Sodium in PDB 5vje: Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
Enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
All present enzymatic activity of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate:
4.1.2.13;
Protein crystallography data
The structure of Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate, PDB code: 5vje
was solved by
M.Coincon,
J.Sygusch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.01 /
1.65
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.250,
71.869,
88.983,
90.00,
108.43,
90.00
|
|
R / Rfree (%)
|
13.8 /
16.4
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
(pdb code 5vje). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate, PDB code: 5vje:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 5vje
Go back to
Sodium Binding Sites List in 5vje
Sodium binding site 1 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
 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 of Escherichia Coli with D-Glucitol 1,6-Bisphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na401
b:21.8
occ:1.00
|
HE2
|
A:HIS107
|
2.2
|
17.0
|
1.0
|
|
HD21
|
A:ASN286
|
2.3
|
22.7
|
1.0
|
|
HZ2
|
A:LYS284
|
2.6
|
16.9
|
1.0
|
|
HZ1
|
A:LYS284
|
2.6
|
16.9
|
1.0
|
|
OD2
|
A:ASP109
|
2.8
|
17.4
|
1.0
|
|
OE2
|
A:GLU172
|
2.8
|
16.3
|
1.0
|
|
NZ
|
A:LYS284
|
2.9
|
14.1
|
1.0
|
|
HE1
|
A:HIS264
|
3.0
|
28.5
|
1.0
|
|
NE2
|
A:HIS107
|
3.0
|
14.1
|
1.0
|
|
HA
|
A:ASP109
|
3.0
|
17.4
|
1.0
|
|
ND2
|
A:ASN286
|
3.1
|
18.9
|
1.0
|
|
OE1
|
A:GLU172
|
3.2
|
15.3
|
1.0
|
|
HZ3
|
A:LYS284
|
3.2
|
16.9
|
1.0
|
|
HE2
|
A:HIS264
|
3.2
|
25.2
|
1.0
|
|
CD
|
A:GLU172
|
3.3
|
14.7
|
1.0
|
|
HB2
|
A:MET142
|
3.4
|
17.2
|
1.0
|
|
HD2
|
A:HIS107
|
3.5
|
16.9
|
1.0
|
|
CE1
|
A:HIS264
|
3.5
|
23.8
|
1.0
|
|
HD22
|
A:ASN286
|
3.6
|
22.7
|
1.0
|
|
SD
|
A:MET142
|
3.6
|
21.0
|
1.0
|
|
NE2
|
A:HIS264
|
3.6
|
21.0
|
1.0
|
|
CD2
|
A:HIS107
|
3.6
|
14.1
|
1.0
|
|
OE1
|
A:GLN59
|
3.6
|
14.1
|
1.0
|
|
HE21
|
A:GLN59
|
3.7
|
17.3
|
1.0
|
|
CG
|
A:ASP109
|
3.8
|
17.4
|
1.0
|
|
CA
|
A:ASP109
|
4.0
|
14.5
|
1.0
|
|
HG11
|
A:VAL262
|
4.0
|
17.6
|
1.0
|
|
CG
|
A:ASN286
|
4.1
|
16.2
|
1.0
|
|
CB
|
A:MET142
|
4.1
|
14.3
|
1.0
|
|
OD1
|
A:ASN286
|
4.1
|
15.2
|
1.0
|
|
HB3
|
A:MET142
|
4.2
|
17.2
|
1.0
|
|
CE1
|
A:HIS107
|
4.2
|
14.9
|
1.0
|
|
NE2
|
A:GLN59
|
4.2
|
14.4
|
1.0
|
|
H
|
A:HIS110
|
4.2
|
24.4
|
0.5
|
|
CG
|
A:MET142
|
4.2
|
17.4
|
1.0
|
|
CD
|
A:GLN59
|
4.3
|
13.2
|
1.0
|
|
H
|
A:HIS110
|
4.3
|
24.4
|
0.5
|
|
CE
|
A:LYS284
|
4.3
|
13.7
|
1.0
|
|
HG3
|
A:MET142
|
4.3
|
20.9
|
1.0
|
|
HE3
|
A:LYS284
|
4.3
|
16.5
|
1.0
|
|
CB
|
A:ASP109
|
4.4
|
15.4
|
1.0
|
|
HE1
|
A:HIS107
|
4.5
|
17.9
|
1.0
|
|
HE3
|
A:MET142
|
4.5
|
28.4
|
1.0
|
|
H32
|
A:GOS403
|
4.6
|
36.8
|
1.0
|
|
HB2
|
A:ASP109
|
4.6
|
18.5
|
1.0
|
|
O
|
A:THR108
|
4.6
|
14.3
|
1.0
|
|
ND1
|
A:HIS264
|
4.6
|
22.1
|
1.0
|
|
OD1
|
A:ASP109
|
4.6
|
17.9
|
1.0
|
|
CE
|
A:MET142
|
4.7
|
23.7
|
1.0
|
|
N
|
A:HIS110
|
4.7
|
20.4
|
0.5
|
|
N
|
A:HIS110
|
4.7
|
20.4
|
0.5
|
|
CG
|
A:GLU172
|
4.7
|
13.8
|
1.0
|
|
HE2
|
A:LYS284
|
4.8
|
16.5
|
1.0
|
|
C
|
A:ASP109
|
4.8
|
18.7
|
1.0
|
|
HE1
|
A:MET142
|
4.8
|
28.4
|
1.0
|
|
CD2
|
A:HIS264
|
4.8
|
21.4
|
1.0
|
|
N
|
A:ASP109
|
4.9
|
13.4
|
1.0
|
|
HG2
|
A:GLU172
|
4.9
|
16.5
|
1.0
|
|
HB3
|
A:GLU172
|
4.9
|
15.3
|
1.0
|
|
CG1
|
A:VAL262
|
4.9
|
14.7
|
1.0
|
|
HE22
|
A:GLN59
|
4.9
|
17.3
|
1.0
|
|
CG
|
A:HIS107
|
4.9
|
13.5
|
1.0
|
|
HD3
|
A:LYS284
|
5.0
|
17.1
|
1.0
|
|
O3
|
A:GOS403
|
5.0
|
30.7
|
1.0
|
|
Sodium binding site 2 out
of 4 in 5vje
Go back to
Sodium Binding Sites List in 5vje
Sodium binding site 2 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
 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 of Escherichia Coli with D-Glucitol 1,6-Bisphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:23.8
occ:1.00
|
O
|
A:GLY227
|
2.2
|
30.1
|
1.0
|
|
O
|
A:SER267
|
2.4
|
32.2
|
1.0
|
|
O12
|
A:GOS403
|
2.4
|
26.0
|
1.0
|
|
O
|
A:HOH790
|
2.5
|
47.1
|
1.0
|
|
O
|
A:VAL225
|
2.6
|
35.6
|
1.0
|
|
O
|
A:GLY265
|
2.7
|
36.5
|
1.0
|
|
HA2
|
A:GLY265
|
3.2
|
44.1
|
1.0
|
|
C
|
A:GLY265
|
3.2
|
35.7
|
1.0
|
|
H
|
A:GLY227
|
3.2
|
36.3
|
0.6
|
|
HB2
|
A:SER267
|
3.3
|
29.6
|
1.0
|
|
C
|
A:GLY227
|
3.4
|
31.9
|
1.0
|
|
C
|
A:SER267
|
3.4
|
31.5
|
1.0
|
|
HA3
|
A:GLY265
|
3.5
|
44.1
|
1.0
|
|
N
|
A:GLY227
|
3.5
|
30.3
|
0.6
|
|
CA
|
A:GLY265
|
3.5
|
36.7
|
1.0
|
|
HA
|
A:HIS226
|
3.6
|
44.7
|
1.0
|
|
N
|
A:SER267
|
3.7
|
27.7
|
1.0
|
|
H
|
A:SER267
|
3.7
|
33.3
|
1.0
|
|
C
|
A:VAL225
|
3.8
|
37.0
|
1.0
|
|
O
|
A:HOH515
|
3.8
|
26.4
|
1.0
|
|
P1
|
A:GOS403
|
3.9
|
26.5
|
1.0
|
|
CA
|
A:SER267
|
3.9
|
26.9
|
1.0
|
|
CA
|
A:GLY227
|
4.0
|
31.0
|
1.0
|
|
C
|
A:HIS226
|
4.0
|
36.2
|
1.0
|
|
CB
|
A:SER267
|
4.1
|
24.7
|
1.0
|
|
N
|
A:GLY266
|
4.1
|
28.7
|
1.0
|
|
C
|
A:GLY266
|
4.1
|
28.2
|
1.0
|
|
HA
|
A:VAL228
|
4.2
|
49.1
|
1.0
|
|
CA
|
A:HIS226
|
4.2
|
37.3
|
1.0
|
|
HG12
|
A:VAL228
|
4.3
|
33.4
|
1.0
|
|
O
|
A:HOH738
|
4.3
|
28.2
|
1.0
|
|
HA3
|
A:GLY268
|
4.4
|
43.8
|
1.0
|
|
O13
|
A:GOS403
|
4.5
|
27.2
|
1.0
|
|
N
|
A:VAL228
|
4.5
|
35.6
|
1.0
|
|
N
|
A:HIS226
|
4.5
|
36.5
|
1.0
|
|
HA2
|
A:GLY227
|
4.5
|
37.2
|
1.0
|
|
H
|
A:VAL225
|
4.5
|
41.1
|
1.0
|
|
HG
|
A:SER269
|
4.5
|
35.4
|
1.0
|
|
O
|
A:GLY266
|
4.6
|
32.4
|
1.0
|
|
O1
|
A:GOS403
|
4.6
|
29.6
|
1.0
|
|
HB3
|
A:SER267
|
4.6
|
29.6
|
1.0
|
|
N
|
A:GLY268
|
4.6
|
35.5
|
1.0
|
|
H
|
A:GLY266
|
4.7
|
34.4
|
1.0
|
|
HG13
|
A:VAL228
|
4.7
|
33.4
|
1.0
|
|
CA
|
A:GLY266
|
4.7
|
26.2
|
1.0
|
|
HB
|
A:VAL225
|
4.7
|
44.0
|
1.0
|
|
O
|
A:HOH736
|
4.8
|
37.5
|
1.0
|
|
HA3
|
A:GLY227
|
4.8
|
37.2
|
1.0
|
|
CA
|
A:VAL228
|
4.8
|
40.9
|
1.0
|
|
HA
|
A:SER267
|
4.9
|
32.2
|
1.0
|
|
O11
|
A:GOS403
|
4.9
|
23.2
|
1.0
|
|
O
|
A:HIS226
|
4.9
|
36.3
|
1.0
|
|
CG1
|
A:VAL228
|
4.9
|
27.9
|
1.0
|
|
HG21
|
A:VAL234
|
4.9
|
51.5
|
1.0
|
|
N
|
A:GLY265
|
4.9
|
30.1
|
1.0
|
|
CA
|
A:GLY268
|
5.0
|
36.5
|
1.0
|
|
Sodium binding site 3 out
of 4 in 5vje
Go back to
Sodium Binding Sites List in 5vje
Sodium binding site 3 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
 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 of Escherichia Coli with D-Glucitol 1,6-Bisphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na401
b:21.2
occ:1.00
|
HE2
|
B:HIS107
|
2.1
|
15.9
|
1.0
|
|
HD21
|
B:ASN286
|
2.3
|
18.5
|
1.0
|
|
HZ3
|
B:LYS284
|
2.6
|
14.3
|
1.0
|
|
HZ1
|
B:LYS284
|
2.7
|
14.3
|
1.0
|
|
OD1
|
B:ASP109
|
2.7
|
15.2
|
1.0
|
|
OE2
|
B:GLU172
|
2.8
|
13.9
|
1.0
|
|
NE2
|
B:HIS107
|
2.9
|
13.2
|
1.0
|
|
NZ
|
B:LYS284
|
3.0
|
11.9
|
1.0
|
|
HE1
|
B:HIS264
|
3.0
|
22.4
|
1.0
|
|
HA
|
B:ASP109
|
3.0
|
17.0
|
1.0
|
|
ND2
|
B:ASN286
|
3.1
|
15.4
|
1.0
|
|
HE2
|
B:HIS264
|
3.2
|
22.6
|
1.0
|
|
OE1
|
B:GLU172
|
3.2
|
12.6
|
1.0
|
|
HB2
|
B:MET142
|
3.3
|
15.7
|
1.0
|
|
CD
|
B:GLU172
|
3.3
|
12.0
|
1.0
|
|
HZ2
|
B:LYS284
|
3.3
|
14.3
|
1.0
|
|
CE1
|
B:HIS264
|
3.5
|
18.7
|
1.0
|
|
SD
|
B:MET142
|
3.5
|
16.0
|
1.0
|
|
HD2
|
B:HIS107
|
3.5
|
15.5
|
1.0
|
|
HD22
|
B:ASN286
|
3.5
|
18.5
|
1.0
|
|
NE2
|
B:HIS264
|
3.6
|
18.9
|
1.0
|
|
CD2
|
B:HIS107
|
3.6
|
12.9
|
1.0
|
|
CG
|
B:ASP109
|
3.7
|
16.1
|
1.0
|
|
OE1
|
B:GLN59
|
3.7
|
12.0
|
1.0
|
|
HE22
|
B:GLN59
|
3.8
|
16.8
|
1.0
|
|
CA
|
B:ASP109
|
4.0
|
14.2
|
1.0
|
|
CE1
|
B:HIS107
|
4.0
|
14.2
|
1.0
|
|
CB
|
B:MET142
|
4.0
|
13.1
|
1.0
|
|
HG11
|
B:VAL262
|
4.1
|
15.5
|
1.0
|
|
CG
|
B:ASN286
|
4.1
|
14.6
|
1.0
|
|
HB3
|
B:MET142
|
4.1
|
15.7
|
1.0
|
|
H
|
B:HIS110
|
4.2
|
18.6
|
1.0
|
|
CG
|
B:MET142
|
4.2
|
16.4
|
1.0
|
|
OD1
|
B:ASN286
|
4.2
|
15.3
|
1.0
|
|
HE1
|
B:HIS107
|
4.3
|
17.0
|
1.0
|
|
HG3
|
B:MET142
|
4.3
|
19.6
|
1.0
|
|
NE2
|
B:GLN59
|
4.3
|
14.0
|
1.0
|
|
CB
|
B:ASP109
|
4.3
|
15.7
|
1.0
|
|
CD
|
B:GLN59
|
4.3
|
12.3
|
1.0
|
|
CE
|
B:LYS284
|
4.3
|
11.2
|
1.0
|
|
HE3
|
B:LYS284
|
4.4
|
13.5
|
1.0
|
|
H32
|
B:GOS403
|
4.5
|
29.6
|
1.0
|
|
HE3
|
B:MET142
|
4.5
|
22.6
|
1.0
|
|
O
|
B:THR108
|
4.5
|
13.9
|
1.0
|
|
HB2
|
B:ASP109
|
4.5
|
18.8
|
1.0
|
|
OD2
|
B:ASP109
|
4.6
|
16.9
|
1.0
|
|
CE
|
B:MET142
|
4.6
|
18.8
|
1.0
|
|
N
|
B:HIS110
|
4.6
|
15.5
|
1.0
|
|
ND1
|
B:HIS264
|
4.7
|
22.3
|
1.0
|
|
CG
|
B:GLU172
|
4.7
|
11.0
|
1.0
|
|
C
|
B:ASP109
|
4.7
|
16.2
|
1.0
|
|
HE1
|
B:MET142
|
4.8
|
22.6
|
1.0
|
|
CD2
|
B:HIS264
|
4.8
|
19.3
|
1.0
|
|
HB3
|
B:GLU172
|
4.8
|
13.6
|
1.0
|
|
HE2
|
B:LYS284
|
4.8
|
13.5
|
1.0
|
|
N
|
B:ASP109
|
4.8
|
13.1
|
1.0
|
|
HG2
|
B:GLU172
|
4.9
|
13.2
|
1.0
|
|
CG
|
B:HIS107
|
4.9
|
12.6
|
1.0
|
|
CG1
|
B:VAL262
|
4.9
|
12.9
|
1.0
|
|
HE21
|
B:GLN59
|
5.0
|
16.8
|
1.0
|
|
Sodium binding site 4 out
of 4 in 5vje
Go back to
Sodium Binding Sites List in 5vje
Sodium binding site 4 out
of 4 in the Class II Fructose-1,6-Bisphosphate Aldolase of Escherichia Coli with D-Glucitol 1,6-Bisphosphate
 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 of Escherichia Coli with D-Glucitol 1,6-Bisphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na402
b:20.7
occ:1.00
|
O
|
B:GLY227
|
2.3
|
21.9
|
1.0
|
|
O
|
B:SER267
|
2.4
|
25.3
|
1.0
|
|
O11
|
B:GOS403
|
2.4
|
19.2
|
1.0
|
|
O
|
B:VAL225
|
2.6
|
28.9
|
1.0
|
|
O
|
B:GLY265
|
2.6
|
23.7
|
1.0
|
|
O
|
B:HOH691
|
2.7
|
34.6
|
1.0
|
|
C
|
B:GLY265
|
3.2
|
24.0
|
1.0
|
|
HB2
|
B:SER267
|
3.2
|
24.6
|
1.0
|
|
HA2
|
B:GLY265
|
3.3
|
28.1
|
1.0
|
|
H
|
B:GLY227
|
3.3
|
29.6
|
1.0
|
|
C
|
B:SER267
|
3.4
|
22.2
|
1.0
|
|
C
|
B:GLY227
|
3.4
|
21.5
|
1.0
|
|
HA3
|
B:GLY265
|
3.5
|
28.1
|
1.0
|
|
N
|
B:GLY227
|
3.5
|
24.6
|
1.0
|
|
CA
|
B:GLY265
|
3.5
|
23.4
|
1.0
|
|
HA
|
B:HIS226
|
3.6
|
34.4
|
1.0
|
|
H
|
B:SER267
|
3.6
|
20.4
|
1.0
|
|
N
|
B:SER267
|
3.6
|
17.0
|
1.0
|
|
C
|
B:VAL225
|
3.8
|
29.4
|
1.0
|
|
CA
|
B:SER267
|
3.9
|
18.3
|
1.0
|
|
O
|
B:HOH552
|
3.9
|
23.8
|
1.0
|
|
P1
|
B:GOS403
|
3.9
|
18.8
|
1.0
|
|
CB
|
B:SER267
|
4.0
|
20.5
|
1.0
|
|
C
|
B:HIS226
|
4.0
|
30.4
|
1.0
|
|
CA
|
B:GLY227
|
4.1
|
21.7
|
1.0
|
|
C
|
B:GLY266
|
4.1
|
19.6
|
1.0
|
|
N
|
B:GLY266
|
4.1
|
21.5
|
1.0
|
|
CA
|
B:HIS226
|
4.1
|
28.6
|
1.0
|
|
HA
|
B:VAL228
|
4.2
|
33.9
|
1.0
|
|
HG12
|
B:VAL228
|
4.4
|
27.6
|
1.0
|
|
O
|
B:HOH707
|
4.4
|
25.5
|
1.0
|
|
N
|
B:HIS226
|
4.4
|
27.1
|
1.0
|
|
HB3
|
B:SER267
|
4.4
|
24.6
|
1.0
|
|
H
|
B:VAL225
|
4.4
|
37.8
|
1.0
|
|
O13
|
B:GOS403
|
4.5
|
19.9
|
1.0
|
|
HA3
|
B:GLY268
|
4.5
|
29.1
|
1.0
|
|
N
|
B:VAL228
|
4.5
|
24.3
|
1.0
|
|
HG
|
B:SER269
|
4.6
|
31.3
|
1.0
|
|
HA2
|
B:GLY227
|
4.6
|
26.1
|
1.0
|
|
O1
|
B:GOS403
|
4.6
|
21.3
|
1.0
|
|
N
|
B:GLY268
|
4.6
|
23.7
|
1.0
|
|
HB
|
B:VAL225
|
4.6
|
46.7
|
1.0
|
|
O
|
B:GLY266
|
4.6
|
21.9
|
1.0
|
|
CA
|
B:GLY266
|
4.7
|
19.9
|
1.0
|
|
HG13
|
B:VAL228
|
4.7
|
27.6
|
1.0
|
|
H
|
B:GLY266
|
4.7
|
25.8
|
1.0
|
|
HA
|
B:SER267
|
4.8
|
22.0
|
1.0
|
|
HA3
|
B:GLY227
|
4.8
|
26.1
|
1.0
|
|
O
|
B:HIS226
|
4.8
|
32.0
|
1.0
|
|
CA
|
B:VAL228
|
4.8
|
28.3
|
1.0
|
|
O12
|
B:GOS403
|
4.8
|
18.3
|
1.0
|
|
CA
|
B:VAL225
|
4.9
|
32.2
|
1.0
|
|
HG
|
B:SER267
|
4.9
|
23.1
|
1.0
|
|
N
|
B:GLY265
|
5.0
|
20.6
|
1.0
|
|
CG1
|
B:VAL228
|
5.0
|
23.0
|
1.0
|
|
O
|
B:HOH702
|
5.0
|
26.6
|
1.0
|
|
HA2
|
B:GLY266
|
5.0
|
23.9
|
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: Tue Oct 8 00:50:48 2024
|
