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Potassium in PDB 4a0m: Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad

Enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad

All present enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad:
1.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad, PDB code: 4a0m was solved by L.Gonzalez-Segura, E.Rudino-Pinera, A.G.Diaz-Sanchez, R.A.Munoz-Clares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.078 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.406, 80.979, 85.540, 79.06, 84.94, 77.99
R / Rfree (%) 21.31 / 24.67

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad (pdb code 4a0m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 8 binding sites of Potassium where determined in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad, PDB code: 4a0m:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Potassium binding site 1 out of 8 in 4a0m

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Potassium binding site 1 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1497

b:85.3
occ:1.00
 O A:ASP96 2.9 44.6 1.0
OD1 A:ASP96 3.0 44.6 1.0
O A:ILE28 3.1 72.4 1.0
O A:HOH2010 3.3 52.3 1.0
O A:LEU186 3.5 57.8 1.0
N A:ILE28 3.8 69.7 1.0
C A:ASP96 3.8 54.6 1.0
C A:ILE28 4.0 76.0 1.0
CA A:ASP96 4.0 57.1 1.0
CG A:ASP96 4.1 53.5 1.0
C A:LEU186 4.3 50.4 1.0
CG2 A:VAL27 4.4 49.1 1.0
CA A:ILE28 4.4 61.6 1.0
CD1 A:ILE334 4.6 38.1 1.0
O A:ILE95 4.6 50.3 1.0
CD A:PRO30 4.7 57.4 1.0
CB A:ASP96 4.7 63.0 1.0
C A:VAL27 4.7 68.4 1.0
CB A:VAL27 4.8 41.4 1.0
CA A:VAL27 4.8 66.3 1.0
O A:ILE334 4.9 42.4 1.0
CG A:PRO30 4.9 57.1 1.0
CA A:ALA187 4.9 41.2 1.0
N A:ALA187 5.0 46.8 1.0
N A:SER97 5.0 55.2 1.0

Potassium binding site 2 out of 8 in 4a0m

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Potassium binding site 2 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1501

b:76.4
occ:1.00
 O A:LYS460 2.8 41.5 1.0
O B:VAL251 2.9 37.1 1.0
O A:HOH2149 3.0 30.4 1.0
CD B:PRO253 3.3 25.7 1.0
C A:LYS460 3.5 43.5 1.0
N A:LYS460 3.6 35.7 1.0
CA A:LYS460 3.7 40.0 1.0
O A:GLY463 3.7 31.9 1.0
C B:VAL251 3.9 28.1 1.0
CG B:PRO253 4.0 19.4 1.0
O A:HOH2148 4.1 33.6 1.0
CA B:LYS252 4.1 32.7 1.0
N B:PRO253 4.3 27.7 1.0
C A:GLY463 4.3 31.9 1.0
C A:ILE459 4.4 28.3 1.0
N B:LYS252 4.4 30.4 1.0
O B:ASP229 4.5 26.8 1.0
CD2 A:PHE464 4.5 25.1 1.0
O B:LEU250 4.5 32.7 1.0
O B:HOH2075 4.5 43.2 1.0
CA A:GLY463 4.6 32.0 1.0
N A:ARG461 4.7 39.9 1.0
C B:LYS252 4.7 30.5 1.0
N A:GLY463 4.7 26.5 1.0
CG1 B:VAL251 4.9 54.2 1.0
CA A:ILE459 4.9 29.8 1.0

Potassium binding site 3 out of 8 in 4a0m

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Potassium binding site 3 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1497

b:63.2
occ:1.00
 O B:LEU186 2.8 66.0 1.0
O B:ASP96 2.8 39.9 1.0
OD1 B:ASP96 3.1 50.3 1.0
C B:LEU186 3.5 57.0 1.0
O B:HOH2011 3.6 72.2 1.0
O B:ILE28 3.8 60.7 1.0
C B:ASP96 3.8 57.1 1.0
CG B:ASP96 4.0 43.4 1.0
CD1 B:ILE334 4.0 44.5 1.0
O B:HOH2037 4.1 59.5 1.0
N B:ALA187 4.1 56.8 1.0
CA B:ALA187 4.2 49.7 1.0
CA B:ASP96 4.3 68.4 1.0
CA B:LEU186 4.3 52.1 1.0
N B:ILE28 4.4 55.0 1.0
CB B:ALA187 4.6 42.6 1.0
OD2 B:ASP96 4.7 43.8 1.0
CB B:ASP96 4.7 59.5 1.0
C B:ILE28 4.8 60.7 1.0
CG1 B:ILE334 4.8 55.9 1.0
CG2 B:VAL27 4.8 55.7 1.0
O B:ILE334 4.9 56.9 1.0
CB B:LEU186 4.9 52.1 1.0
N B:SER97 5.0 52.0 1.0

Potassium binding site 4 out of 8 in 4a0m

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Potassium binding site 4 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1499

b:69.9
occ:1.00
 O A:VAL251 2.6 33.8 1.0
O B:LYS460 2.8 36.4 1.0
O A:HOH2070 2.8 46.1 1.0
O B:HOH2121 3.0 42.6 1.0
O B:GLY463 3.1 35.4 1.0
CD A:PRO253 3.4 32.1 1.0
C B:LYS460 3.7 37.9 1.0
C B:GLY463 3.7 39.0 1.0
C A:VAL251 3.7 33.4 1.0
N B:LYS460 3.8 30.6 1.0
CD2 B:PHE464 4.0 26.7 1.0
CA B:LYS460 4.0 40.3 1.0
CG A:PRO253 4.0 24.1 1.0
CA B:GLY463 4.0 36.0 1.0
CA A:LYS252 4.1 26.5 1.0
N A:PRO253 4.2 29.8 1.0
N B:GLY463 4.3 40.2 1.0
N A:LYS252 4.3 22.8 1.0
C B:ILE459 4.4 41.4 1.0
CG1 A:VAL251 4.4 51.0 1.0
CB B:PHE464 4.5 30.2 1.0
O A:LEU250 4.6 31.7 1.0
C A:LYS252 4.6 32.5 1.0
N B:PHE464 4.7 29.8 1.0
O A:HOH2072 4.7 37.1 1.0
CG B:PHE464 4.8 24.4 1.0
CA B:ILE459 4.8 35.5 1.0
N B:ARG461 4.8 35.4 1.0
CE2 B:PHE464 4.8 27.1 1.0
O A:ASP229 4.9 39.5 1.0
CA A:VAL251 4.9 34.5 1.0
CB A:VAL251 5.0 37.5 1.0

Potassium binding site 5 out of 8 in 4a0m

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Potassium binding site 5 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1497

b:85.0
occ:1.00
 OD1 C:ASP96 2.9 62.4 1.0
O C:ASP96 3.1 58.2 1.0
O C:LEU186 3.2 54.6 1.0
O C:HOH2005 3.3 74.4 0.9
O C:ILE28 3.4 74.0 1.0
O C:HOH2008 3.4 70.8 1.0
N C:ILE28 3.8 61.6 1.0
C C:LEU186 3.9 61.0 1.0
CG C:ASP96 4.0 54.0 1.0
C C:ASP96 4.1 57.4 1.0
C C:ILE28 4.2 75.6 1.0
CA C:ASP96 4.3 59.5 1.0
O C:HOH2006 4.4 51.2 1.0
CD1 C:ILE334 4.4 47.6 1.0
CG2 C:VAL27 4.5 58.7 1.0
N C:ALA187 4.5 57.0 1.0
CA C:ILE28 4.6 65.5 1.0
CA C:LEU186 4.6 45.9 1.0
CA C:ALA187 4.7 51.4 1.0
CA C:VAL27 4.7 68.5 1.0
C C:VAL27 4.8 64.0 1.0
CB C:VAL27 4.8 68.4 1.0
CB C:ASP96 4.8 57.5 1.0
OD2 C:ASP96 4.8 40.9 1.0
O C:ILE334 4.8 46.3 1.0

Potassium binding site 6 out of 8 in 4a0m

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Potassium binding site 6 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1500

b:69.8
occ:1.00
 O C:HOH2053 2.6 43.2 1.0
O D:LYS460 2.9 48.1 1.0
O C:VAL251 2.9 39.7 0.5
O C:VAL251 3.0 39.7 0.5
CD C:PRO253 3.2 38.9 1.0
O D:GLY463 3.3 30.7 1.0
N D:LYS460 3.6 35.8 1.0
C D:LYS460 3.7 47.5 1.0
CA D:LYS460 3.8 39.0 1.0
CG C:PRO253 3.8 29.6 1.0
C C:VAL251 3.9 36.2 0.5
C C:VAL251 4.0 36.1 0.5
C D:GLY463 4.0 47.8 1.0
CA C:LYS252 4.1 41.3 1.0
N C:PRO253 4.2 34.7 1.0
C D:ILE459 4.3 38.4 1.0
CD2 D:PHE464 4.3 37.6 1.0
N C:LYS252 4.4 37.3 1.0
O C:ASP229 4.5 43.6 1.0
CA D:GLY463 4.5 45.2 1.0
C C:LYS252 4.6 34.9 1.0
N D:GLY463 4.6 46.9 1.0
O C:LEU250 4.7 37.7 1.0
CA D:ILE459 4.7 33.1 1.0
CB D:PHE464 4.7 28.1 1.0
CG2 C:VAL251 4.8 35.7 0.5
CG1 C:VAL251 4.8 43.1 0.5
N D:ARG461 4.9 39.3 1.0
O C:HOH2054 5.0 38.6 1.0
N D:PHE464 5.0 26.6 1.0
O D:ILE459 5.0 42.4 1.0

Potassium binding site 7 out of 8 in 4a0m

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Potassium binding site 7 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1501

b:64.0
occ:1.00
 O D:VAL251 2.7 39.8 1.0
O C:LYS460 2.8 31.9 1.0
O D:HOH2053 2.9 44.2 1.0
O C:HOH2118 3.1 47.5 1.0
CD D:PRO253 3.4 39.9 1.0
C C:LYS460 3.5 32.5 1.0
O C:GLY463 3.6 23.4 1.0
N C:LYS460 3.7 30.1 1.0
C D:VAL251 3.7 38.7 1.0
CA C:LYS460 3.8 31.9 1.0
CA D:LYS252 3.9 44.9 1.0
CG D:PRO253 4.1 29.4 1.0
N D:LYS252 4.2 41.3 1.0
N D:PRO253 4.3 36.2 1.0
C C:GLY463 4.3 25.5 1.0
O D:LEU250 4.4 39.5 1.0
CD2 C:PHE464 4.4 30.2 1.0
C C:ILE459 4.5 30.0 1.0
O D:ASP229 4.5 37.7 1.0
C D:LYS252 4.6 37.7 1.0
CA C:GLY463 4.6 29.1 1.0
O C:HOH2116 4.7 39.4 1.0
N C:ARG461 4.7 32.1 1.0
N C:GLY463 4.7 44.6 1.0
CG1 D:VAL251 4.7 53.3 1.0
O D:HOH2054 4.9 38.7 1.0
CA C:ILE459 5.0 31.1 1.0
CA D:VAL251 5.0 29.6 1.0

Potassium binding site 8 out of 8 in 4a0m

Go back to Potassium Binding Sites List in 4a0m
Potassium binding site 8 out of 8 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach in Complex with Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1497

b:94.5
occ:1.00
 OD1 D:ASP96 2.4 69.2 1.0
O D:LEU186 3.0 65.2 1.0
O D:ASP96 3.0 67.9 1.0
O D:HOH2004 3.5 65.8 1.0
O D:ILE28 3.5 81.7 1.0
CG D:ASP96 3.6 62.4 1.0
O D:HOH2011 3.6 61.0 1.0
C D:LEU186 3.7 62.3 1.0
C D:ASP96 4.1 68.7 1.0
CD1 D:ILE334 4.1 59.1 1.0
N D:ILE28 4.1 53.6 1.0
OD2 D:ASP96 4.1 62.2 1.0
CA D:LEU186 4.4 42.0 1.0
C D:ILE28 4.4 78.4 1.0
N D:ALA187 4.5 65.6 1.0
CA D:ASP96 4.5 68.6 1.0
O D:ILE334 4.5 60.0 1.0
CA D:ALA187 4.6 56.3 1.0
CB D:ASP96 4.6 51.4 1.0
CG1 D:ILE334 4.7 45.7 1.0
CA D:ILE28 4.8 61.2 1.0
CG2 D:VAL27 4.9 55.5 1.0
CB D:LEU186 4.9 50.4 1.0
CB D:ALA187 5.0 58.3 1.0

Reference:

A.G.Diaz-Sanchez, L.Gonzalez-Segura, C.Mujica-Jimenez, E.Rudino-Pinera, C.Montiel, L.P.Martinez-Castilla, R.A.Munoz-Clares. Amino Acid Residues Critical For the Specificity For Betaine Aldehyde of the Plant ALDH10 Isoenzyme Involved in the Synthesis of Glycine Betaine. Plant Physiol. V. 158 1570 2012.
ISSN: ISSN 0032-0889
PubMed: 22345508
DOI: 10.1104/PP.112.194514
Page generated: Sun Dec 13 23:26:09 2020

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