Sodium in PDB 1ebu: Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
Enzymatic activity of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
All present enzymatic activity of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine:
1.1.1.3;
Protein crystallography data
The structure of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine, PDB code: 1ebu
was solved by
B.Delabarre,
P.R.Thompson,
G.D.Wright,
A.M.Berghuis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.40 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.780,
104.090,
120.640,
90.00,
91.93,
90.00
|
R / Rfree (%)
|
21.5 /
28.3
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
(pdb code 1ebu). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine, PDB code: 1ebu:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1ebu
Go back to
Sodium Binding Sites List in 1ebu
Sodium binding site 1 out
of 4 in the Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na901
b:24.8
occ:1.00
|
O
|
A:LEU150
|
2.4
|
18.7
|
1.0
|
O
|
A:ALA148
|
2.4
|
18.7
|
1.0
|
O
|
A:GLU143
|
2.6
|
23.4
|
1.0
|
OE2
|
A:GLU143
|
2.7
|
21.8
|
1.0
|
CG
|
A:GLU143
|
3.2
|
12.5
|
1.0
|
N
|
A:GLY147
|
3.3
|
7.8
|
1.0
|
CD
|
A:GLU143
|
3.3
|
20.2
|
1.0
|
C
|
A:GLU143
|
3.5
|
21.1
|
1.0
|
C
|
A:GLY147
|
3.5
|
18.3
|
1.0
|
C
|
A:ALA148
|
3.5
|
16.7
|
1.0
|
C
|
A:LEU150
|
3.6
|
18.1
|
1.0
|
O
|
A:GLY147
|
3.7
|
11.7
|
1.0
|
CA
|
A:GLY147
|
3.7
|
16.7
|
1.0
|
N
|
A:ALA148
|
3.7
|
20.0
|
1.0
|
N
|
A:LEU150
|
3.9
|
17.4
|
1.0
|
N
|
A:ILE152
|
4.1
|
15.8
|
1.0
|
C
|
A:GLY149
|
4.1
|
17.7
|
1.0
|
CA
|
A:LEU150
|
4.2
|
18.2
|
1.0
|
CA
|
A:GLU143
|
4.2
|
18.8
|
1.0
|
C
|
A:VAL146
|
4.2
|
23.9
|
1.0
|
CA
|
A:ALA148
|
4.3
|
25.7
|
1.0
|
CB
|
A:GLU143
|
4.3
|
10.7
|
1.0
|
N
|
A:ALA144
|
4.3
|
17.5
|
1.0
|
CB
|
A:ILE152
|
4.3
|
11.2
|
1.0
|
N
|
A:GLY149
|
4.4
|
13.6
|
1.0
|
CD1
|
A:ILE152
|
4.5
|
20.3
|
1.0
|
N
|
A:VAL146
|
4.5
|
13.3
|
1.0
|
CA
|
A:ALA144
|
4.5
|
17.9
|
1.0
|
CB
|
A:LEU150
|
4.5
|
17.9
|
1.0
|
OE1
|
A:GLU143
|
4.5
|
17.3
|
1.0
|
CA
|
A:GLY149
|
4.6
|
12.7
|
1.0
|
CB
|
A:VAL146
|
4.6
|
18.9
|
1.0
|
O
|
A:GLY149
|
4.6
|
24.4
|
1.0
|
CG1
|
A:ILE152
|
4.6
|
12.7
|
1.0
|
CA
|
A:VAL146
|
4.6
|
18.4
|
1.0
|
N
|
A:ILE153
|
4.7
|
15.2
|
1.0
|
N
|
A:PRO151
|
4.7
|
14.4
|
1.0
|
CA
|
A:ILE152
|
4.7
|
16.3
|
1.0
|
CD1
|
A:ILE153
|
4.9
|
25.6
|
1.0
|
CA
|
A:PRO151
|
5.0
|
10.1
|
1.0
|
C
|
A:ALA144
|
5.0
|
21.0
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1ebu
Go back to
Sodium Binding Sites List in 1ebu
Sodium binding site 2 out
of 4 in the Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na902
b:21.6
occ:1.00
|
O
|
B:ALA148
|
2.3
|
22.9
|
1.0
|
O
|
B:VAL146
|
2.5
|
12.0
|
1.0
|
O
|
B:LEU150
|
2.5
|
18.1
|
1.0
|
O
|
B:GLU143
|
2.5
|
20.4
|
1.0
|
OE2
|
B:GLU143
|
2.5
|
21.7
|
1.0
|
C
|
B:ALA148
|
3.3
|
16.5
|
1.0
|
CD
|
B:GLU143
|
3.4
|
18.2
|
1.0
|
C
|
B:GLU143
|
3.4
|
9.2
|
1.0
|
CG
|
B:GLU143
|
3.4
|
12.9
|
1.0
|
C
|
B:VAL146
|
3.5
|
11.0
|
1.0
|
C
|
B:LEU150
|
3.6
|
15.8
|
1.0
|
N
|
B:ALA148
|
3.7
|
18.5
|
1.0
|
C
|
B:GLY147
|
3.8
|
17.5
|
1.0
|
N
|
B:LEU150
|
3.8
|
16.4
|
1.0
|
CA
|
B:ALA148
|
4.0
|
16.0
|
1.0
|
C
|
B:GLY149
|
4.1
|
22.1
|
1.0
|
N
|
B:ILE152
|
4.1
|
12.5
|
1.0
|
CG1
|
B:ILE152
|
4.1
|
16.5
|
1.0
|
O
|
B:GLY147
|
4.1
|
20.8
|
1.0
|
N
|
B:ALA144
|
4.2
|
9.2
|
1.0
|
CA
|
B:GLU143
|
4.2
|
12.3
|
1.0
|
CA
|
B:LEU150
|
4.2
|
16.2
|
1.0
|
N
|
B:GLY149
|
4.2
|
23.6
|
1.0
|
CA
|
B:GLY147
|
4.2
|
11.5
|
1.0
|
N
|
B:GLY147
|
4.3
|
13.8
|
1.0
|
CB
|
B:ILE152
|
4.3
|
17.1
|
1.0
|
CA
|
B:ALA144
|
4.3
|
8.4
|
1.0
|
CB
|
B:GLU143
|
4.3
|
3.5
|
1.0
|
N
|
B:VAL146
|
4.3
|
19.5
|
1.0
|
CA
|
B:VAL146
|
4.4
|
12.1
|
1.0
|
CA
|
B:GLY149
|
4.4
|
19.6
|
1.0
|
CB
|
B:LEU150
|
4.5
|
12.8
|
1.0
|
CD1
|
B:ILE153
|
4.6
|
23.9
|
1.0
|
OE1
|
B:GLU143
|
4.6
|
16.3
|
1.0
|
O
|
B:GLY149
|
4.6
|
26.5
|
1.0
|
C
|
B:ALA144
|
4.7
|
4.2
|
1.0
|
N
|
B:PRO151
|
4.7
|
15.6
|
1.0
|
CA
|
B:ILE152
|
4.8
|
14.7
|
1.0
|
N
|
B:ILE153
|
4.9
|
14.9
|
1.0
|
CB
|
B:VAL146
|
5.0
|
15.6
|
1.0
|
CA
|
B:PRO151
|
5.0
|
12.6
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1ebu
Go back to
Sodium Binding Sites List in 1ebu
Sodium binding site 3 out
of 4 in the Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na903
b:22.0
occ:1.00
|
O
|
C:ALA148
|
2.2
|
14.9
|
1.0
|
O
|
C:GLU143
|
2.3
|
28.2
|
1.0
|
O
|
C:LEU150
|
2.5
|
19.8
|
1.0
|
O
|
C:VAL146
|
2.9
|
24.7
|
1.0
|
OE2
|
C:GLU143
|
2.9
|
17.8
|
1.0
|
C
|
C:ALA148
|
3.1
|
11.7
|
1.0
|
C
|
C:GLU143
|
3.3
|
16.4
|
1.0
|
CG
|
C:GLU143
|
3.4
|
9.7
|
1.0
|
N
|
C:LEU150
|
3.5
|
14.7
|
1.0
|
C
|
C:GLY147
|
3.5
|
17.8
|
1.0
|
C
|
C:LEU150
|
3.6
|
13.7
|
1.0
|
CD
|
C:GLU143
|
3.6
|
24.4
|
1.0
|
O
|
C:GLY147
|
3.6
|
13.1
|
1.0
|
N
|
C:ALA148
|
3.7
|
13.2
|
1.0
|
C
|
C:VAL146
|
3.7
|
14.7
|
1.0
|
C
|
C:GLY149
|
3.7
|
16.2
|
1.0
|
N
|
C:GLY149
|
3.8
|
12.3
|
1.0
|
CA
|
C:GLY149
|
3.9
|
6.2
|
1.0
|
CA
|
C:ALA148
|
4.0
|
15.5
|
1.0
|
CA
|
C:LEU150
|
4.0
|
17.3
|
1.0
|
CA
|
C:GLY147
|
4.1
|
14.8
|
1.0
|
N
|
C:ALA144
|
4.1
|
14.6
|
1.0
|
CA
|
C:GLU143
|
4.2
|
12.2
|
1.0
|
N
|
C:GLY147
|
4.2
|
20.0
|
1.0
|
CA
|
C:ALA144
|
4.2
|
16.9
|
1.0
|
CB
|
C:GLU143
|
4.3
|
15.8
|
1.0
|
O
|
C:GLY149
|
4.3
|
14.4
|
1.0
|
CB
|
C:LEU150
|
4.4
|
17.7
|
1.0
|
N
|
C:VAL146
|
4.5
|
9.7
|
1.0
|
N
|
C:ILE152
|
4.5
|
14.8
|
1.0
|
CA
|
C:VAL146
|
4.7
|
16.3
|
1.0
|
N
|
C:PRO151
|
4.7
|
25.1
|
1.0
|
C
|
C:ALA144
|
4.8
|
14.9
|
1.0
|
OE1
|
C:GLU143
|
4.8
|
15.3
|
1.0
|
CB
|
C:ILE152
|
4.9
|
18.1
|
1.0
|
CD1
|
C:ILE152
|
4.9
|
22.8
|
1.0
|
N
|
C:THR145
|
4.9
|
13.8
|
1.0
|
CG1
|
C:ILE152
|
4.9
|
16.4
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1ebu
Go back to
Sodium Binding Sites List in 1ebu
Sodium binding site 4 out
of 4 in the Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Homoserine Dehydrogenase Complex with Nad Analogue and L- Homoserine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na904
b:16.6
occ:1.00
|
O
|
D:VAL146
|
2.2
|
16.9
|
1.0
|
OE2
|
D:GLU143
|
2.4
|
14.6
|
1.0
|
O
|
D:LEU150
|
2.4
|
19.1
|
1.0
|
O
|
D:GLU143
|
2.5
|
22.3
|
1.0
|
O
|
D:ALA148
|
2.5
|
21.4
|
1.0
|
CD
|
D:GLU143
|
3.3
|
14.0
|
1.0
|
C
|
D:VAL146
|
3.4
|
12.4
|
1.0
|
C
|
D:GLU143
|
3.4
|
7.2
|
1.0
|
CG
|
D:GLU143
|
3.5
|
6.8
|
1.0
|
C
|
D:ALA148
|
3.5
|
14.2
|
1.0
|
C
|
D:LEU150
|
3.6
|
8.4
|
1.0
|
C
|
D:GLY147
|
3.9
|
12.4
|
1.0
|
N
|
D:LEU150
|
3.9
|
13.8
|
1.0
|
N
|
D:ALA148
|
3.9
|
10.3
|
1.0
|
O
|
D:GLY147
|
4.1
|
10.0
|
1.0
|
N
|
D:ILE152
|
4.1
|
16.1
|
1.0
|
CA
|
D:GLU143
|
4.1
|
9.3
|
1.0
|
N
|
D:VAL146
|
4.1
|
9.2
|
1.0
|
CA
|
D:VAL146
|
4.2
|
10.6
|
1.0
|
CA
|
D:LEU150
|
4.3
|
13.9
|
1.0
|
CA
|
D:ALA148
|
4.3
|
9.7
|
1.0
|
C
|
D:GLY149
|
4.3
|
15.2
|
1.0
|
N
|
D:ALA144
|
4.3
|
4.6
|
1.0
|
N
|
D:GLY147
|
4.3
|
12.0
|
1.0
|
CA
|
D:GLY147
|
4.3
|
9.5
|
1.0
|
CB
|
D:GLU143
|
4.4
|
3.5
|
1.0
|
CG1
|
D:ILE152
|
4.4
|
19.6
|
1.0
|
CB
|
D:ILE152
|
4.4
|
22.2
|
1.0
|
OE1
|
D:GLU143
|
4.4
|
11.8
|
1.0
|
CA
|
D:ALA144
|
4.5
|
12.4
|
1.0
|
N
|
D:GLY149
|
4.5
|
19.1
|
1.0
|
CB
|
D:VAL146
|
4.6
|
14.7
|
1.0
|
N
|
D:PRO151
|
4.6
|
9.0
|
1.0
|
N
|
D:ILE153
|
4.6
|
15.0
|
1.0
|
CA
|
D:GLY149
|
4.7
|
10.6
|
1.0
|
CB
|
D:LEU150
|
4.7
|
15.7
|
1.0
|
CA
|
D:ILE152
|
4.8
|
16.2
|
1.0
|
O
|
D:GLY149
|
4.8
|
19.7
|
1.0
|
C
|
D:ALA144
|
4.9
|
10.8
|
1.0
|
N
|
D:THR145
|
4.9
|
16.1
|
1.0
|
C
|
D:PRO151
|
4.9
|
16.8
|
1.0
|
CA
|
D:PRO151
|
4.9
|
6.9
|
1.0
|
|
Reference:
B.Delabarre,
P.R.Thompson,
G.D.Wright,
A.M.Berghuis.
Crystal Structures of Homoserine Dehydrogenase Suggest A Novel Catalytic Mechanism For Oxidoreductases. Nat.Struct.Biol. V. 7 238 2000.
ISSN: ISSN 1072-8368
PubMed: 10700284
DOI: 10.1038/73359
Page generated: Sun Oct 6 18:22:28 2024
|