.0
|
1.0
|
|
OE1
|
K:GLU132
|
3.2
|
18.0
|
1.0
|
|
CE1
|
K:HIS210
|
3.3
|
17.0
|
1.0
|
|
HB2
|
K:MET102
|
3.3
|
11.4
|
1.0
|
|
HA
|
K:ASP82
|
3.3
|
14.4
|
1.0
|
|
NE2
|
K:HIS210
|
3.3
|
12.1
|
1.0
|
|
CD
|
K:GLU132
|
3.4
|
21.8
|
1.0
|
|
HZ3
|
K:LYS251
|
3.5
|
19.3
|
1.0
|
|
HD22
|
K:ASN253
|
3.5
|
19.2
|
1.0
|
|
SD
|
K:MET102
|
3.5
|
12.9
|
1.0
|
|
OE1
|
K:GLN47
|
3.5
|
21.3
|
1.0
|
|
HD2
|
K:HIS80
|
3.6
|
15.2
|
1.0
|
|
CD2
|
K:HIS80
|
3.7
|
12.7
|
1.0
|
|
H
|
K:HIS83
|
3.7
|
10.6
|
1.0
|
|
CG
|
K:ASP82
|
3.9
|
23.9
|
1.0
|
|
CB
|
K:MET102
|
4.0
|
9.6
|
1.0
|
|
HG11
|
K:VAL208
|
4.0
|
14.2
|
1.0
|
|
HB3
|
K:MET102
|
4.0
|
11.4
|
1.0
|
|
CE1
|
K:HIS80
|
4.1
|
13.9
|
1.0
|
|
CG
|
K:ASN253
|
4.2
|
13.2
|
1.0
|
|
CG
|
K:MET102
|
4.2
|
13.9
|
1.0
|
|
HG3
|
K:MET102
|
4.2
|
16.6
|
1.0
|
|
CA
|
K:ASP82
|
4.2
|
12.0
|
1.0
|
|
OD1
|
K:ASN253
|
4.3
|
12.5
|
1.0
|
|
HE1
|
K:HIS80
|
4.3
|
16.7
|
1.0
|
|
CE
|
K:LYS251
|
4.4
|
15.9
|
1.0
|
|
ND1
|
K:HIS210
|
4.4
|
13.9
|
1.0
|
|
CB
|
K:ASP82
|
4.5
|
12.9
|
1.0
|
|
HE21
|
K:GLN47
|
4.5
|
22.1
|
1.0
|
|
N
|
K:HIS83
|
4.5
|
8.9
|
1.0
|
|
HE3
|
K:LYS251
|
4.5
|
19.0
|
1.0
|
|
HB2
|
K:ASP82
|
4.5
|
15.4
|
1.0
|
|
CD
|
K:GLN47
|
4.5
|
13.9
|
1.0
|
|
HE3
|
K:MET102
|
4.5
|
19.9
|
1.0
|
|
CD2
|
K:HIS210
|
4.5
|
12.8
|
1.0
|
|
CE
|
K:MET102
|
4.6
|
16.6
|
1.0
|
|
HB3
|
K:GLU132
|
4.8
|
15.9
|
1.0
|
|
CG
|
K:GLU132
|
4.8
|
10.7
|
1.0
|
|
HE1
|
K:MET102
|
4.8
|
19.9
|
1.0
|
|
CG1
|
K:VAL208
|
4.9
|
11.8
|
1.0
|
|
NE2
|
K:GLN47
|
4.9
|
18.4
|
1.0
|
|
OD2
|
K:ASP82
|
4.9
|
27.5
|
1.0
|
|
C
|
K:ASP82
|
4.9
|
15.0
|
1.0
|
|
CG
|
K:HIS80
|
4.9
|
12.1
|
1.0
|
|
O
|
K:LEU81
|
4.9
|
12.9
|
1.0
|
|
HE2
|
K:LYS251
|
4.9
|
19.0
|
1.0
|
|
Sodium binding site 4 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:30.1
occ:1.00
|
HE2
|
P:HIS80
|
2.2
|
19.9
|
1.0
|
|
HD21
|
P:ASN253
|
2.3
|
19.4
|
1.0
|
|
HZ1
|
P:LYS251
|
2.7
|
14.6
|
1.0
|
|
HZ2
|
P:LYS251
|
2.8
|
14.6
|
1.0
|
|
HE1
|
P:HIS210
|
2.9
|
19.0
|
1.0
|
|
OD1
|
P:ASP82
|
2.9
|
21.5
|
1.0
|
|
HE2
|
P:HIS210
|
2.9
|
15.2
|
1.0
|
|
OE2
|
P:GLU132
|
3.0
|
17.6
|
1.0
|
|
NE2
|
P:HIS80
|
3.0
|
16.6
|
1.0
|
|
NZ
|
P:LYS251
|
3.1
|
12.2
|
1.0
|
|
ND2
|
P:ASN253
|
3.1
|
16.1
|
1.0
|
|
OE1
|
P:GLU132
|
3.2
|
15.6
|
1.0
|
|
HA
|
P:ASP82
|
3.2
|
13.5
|
1.0
|
|
CE1
|
P:HIS210
|
3.3
|
15.9
|
1.0
|
|
NE2
|
P:HIS210
|
3.3
|
12.7
|
1.0
|
|
HB2
|
P:MET102
|
3.3
|
12.6
|
1.0
|
|
HZ3
|
P:LYS251
|
3.4
|
14.6
|
1.0
|
|
CD
|
P:GLU132
|
3.4
|
17.2
|
1.0
|
|
SD
|
P:MET102
|
3.5
|
13.2
|
1.0
|
|
OE1
|
P:GLN47
|
3.5
|
21.6
|
1.0
|
|
HD22
|
P:ASN253
|
3.5
|
19.4
|
1.0
|
|
HD2
|
P:HIS80
|
3.6
|
16.2
|
1.0
|
|
H
|
P:HIS83
|
3.7
|
9.7
|
1.0
|
|
CD2
|
P:HIS80
|
3.7
|
13.5
|
1.0
|
|
CG
|
P:ASP82
|
3.9
|
24.1
|
1.0
|
|
HB3
|
P:MET102
|
4.0
|
12.6
|
1.0
|
|
CB
|
P:MET102
|
4.0
|
10.5
|
1.0
|
|
HG11
|
P:VAL208
|
4.0
|
10.6
|
1.0
|
|
CE1
|
P:HIS80
|
4.1
|
11.9
|
1.0
|
|
CG
|
P:ASN253
|
4.1
|
17.3
|
1.0
|
|
CA
|
P:ASP82
|
4.1
|
11.3
|
1.0
|
|
CG
|
P:MET102
|
4.2
|
16.2
|
1.0
|
|
HG3
|
P:MET102
|
4.3
|
19.4
|
1.0
|
|
OD1
|
P:ASN253
|
4.3
|
11.4
|
1.0
|
|
HE1
|
P:HIS80
|
4.3
|
14.2
|
1.0
|
|
HE21
|
P:GLN47
|
4.4
|
22.9
|
1.0
|
|
ND1
|
P:HIS210
|
4.4
|
11.5
|
1.0
|
|
HE3
|
P:MET102
|
4.4
|
15.7
|
1.0
|
|
N
|
P:HIS83
|
4.4
|
8.1
|
1.0
|
|
CD
|
P:GLN47
|
4.5
|
16.4
|
1.0
|
|
CE
|
P:LYS251
|
4.5
|
13.2
|
1.0
|
|
CB
|
P:ASP82
|
4.5
|
14.6
|
1.0
|
|
CD2
|
P:HIS210
|
4.5
|
10.1
|
1.0
|
|
HB2
|
P:ASP82
|
4.5
|
17.5
|
1.0
|
|
HE3
|
P:LYS251
|
4.5
|
15.8
|
1.0
|
|
CE
|
P:MET102
|
4.6
|
13.1
|
1.0
|
|
HE1
|
P:MET102
|
4.7
|
15.7
|
1.0
|
|
CG
|
P:GLU132
|
4.8
|
9.0
|
1.0
|
|
HB3
|
P:GLU132
|
4.8
|
14.2
|
1.0
|
|
NE2
|
P:GLN47
|
4.8
|
19.1
|
1.0
|
|
CG1
|
P:VAL208
|
4.9
|
8.8
|
1.0
|
|
C
|
P:ASP82
|
4.9
|
14.8
|
1.0
|
|
OD2
|
P:ASP82
|
4.9
|
28.0
|
1.0
|
|
HE2
|
P:LYS251
|
4.9
|
15.8
|
1.0
|
|
CG
|
P:HIS80
|
4.9
|
11.9
|
1.0
|
|
O
|
P:LEU81
|
5.0
|
13.4
|
1.0
|
|
HG2
|
P:GLU132
|
5.0
|
10.8
|
1.0
|
|
Sodium binding site 5 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:39.5
occ:1.00
|
HD21
|
U:ASN253
|
2.4
|
29.4
|
1.0
|
|
HE2
|
U:HIS80
|
2.4
|
36.8
|
1.0
|
|
HZ1
|
U:LYS251
|
2.8
|
26.7
|
1.0
|
|
OD1
|
U:ASP82
|
2.9
|
29.9
|
1.0
|
|
HE1
|
U:HIS210
|
2.9
|
32.5
|
1.0
|
|
HZ2
|
U:LYS251
|
3.0
|
26.7
|
1.0
|
|
OE2
|
U:GLU132
|
3.1
|
25.1
|
1.0
|
|
NE2
|
U:HIS80
|
3.2
|
30.7
|
1.0
|
|
HA
|
U:ASP82
|
3.2
|
27.3
|
1.0
|
|
ND2
|
U:ASN253
|
3.2
|
24.6
|
1.0
|
|
HE2
|
U:HIS210
|
3.2
|
28.8
|
1.0
|
|
HB2
|
U:MET102
|
3.3
|
33.0
|
1.0
|
|
NZ
|
U:LYS251
|
3.3
|
22.2
|
1.0
|
|
OE1
|
U:GLU132
|
3.3
|
24.4
|
1.0
|
|
CE1
|
U:HIS210
|
3.4
|
27.1
|
1.0
|
|
HD2
|
U:HIS80
|
3.5
|
34.3
|
1.0
|
|
SD
|
U:MET102
|
3.5
|
31.7
|
1.0
|
|
CD
|
U:GLU132
|
3.5
|
28.0
|
1.0
|
|
H
|
U:HIS83
|
3.5
|
33.6
|
1.0
|
|
HD22
|
U:ASN253
|
3.5
|
29.4
|
1.0
|
|
NE2
|
U:HIS210
|
3.5
|
24.0
|
1.0
|
|
OE1
|
U:GLN47
|
3.6
|
31.7
|
1.0
|
|
HZ3
|
U:LYS251
|
3.6
|
26.7
|
1.0
|
|
CD2
|
U:HIS80
|
3.7
|
28.6
|
1.0
|
|
HB3
|
U:MET102
|
3.9
|
33.0
|
1.0
|
|
CB
|
U:MET102
|
3.9
|
27.5
|
1.0
|
|
CG
|
U:ASP82
|
4.0
|
34.3
|
1.0
|
|
CA
|
U:ASP82
|
4.1
|
22.8
|
1.0
|
|
CG
|
U:MET102
|
4.2
|
25.4
|
1.0
|
|
HG11
|
U:VAL208
|
4.2
|
25.1
|
1.0
|
|
HE21
|
U:GLN47
|
4.2
|
30.9
|
1.0
|
|
N
|
U:HIS83
|
4.3
|
28.0
|
1.0
|
|
CG
|
U:ASN253
|
4.3
|
26.5
|
1.0
|
|
HG3
|
U:MET102
|
4.3
|
30.5
|
1.0
|
|
HE3
|
U:MET102
|
4.3
|
38.2
|
1.0
|
|
CE1
|
U:HIS80
|
4.3
|
28.8
|
1.0
|
|
CD
|
U:GLN47
|
4.4
|
26.5
|
1.0
|
|
CE
|
U:MET102
|
4.5
|
31.8
|
1.0
|
|
ND1
|
U:HIS210
|
4.5
|
28.2
|
1.0
|
|
OD1
|
U:ASN253
|
4.5
|
22.2
|
1.0
|
|
CB
|
U:ASP82
|
4.5
|
26.1
|
1.0
|
|
HB2
|
U:ASP82
|
4.6
|
31.3
|
1.0
|
|
CE
|
U:LYS251
|
4.6
|
25.6
|
1.0
|
|
HE1
|
U:MET102
|
4.6
|
38.2
|
1.0
|
|
HE3
|
U:LYS251
|
4.6
|
30.7
|
1.0
|
|
NE2
|
U:GLN47
|
4.7
|
25.8
|
1.0
|
|
HE1
|
U:HIS80
|
4.7
|
34.5
|
1.0
|
|
O
|
U:LEU81
|
4.7
|
22.5
|
1.0
|
|
CD2
|
U:HIS210
|
4.7
|
22.7
|
1.0
|
|
O01
|
U:TD3311
|
4.7
|
44.8
|
1.0
|
|
C
|
U:ASP82
|
4.8
|
25.5
|
1.0
|
|
HB3
|
U:GLU132
|
4.8
|
31.1
|
1.0
|
|
CG
|
U:GLU132
|
4.8
|
24.2
|
1.0
|
|
HD2
|
U:HIS83
|
4.9
|
33.6
|
1.0
|
|
CD2
|
U:HIS83
|
4.9
|
28.0
|
1.0
|
|
CG
|
U:HIS80
|
5.0
|
23.3
|
1.0
|
|
Sodium binding site 6 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:34.3
occ:1.00
|
HE2
|
Z:HIS80
|
2.3
|
25.7
|
1.0
|
|
HD21
|
Z:ASN253
|
2.4
|
29.0
|
1.0
|
|
HZ1
|
Z:LYS251
|
2.8
|
23.5
|
1.0
|
|
HE1
|
Z:HIS210
|
2.8
|
26.7
|
1.0
|
|
OD1
|
Z:ASP82
|
2.9
|
29.3
|
1.0
|
|
HZ2
|
Z:LYS251
|
2.9
|
23.5
|
1.0
|
|
OE2
|
Z:GLU132
|
3.0
|
26.5
|
1.0
|
|
NE2
|
Z:HIS80
|
3.0
|
21.4
|
1.0
|
|
HA
|
Z:ASP82
|
3.2
|
18.9
|
1.0
|
|
HB2
|
Z:MET102
|
3.2
|
15.0
|
1.0
|
|
HE2
|
Z:HIS210
|
3.2
|
30.5
|
1.0
|
|
NZ
|
Z:LYS251
|
3.3
|
19.6
|
1.0
|
|
ND2
|
Z:ASN253
|
3.3
|
24.2
|
1.0
|
|
OE1
|
Z:GLU132
|
3.3
|
23.1
|
1.0
|
|
CE1
|
Z:HIS210
|
3.3
|
22.3
|
1.0
|
|
HD2
|
Z:HIS80
|
3.4
|
23.0
|
1.0
|
|
CD
|
Z:GLU132
|
3.5
|
27.9
|
1.0
|
|
OE1
|
Z:GLN47
|
3.5
|
24.8
|
1.0
|
|
SD
|
Z:MET102
|
3.5
|
25.4
|
1.0
|
|
NE2
|
Z:HIS210
|
3.5
|
25.4
|
1.0
|
|
CD2
|
Z:HIS80
|
3.6
|
19.1
|
1.0
|
|
HD22
|
Z:ASN253
|
3.6
|
29.0
|
1.0
|
|
H
|
Z:HIS83
|
3.6
|
19.4
|
1.0
|
|
HZ3
|
Z:LYS251
|
3.6
|
23.5
|
1.0
|
|
CB
|
Z:MET102
|
3.8
|
12.5
|
1.0
|
|
HB3
|
Z:MET102
|
3.9
|
15.0
|
1.0
|
|
CG
|
Z:ASP82
|
3.9
|
25.6
|
1.0
|
|
CG
|
Z:MET102
|
4.1
|
19.1
|
1.0
|
|
CA
|
Z:ASP82
|
4.1
|
15.8
|
1.0
|
|
HG3
|
Z:MET102
|
4.1
|
22.8
|
1.0
|
|
HG11
|
Z:VAL208
|
4.2
|
20.3
|
1.0
|
|
CE1
|
Z:HIS80
|
4.2
|
22.0
|
1.0
|
|
CG
|
Z:ASN253
|
4.3
|
27.4
|
1.0
|
|
N
|
Z:HIS83
|
4.4
|
16.2
|
1.0
|
|
HE21
|
Z:GLN47
|
4.4
|
27.3
|
1.0
|
|
CB
|
Z:ASP82
|
4.4
|
18.5
|
1.0
|
|
OD1
|
Z:ASN253
|
4.4
|
20.5
|
1.0
|
|
CD
|
Z:GLN47
|
4.4
|
24.6
|
1.0
|
|
HE3
|
Z:MET102
|
4.4
|
32.1
|
1.0
|
|
HB2
|
Z:ASP82
|
4.4
|
22.2
|
1.0
|
|
ND1
|
Z:HIS210
|
4.4
|
22.2
|
1.0
|
|
HE3
|
Z:LYS251
|
4.5
|
22.5
|
1.0
|
|
CE
|
Z:LYS251
|
4.5
|
18.8
|
1.0
|
|
HE1
|
Z:HIS80
|
4.5
|
26.4
|
1.0
|
|
CE
|
Z:MET102
|
4.6
|
26.8
|
1.0
|
|
CD2
|
Z:HIS210
|
4.7
|
21.6
|
1.0
|
|
O
|
Z:LEU81
|
4.7
|
18.3
|
1.0
|
|
HB3
|
Z:GLU132
|
4.8
|
15.6
|
1.0
|
|
C
|
Z:ASP82
|
4.8
|
21.0
|
1.0
|
|
NE2
|
Z:GLN47
|
4.8
|
22.8
|
1.0
|
|
CG
|
Z:GLU132
|
4.8
|
14.7
|
1.0
|
|
HE1
|
Z:MET102
|
4.8
|
32.1
|
1.0
|
|
CG
|
Z:HIS80
|
4.9
|
17.6
|
1.0
|
|
OD2
|
Z:ASP82
|
4.9
|
31.3
|
1.0
|
|
HG2
|
Z:GLU132
|
5.0
|
17.6
|
1.0
|
|
HG2
|
Z:MET102
|
5.0
|
22.8
|
1.0
|
|
Sodium binding site 7 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:36.8
occ:1.00
|
HD21
|
e:ASN253
|
2.4
|
33.3
|
1.0
|
|
HE2
|
e:HIS80
|
2.5
|
35.5
|
1.0
|
|
HZ1
|
e:LYS251
|
2.8
|
23.4
|
1.0
|
|
HE1
|
e:HIS210
|
2.8
|
29.1
|
1.0
|
|
OD1
|
e:ASP82
|
2.8
|
35.3
|
1.0
|
|
HZ2
|
e:LYS251
|
3.0
|
23.4
|
1.0
|
|
OE2
|
e:GLU132
|
3.1
|
25.3
|
1.0
|
|
HA
|
e:ASP82
|
3.2
|
24.1
|
1.0
|
|
NE2
|
e:HIS80
|
3.2
|
29.6
|
1.0
|
|
ND2
|
e:ASN253
|
3.2
|
27.7
|
1.0
|
|
HE2
|
e:HIS210
|
3.3
|
28.3
|
1.0
|
|
NZ
|
e:LYS251
|
3.3
|
19.6
|
1.0
|
|
HB2
|
e:MET102
|
3.3
|
34.9
|
1.0
|
|
HD2
|
e:HIS80
|
3.3
|
35.0
|
1.0
|
|
CE1
|
e:HIS210
|
3.3
|
24.3
|
1.0
|
|
OE1
|
e:GLU132
|
3.4
|
27.8
|
1.0
|
|
H
|
e:HIS83
|
3.5
|
31.0
|
1.0
|
|
CD
|
e:GLU132
|
3.5
|
32.6
|
1.0
|
|
HD22
|
e:ASN253
|
3.5
|
33.3
|
1.0
|
|
SD
|
e:MET102
|
3.5
|
33.3
|
1.0
|
|
NE2
|
e:HIS210
|
3.6
|
23.6
|
1.0
|
|
HZ3
|
e:LYS251
|
3.6
|
23.4
|
1.0
|
|
CD2
|
e:HIS80
|
3.6
|
29.2
|
1.0
|
|
OE1
|
e:GLN47
|
3.8
|
30.4
|
1.0
|
|
CG
|
e:ASP82
|
3.9
|
37.0
|
1.0
|
|
HB3
|
e:MET102
|
3.9
|
34.9
|
1.0
|
|
CB
|
e:MET102
|
3.9
|
29.1
|
1.0
|
|
CA
|
e:ASP82
|
4.0
|
20.1
|
1.0
|
|
HE21
|
e:GLN47
|
4.2
|
38.0
|
1.0
|
|
CG
|
e:MET102
|
4.2
|
30.2
|
1.0
|
|
HG11
|
e:VAL208
|
4.2
|
21.3
|
1.0
|
|
CG
|
e:ASN253
|
4.2
|
24.7
|
1.0
|
|
N
|
e:HIS83
|
4.3
|
25.8
|
1.0
|
|
HG3
|
e:MET102
|
4.3
|
36.3
|
1.0
|
|
CB
|
e:ASP82
|
4.4
|
28.3
|
1.0
|
|
HB2
|
e:ASP82
|
4.4
|
33.9
|
1.0
|
|
CE1
|
e:HIS80
|
4.4
|
28.8
|
1.0
|
|
OD1
|
e:ASN253
|
4.4
|
23.9
|
1.0
|
|
ND1
|
e:HIS210
|
4.5
|
23.8
|
1.0
|
|
HE3
|
e:MET102
|
4.5
|
35.7
|
1.0
|
|
CD
|
e:GLN47
|
4.6
|
30.7
|
1.0
|
|
CE
|
e:LYS251
|
4.6
|
26.0
|
1.0
|
|
CE
|
e:MET102
|
4.6
|
29.8
|
1.0
|
|
NE2
|
e:GLN47
|
4.6
|
31.7
|
1.0
|
|
HE3
|
e:LYS251
|
4.7
|
31.2
|
1.0
|
|
O01
|
e:TD3311
|
4.7
|
43.8
|
1.0
|
|
C
|
e:ASP82
|
4.7
|
26.3
|
1.0
|
|
HE1
|
e:HIS80
|
4.7
|
34.5
|
1.0
|
|
CD2
|
e:HIS210
|
4.8
|
24.7
|
1.0
|
|
O
|
e:LEU81
|
4.8
|
23.0
|
1.0
|
|
HE1
|
e:MET102
|
4.8
|
35.7
|
1.0
|
|
CG
|
e:GLU132
|
4.9
|
25.6
|
1.0
|
|
HB3
|
e:GLU132
|
4.9
|
31.4
|
1.0
|
|
OD2
|
e:ASP82
|
4.9
|
38.2
|
1.0
|
|
CG
|
e:HIS80
|
4.9
|
25.9
|
1.0
|
|
HD2
|
e:HIS83
|
4.9
|
33.4
|
1.0
|
|
CD2
|
e:HIS83
|
5.0
|
27.8
|
1.0
|
|
Sodium binding site 8 out
of 8 in 3n9r
Go back to
Sodium Binding Sites List in 3n9r
Sodium 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 Sodium with other atoms in the Na 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:Na309
b:33.8
occ:1.00
|
HE2
|
j:HIS80
|
2.3
|
22.5
|
1.0
|
|
HD21
|
j:ASN253
|
2.5
|
27.3
|
1.0
|
|
HE1
|
j:HIS210
|
2.7
|
24.5
|
1.0
|
|
HZ1
|
j:LYS251
|
2.8
|
21.0
|
1.0
|
|
OD1
|
j:ASP82
|
2.8
|
34.3
|
1.0
|
|
HZ2
|
j:LYS251
|
3.0
|
21.0
|
1.0
|
|
NE2
|
j:HIS80
|
3.1
|
18.8
|
1.0
|
|
HE2
|
j:HIS210
|
3.1
|
23.7
|
1.0
|
|
OE2
|
j:GLU132
|
3.1
|
28.0
|
1.0
|
|
HA
|
j:ASP82
|
3.1
|
17.8
|
1.0
|
|
HB2
|
j:MET102
|
3.2
|
16.0
|
1.0
|
|
CE1
|
j:HIS210
|
3.2
|
20.4
|
1.0
|
|
NZ
|
j:LYS251
|
3.3
|
17.6
|
1.0
|
|
OE1
|
j:GLU132
|
3.3
|
26.6
|
1.0
|
|
ND2
|
j:ASN253
|
3.3
|
22.8
|
1.0
|
|
NE2
|
j:HIS210
|
3.4
|
19.7
|
1.0
|
|
HD2
|
j:HIS80
|
3.4
|
24.2
|
1.0
|
|
SD
|
j:MET102
|
3.4
|
25.2
|
1.0
|
|
CD
|
j:GLU132
|
3.5
|
28.6
|
1.0
|
|
H
|
j:HIS83
|
3.6
|
17.1
|
1.0
|
|
CD2
|
j:HIS80
|
3.6
|
20.2
|
1.0
|
|
HZ3
|
j:LYS251
|
3.6
|
21.0
|
1.0
|
|
HD22
|
j:ASN253
|
3.6
|
27.3
|
1.0
|
|
OE1
|
j:GLN47
|
3.7
|
24.6
|
1.0
|
|
CG
|
j:ASP82
|
3.8
|
26.1
|
1.0
|
|
CB
|
j:MET102
|
3.9
|
13.4
|
1.0
|
|
HB3
|
j:MET102
|
3.9
|
16.0
|
1.0
|
|
CA
|
j:ASP82
|
4.0
|
14.9
|
1.0
|
|
CG
|
j:MET102
|
4.0
|
23.2
|
1.0
|
|
HG3
|
j:MET102
|
4.1
|
27.9
|
1.0
|
|
HG11
|
j:VAL208
|
4.2
|
19.1
|
1.0
|
|
CE1
|
j:HIS80
|
4.2
|
16.1
|
1.0
|
|
N
|
j:HIS83
|
4.3
|
14.3
|
1.0
|
|
CG
|
j:ASN253
|
4.3
|
24.3
|
1.0
|
|
CB
|
j:ASP82
|
4.3
|
17.3
|
1.0
|
|
HE21
|
j:GLN47
|
4.3
|
29.3
|
1.0
|
|
HB2
|
j:ASP82
|
4.4
|
20.8
|
1.0
|
|
ND1
|
j:HIS210
|
4.4
|
21.5
|
1.0
|
|
OD1
|
j:ASN253
|
4.5
|
19.4
|
1.0
|
|
HE3
|
j:MET102
|
4.5
|
31.5
|
1.0
|
|
HE3
|
j:LYS251
|
4.5
|
23.8
|
1.0
|
|
CD
|
j:GLN47
|
4.5
|
24.8
|
1.0
|
|
HE1
|
j:HIS80
|
4.5
|
19.3
|
1.0
|
|
CE
|
j:LYS251
|
4.5
|
19.8
|
1.0
|
|
CE
|
j:MET102
|
4.6
|
26.3
|
1.0
|
|
CD2
|
j:HIS210
|
4.6
|
21.9
|
1.0
|
|
OD2
|
j:ASP82
|
4.7
|
30.6
|
1.0
|
|
C
|
j:ASP82
|
4.7
|
20.4
|
1.0
|
|
O
|
j:LEU81
|
4.8
|
18.8
|
1.0
|
|
HE1
|
j:MET102
|
4.8
|
31.5
|
1.0
|
|
NE2
|
j:GLN47
|
4.8
|
24.4
|
1.0
|
|
HB3
|
j:GLU132
|
4.8
|
18.3
|
1.0
|
|
CG
|
j:GLU132
|
4.8
|
18.7
|
1.0
|
|
CG
|
j:HIS80
|
4.9
|
16.8
|
1.0
|
|
HG2
|
j:MET102
|
5.0
|
27.9
|
1.0
|
|
HG2
|
j:GLU132
|
5.0
|
22.4
|
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: Mon Oct 7 11:45:23 2024
|
