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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: Tue Dec 15 05:23:31 2020

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