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Sodium in PDB 5l13: Structure of ALDH2 in Complex with 2P3

Enzymatic activity of Structure of ALDH2 in Complex with 2P3

All present enzymatic activity of Structure of ALDH2 in Complex with 2P3:
1.2.1.3;

Protein crystallography data

The structure of Structure of ALDH2 in Complex with 2P3, PDB code: 5l13 was solved by C.D.Buchman, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.412, 127.049, 294.847, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of ALDH2 in Complex with 2P3 (pdb code 5l13). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of ALDH2 in Complex with 2P3, PDB code: 5l13:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5l13

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Sodium binding site 1 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:32.4
occ:1.00
 O A:VAL40 2.3 23.1 1.0
O A:ASP109 2.4 22.1 1.0
O A:HOH707 2.4 27.5 1.0
O A:GLN196 2.5 25.4 1.0
OD1 A:ASP109 2.5 27.0 1.0
O A:HOH871 3.1 29.3 1.0
OG1 A:THR39 3.4 30.4 1.0
C A:ASP109 3.4 22.8 1.0
C A:VAL40 3.5 23.1 1.0
CG A:ASP109 3.5 26.9 1.0
C A:GLN196 3.6 24.8 1.0
N A:VAL40 3.8 24.2 1.0
CA A:ASP109 3.8 23.8 1.0
CA A:VAL40 4.2 23.6 1.0
CB A:ASP109 4.2 24.3 1.0
CD A:PRO42 4.3 21.2 1.0
CA A:GLN196 4.3 26.3 1.0
OD2 A:ASP109 4.4 27.6 1.0
N A:ASN41 4.6 22.6 1.0
N A:ASN110 4.6 22.1 1.0
C A:THR39 4.6 24.9 1.0
N A:THR197 4.7 23.0 1.0
CG2 A:THR197 4.7 21.0 1.0
CB A:GLN196 4.7 27.8 1.0
CB A:THR39 4.7 28.1 1.0
O A:VAL345 4.7 22.3 1.0
CB A:VAL40 4.8 25.5 1.0
CA A:THR197 4.9 23.0 1.0
CA A:ASN41 4.9 21.6 1.0
CA A:THR39 5.0 26.6 1.0

Sodium binding site 2 out of 8 in 5l13

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Sodium binding site 2 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:32.6
occ:1.00
 O B:ASP109 2.3 28.9 1.0
O B:GLN196 2.3 33.9 1.0
O B:VAL40 2.4 29.7 1.0
OD1 B:ASP109 2.7 35.4 1.0
C B:ASP109 3.4 27.8 1.0
OG1 B:THR39 3.4 29.4 1.0
O B:HOH905 3.5 31.4 1.0
C B:VAL40 3.5 29.9 1.0
C B:GLN196 3.5 30.8 1.0
CG B:ASP109 3.6 32.7 1.0
N B:VAL40 3.8 29.1 1.0
CA B:ASP109 3.8 29.1 1.0
CD B:PRO42 4.2 25.8 1.0
CA B:VAL40 4.2 30.0 1.0
CB B:ASP109 4.2 29.8 1.0
CA B:GLN196 4.3 29.4 1.0
OD2 B:ASP109 4.5 31.5 1.0
N B:ASN110 4.5 26.8 1.0
CG2 B:THR197 4.5 31.9 1.0
N B:THR197 4.6 29.6 1.0
N B:ASN41 4.6 29.0 1.0
C B:THR39 4.6 28.6 1.0
CB B:THR39 4.7 27.4 1.0
CB B:GLN196 4.7 29.6 1.0
CA B:THR197 4.7 29.2 1.0
O B:VAL345 4.8 24.3 1.0
CB B:VAL40 4.9 32.2 1.0
CA B:ASN41 4.9 28.0 1.0
CD1 B:ILE48 4.9 32.1 1.0
CA B:ASN110 5.0 25.9 1.0
CG B:PRO42 5.0 25.3 1.0
N B:PRO42 5.0 25.9 1.0

Sodium binding site 3 out of 8 in 5l13

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Sodium binding site 3 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:31.2
occ:1.00
 O C:GLN196 2.3 28.8 1.0
O C:VAL40 2.4 26.4 1.0
O C:ASP109 2.5 27.2 1.0
O C:HOH880 2.5 28.2 1.0
OD1 C:ASP109 2.7 32.0 1.0
C C:GLN196 3.4 29.7 1.0
OG1 C:THR39 3.4 33.9 1.0
C C:ASP109 3.6 27.9 1.0
C C:VAL40 3.6 28.4 1.0
CG C:ASP109 3.7 32.4 1.0
N C:VAL40 3.8 29.1 1.0
CA C:GLN196 4.0 30.5 1.0
CA C:ASP109 4.0 29.2 1.0
CA C:VAL40 4.2 28.5 1.0
CD C:PRO42 4.3 26.7 1.0
CB C:GLN196 4.4 32.0 1.0
CB C:ASP109 4.5 31.1 1.0
N C:THR197 4.5 28.9 1.0
OD2 C:ASP109 4.6 31.1 1.0
C C:THR39 4.7 29.4 1.0
N C:ASN41 4.7 27.3 1.0
O C:VAL345 4.7 23.3 1.0
CB C:THR39 4.7 30.1 1.0
N C:ASN110 4.7 28.0 1.0
CG2 C:THR197 4.8 27.8 1.0
CA C:THR197 4.8 27.5 1.0
CB C:VAL40 4.8 29.4 1.0
N C:PRO42 4.9 27.1 1.0
CG C:PRO42 4.9 26.6 1.0
CA C:ASN41 5.0 26.1 1.0
CA C:THR39 5.0 29.2 1.0

Sodium binding site 4 out of 8 in 5l13

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Sodium binding site 4 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:26.3
occ:1.00
 O D:GLN196 2.1 25.5 1.0
O D:HOH795 2.3 25.0 1.0
O D:VAL40 2.4 26.2 1.0
OD1 D:ASP109 2.4 29.1 1.0
O D:HOH832 2.5 27.4 1.0
O D:ASP109 2.6 25.9 1.0
OG1 D:THR39 2.9 29.5 1.0
C D:GLN196 3.3 25.6 1.0
C D:VAL40 3.5 25.3 1.0
CG D:ASP109 3.5 28.6 1.0
N D:VAL40 3.7 24.1 1.0
C D:ASP109 3.7 25.1 1.0
CA D:GLN196 3.9 27.7 1.0
CA D:ASP109 4.0 25.3 1.0
CA D:VAL40 4.1 25.3 1.0
CB D:THR39 4.3 27.1 1.0
OD2 D:ASP109 4.3 28.8 1.0
CB D:ASP109 4.3 26.3 1.0
N D:THR197 4.4 22.7 1.0
C D:THR39 4.5 25.2 1.0
CB D:GLN196 4.5 29.5 1.0
CD D:PRO42 4.6 23.1 1.0
N D:ASN41 4.6 25.3 1.0
CA D:THR39 4.7 26.1 1.0
CA D:THR197 4.7 21.7 1.0
CG2 D:THR197 4.7 22.6 1.0
CB D:VAL40 4.7 26.4 1.0
N D:ASN110 4.9 23.0 1.0
CD1 D:ILE48 5.0 27.0 1.0

Sodium binding site 5 out of 8 in 5l13

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Sodium binding site 5 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:21.9
occ:1.00
 O E:HOH718 2.2 32.2 1.0
O E:VAL40 2.3 28.6 1.0
O E:ASP109 2.5 26.4 1.0
O E:GLN196 2.5 23.2 1.0
OD1 E:ASP109 2.6 33.3 1.0
O E:HOH847 2.7 32.7 1.0
OG1 E:THR39 3.4 30.2 1.0
C E:VAL40 3.4 28.1 1.0
C E:ASP109 3.5 28.9 1.0
CG E:ASP109 3.5 33.7 1.0
C E:GLN196 3.7 24.4 1.0
N E:VAL40 3.7 29.2 1.0
CA E:ASP109 3.9 29.0 1.0
CA E:VAL40 4.1 28.6 1.0
CD E:PRO42 4.2 24.9 1.0
CB E:ASP109 4.3 31.0 1.0
OD2 E:ASP109 4.3 36.1 1.0
CA E:GLN196 4.3 24.8 1.0
N E:ASN41 4.5 27.2 1.0
C E:THR39 4.5 28.6 1.0
CB E:THR39 4.7 28.8 1.0
CB E:VAL40 4.7 30.2 1.0
N E:ASN110 4.7 29.2 1.0
N E:THR197 4.7 24.7 1.0
O E:VAL345 4.7 27.1 1.0
CB E:GLN196 4.7 25.8 1.0
CG2 E:THR197 4.8 26.6 1.0
CA E:ASN41 4.9 25.3 1.0
CD1 E:ILE48 4.9 27.7 1.0
CA E:THR39 4.9 28.6 1.0
CA E:THR197 4.9 25.8 1.0
N E:PRO42 4.9 25.3 1.0

Sodium binding site 6 out of 8 in 5l13

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Sodium binding site 6 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:31.8
occ:1.00
 O F:GLN196 2.3 29.9 1.0
O F:VAL40 2.4 22.3 1.0
OD1 F:ASP109 2.7 29.4 1.0
O F:ASP109 2.7 30.7 1.0
OG1 F:THR39 2.9 32.8 1.0
C F:VAL40 3.4 25.2 1.0
C F:GLN196 3.5 30.5 1.0
N F:VAL40 3.5 26.0 1.0
CG F:ASP109 3.6 28.9 1.0
C F:ASP109 3.7 28.0 1.0
CA F:VAL40 4.0 26.2 1.0
CA F:ASP109 4.1 27.7 1.0
CA F:GLN196 4.2 30.5 1.0
CB F:THR39 4.3 31.0 1.0
C F:THR39 4.3 27.0 1.0
OD2 F:ASP109 4.4 28.1 1.0
CB F:ASP109 4.4 27.2 1.0
CD F:PRO42 4.5 23.6 1.0
N F:THR197 4.5 29.9 1.0
N F:ASN41 4.6 26.8 1.0
CA F:THR39 4.6 28.6 1.0
CB F:GLN196 4.7 29.5 1.0
CB F:VAL40 4.7 26.4 1.0
CD1 F:ILE48 4.8 35.0 1.0
CA F:THR197 4.8 30.0 1.0
CG2 F:THR197 4.9 33.4 1.0
O F:VAL345 4.9 26.9 1.0
N F:ASN110 4.9 27.5 1.0
CA F:ASN41 5.0 27.3 1.0

Sodium binding site 7 out of 8 in 5l13

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Sodium binding site 7 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:33.0
occ:1.00
 O G:VAL40 2.3 32.7 1.0
O G:GLN196 2.4 26.2 1.0
O G:ASP109 2.6 24.8 1.0
OD1 G:ASP109 2.7 34.3 1.0
OG1 G:THR39 3.3 35.2 1.0
C G:VAL40 3.4 31.4 1.0
C G:GLN196 3.5 25.2 1.0
N G:VAL40 3.6 31.8 1.0
C G:ASP109 3.7 25.5 1.0
CG G:ASP109 3.7 31.9 1.0
CA G:VAL40 4.0 31.8 1.0
CA G:ASP109 4.1 26.2 1.0
CA G:GLN196 4.1 26.5 1.0
CD G:PRO42 4.3 26.4 1.0
C G:THR39 4.5 33.0 1.0
CB G:ASP109 4.5 28.8 1.0
N G:ASN41 4.5 29.6 1.0
CB G:GLN196 4.5 26.1 1.0
CB G:VAL40 4.6 33.8 1.0
N G:THR197 4.6 24.9 1.0
CB G:THR39 4.6 34.5 1.0
OD2 G:ASP109 4.6 33.8 1.0
O G:VAL345 4.7 23.4 1.0
CG2 G:THR197 4.8 26.0 1.0
N G:ASN110 4.8 24.1 1.0
CA G:THR39 4.9 34.2 1.0
CA G:THR197 4.9 25.9 1.0
CA G:ASN41 4.9 27.8 1.0
CD1 G:ILE48 5.0 28.7 1.0
N G:PRO42 5.0 27.2 1.0

Sodium binding site 8 out of 8 in 5l13

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Sodium binding site 8 out of 8 in the Structure of ALDH2 in Complex with 2P3


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of ALDH2 in Complex with 2P3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:28.6
occ:1.00
 O H:VAL40 2.3 20.9 1.0
O H:HOH728 2.4 24.5 1.0
O H:GLN196 2.4 22.7 1.0
O H:ASP109 2.5 24.9 1.0
OD1 H:ASP109 2.7 27.4 1.0
C H:VAL40 3.4 21.6 1.0
OG1 H:THR39 3.5 26.4 1.0
C H:ASP109 3.5 24.9 1.0
C H:GLN196 3.5 23.9 1.0
CG H:ASP109 3.6 29.0 1.0
N H:VAL40 3.7 21.7 1.0
CA H:ASP109 3.9 26.1 1.0
CA H:VAL40 4.1 21.7 1.0
CD H:PRO42 4.2 20.6 1.0
CA H:GLN196 4.2 24.7 1.0
CB H:ASP109 4.3 26.9 1.0
OD2 H:ASP109 4.4 29.9 1.0
N H:ASN41 4.5 22.3 1.0
C H:THR39 4.6 22.3 1.0
N H:THR197 4.6 23.8 1.0
CB H:VAL40 4.7 22.4 1.0
CB H:GLN196 4.7 24.8 1.0
N H:ASN110 4.7 23.3 1.0
CB H:THR39 4.7 23.6 1.0
CA H:THR197 4.8 25.2 1.0
CA H:ASN41 4.9 21.8 1.0
CG2 H:THR197 4.9 25.6 1.0
N H:PRO42 4.9 21.1 1.0
O H:VAL345 4.9 19.3 1.0
CG H:PRO42 4.9 20.1 1.0
CD1 H:ILE48 5.0 24.1 1.0
CA H:THR39 5.0 22.8 1.0

Reference:

C.D.Buchman, T.D.Hurley. Inhibition of the Aldehyde Dehydrogenase 1/2 Family By Psoralen and Coumarin Derivatives. J. Med. Chem. V. 60 2439 2017.
ISSN: ISSN 1520-4804
PubMed: 28219011
DOI: 10.1021/ACS.JMEDCHEM.6B01825
Page generated: Mon Oct 7 22:15:24 2024

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