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Potassium in PDB 5a2d: Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde

Enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde

All present enzymatic activity of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde:
1.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde, PDB code: 5a2d was solved by A.Zarate-Romero, R.A.Munoz-Clares, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.70 / 1.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.720, 82.286, 87.717, 79.41, 84.75, 77.40
R / Rfree (%) 19.4 / 23.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde (pdb code 5a2d). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde, PDB code: 5a2d:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 5a2d

Go back to Potassium Binding Sites List in 5a2d
Potassium binding site 1 out of 4 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1499

b:43.4
occ:1.00
 O A:ASP96 2.6 36.5 1.0
O A:LEU186 2.6 34.0 1.0
OD1 A:ASP96 2.7 43.5 1.0
O A:HOH2022 2.9 33.7 1.0
O A:HOH2023 2.9 54.1 1.0
O A:ILE28 3.1 32.1 1.0
C A:ASP96 3.6 36.9 1.0
CG A:ASP96 3.8 44.4 1.0
C A:LEU186 3.8 32.6 1.0
CA A:ASP96 4.0 38.8 1.0
C A:ILE28 4.2 37.4 1.0
N A:ILE28 4.3 33.3 1.0
O A:HOH2072 4.3 34.6 1.0
CD A:PRO30 4.3 31.8 1.0
CG1 A:VAL27 4.4 33.6 1.0
CD1 A:ILE334 4.4 30.2 1.0
CB A:ASP96 4.5 41.9 1.0
CA A:ALA187 4.5 34.7 1.0
O A:HOH2020 4.5 33.2 1.0
O A:HOH2008 4.6 45.1 1.0
N A:ALA187 4.6 33.0 1.0
OD2 A:ASP96 4.7 43.4 1.0
N A:SER97 4.7 32.0 1.0
CA A:ILE28 4.7 35.5 1.0
CA A:LEU186 4.7 29.6 1.0
CB A:ALA187 4.8 31.7 1.0
O A:ILE334 5.0 32.2 1.0
CG A:PRO30 5.0 37.8 1.0

Potassium binding site 2 out of 4 in 5a2d

Go back to Potassium Binding Sites List in 5a2d
Potassium binding site 2 out of 4 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1499

b:45.7
occ:0.63
 O B:HOH2018 2.4 68.4 1.0
O B:ASP96 2.6 60.8 1.0
OD1 B:ASP96 2.7 55.5 1.0
O B:LEU186 2.7 48.4 1.0
O B:HOH2015 2.9 51.2 1.0
O B:ILE28 3.0 55.5 1.0
C B:ASP96 3.4 60.9 1.0
CA B:ASP96 3.4 64.3 1.0
CG B:ASP96 3.6 58.0 1.0
C B:LEU186 3.9 49.0 1.0
C B:ILE28 4.0 61.6 1.0
N B:ILE28 4.1 62.7 1.0
CB B:ASP96 4.1 61.7 1.0
O B:HOH2046 4.3 42.3 1.0
CG1 B:VAL27 4.3 53.8 1.0
CD B:PRO30 4.4 56.6 1.0
O B:HOH2016 4.4 53.2 1.0
OD2 B:ASP96 4.5 56.9 1.0
N B:SER97 4.6 58.9 1.0
CA B:ILE28 4.6 64.8 1.0
N B:ASP96 4.6 70.8 1.0
CD1 B:ILE334 4.6 53.1 1.0
CA B:ALA187 4.6 47.4 1.0
N B:ALA187 4.7 47.2 1.0
CA B:LEU186 4.9 48.2 1.0
C B:VAL27 4.9 61.8 1.0

Potassium binding site 3 out of 4 in 5a2d

Go back to Potassium Binding Sites List in 5a2d
Potassium binding site 3 out of 4 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1498

b:48.6
occ:0.65
 O C:LEU186 2.8 65.8 1.0
OD1 C:ASP96 2.8 71.5 1.0
O C:HOH2037 2.9 56.0 1.0
O C:ASP96 2.9 72.1 1.0
O C:ILE28 3.0 77.0 1.0
CG2 C:VAL27 3.5 79.9 1.0
N C:ILE28 3.7 75.4 1.0
C C:LEU186 3.9 63.4 1.0
C C:ASP96 3.9 73.6 1.0
CG C:ASP96 4.0 72.7 1.0
C C:ILE28 4.0 79.0 1.0
O C:HOH2017 4.1 45.9 1.0
CA C:ASP96 4.2 77.5 1.0
CA C:ILE28 4.4 77.6 1.0
CB C:VAL27 4.5 79.4 1.0
CA C:VAL27 4.5 74.5 1.0
C C:VAL27 4.6 77.3 1.0
CA C:LEU186 4.6 60.0 1.0
CB C:ASP96 4.7 74.4 1.0
N C:ALA187 4.8 64.3 1.0
OD2 C:ASP96 4.9 71.2 1.0
CA C:ALA187 4.9 67.4 1.0
CD1 C:ILE334 4.9 63.2 1.0
O C:ILE334 4.9 64.9 1.0
O C:ILE95 4.9 86.5 1.0
CD C:PRO30 5.0 85.5 1.0

Potassium binding site 4 out of 4 in 5a2d

Go back to Potassium Binding Sites List in 5a2d
Potassium binding site 4 out of 4 in the Crystal Structure of Betaine Aldehyde Dehydrogenase From Spinach Showing A Thiohemiacetal with Betaine Aldehyde


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 Showing A Thiohemiacetal with Betaine Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1499

b:43.4
occ:0.62
 O D:ASP96 2.6 46.6 1.0
OD1 D:ASP96 2.7 46.3 1.0
O D:LEU186 2.7 46.0 1.0
O D:HOH2088 2.8 52.4 1.0
O D:HOH2019 2.9 46.4 1.0
O D:ILE28 3.0 46.8 1.0
C D:ASP96 3.6 44.5 1.0
CG D:ASP96 3.8 46.7 1.0
C D:LEU186 3.8 45.3 1.0
CA D:ASP96 4.0 43.9 1.0
C D:ILE28 4.1 48.1 1.0
N D:ILE28 4.2 48.7 1.0
CG1 D:VAL27 4.3 38.4 1.0
O D:HOH2056 4.3 34.6 1.0
CB D:ASP96 4.5 44.3 1.0
CA D:ALA187 4.6 45.8 1.0
CD1 D:ILE334 4.6 38.9 1.0
OD2 D:ASP96 4.6 43.9 1.0
CD D:PRO30 4.6 39.9 1.0
N D:ALA187 4.7 45.2 1.0
CA D:ILE28 4.7 49.6 1.0
N D:SER97 4.8 44.1 1.0
CA D:LEU186 4.8 41.4 1.0
C D:VAL27 5.0 46.2 1.0

Reference:

A.Zarate-Romero, D.S.Murillo-Melo, C.Mujica-Jimenez, C.Montiel, R.A.Munoz-Clares. Reversible, Partial Inactivation of Plant Betaine Aldehyde Dehydrogenase By Betaine Aldehyde: Mechanism and Possible Physiological Implications. Biochem.J. V. 473 873 2016.
ISSN: ISSN 0264-6021
PubMed: 26792760
DOI: 10.1042/BJ20151084
Page generated: Mon Aug 12 12:51:07 2024

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