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Sodium in PDB 3sz9: Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One

Enzymatic activity of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One

All present enzymatic activity of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One:
1.2.1.3;

Protein crystallography data

The structure of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One, PDB code: 3sz9 was solved by S.Perez-Miller, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 140.522, 151.052, 177.021, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One (pdb code 3sz9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One, PDB code: 3sz9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3sz9

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Sodium binding site 1 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:34.4
occ:1.00
 O A:GLN196 2.2 34.9 1.0
OD1 A:ASP109 2.4 39.0 1.0
O A:VAL40 2.5 41.1 1.0
O A:ASP109 2.6 31.5 1.0
OG1 A:THR39 3.0 44.9 1.0
C A:GLN196 3.4 35.4 1.0
CG A:ASP109 3.4 34.0 1.0
C A:ASP109 3.5 31.4 1.0
C A:VAL40 3.6 40.2 1.0
N A:VAL40 3.7 41.5 1.0
CA A:ASP109 3.8 30.7 1.0
CA A:GLN196 4.0 35.8 1.0
CB A:ASP109 4.2 30.7 1.0
OD2 A:ASP109 4.2 30.0 1.0
CD A:PRO42 4.2 40.0 1.0
CA A:VAL40 4.2 40.4 1.0
CB A:THR39 4.4 42.8 1.0
N A:THR197 4.4 34.1 1.0
CB A:GLN196 4.5 37.1 1.0
C A:THR39 4.5 41.9 1.0
CA A:THR197 4.7 33.1 1.0
N A:ASN41 4.7 39.2 1.0
CG2 A:THR197 4.7 28.1 1.0
N A:ASN110 4.8 30.5 1.0
O A:VAL345 4.8 37.9 1.0
CA A:THR39 4.8 42.5 1.0
CB A:VAL40 4.9 40.4 1.0
CD1 A:ILE48 4.9 33.4 1.0

Sodium binding site 2 out of 8 in 3sz9

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Sodium binding site 2 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:29.6
occ:1.00
 O B:GLN196 2.3 24.2 1.0
O B:HOH2061 2.3 32.1 1.0
OD1 B:ASP109 2.3 25.9 1.0
O B:ASP109 2.4 19.6 1.0
O B:VAL40 2.4 23.1 1.0
OG1 B:THR39 3.0 27.1 1.0
CG B:ASP109 3.4 21.8 1.0
C B:ASP109 3.5 20.6 1.0
C B:GLN196 3.5 25.2 1.0
C B:VAL40 3.6 25.0 1.0
N B:VAL40 3.6 25.7 1.0
CA B:ASP109 3.9 20.8 1.0
OD2 B:ASP109 4.2 27.2 1.0
CB B:ASP109 4.2 20.6 1.0
CA B:VAL40 4.2 24.6 1.0
CA B:GLN196 4.2 25.1 1.0
CB B:THR39 4.4 26.6 1.0
C B:THR39 4.5 25.6 1.0
CD B:PRO42 4.5 23.6 1.0
N B:THR197 4.5 24.0 1.0
CD1 B:ILE48 4.6 25.3 1.0
N B:ASN110 4.7 20.0 1.0
CB B:GLN196 4.7 25.0 1.0
N B:ASN41 4.7 22.6 1.0
CG2 B:THR197 4.7 21.1 1.0
CA B:THR197 4.8 23.8 1.0
CB B:VAL40 4.8 26.6 1.0
CA B:THR39 4.8 26.3 1.0
O B:VAL345 5.0 21.9 1.0

Sodium binding site 3 out of 8 in 3sz9

Go back to Sodium Binding Sites List in 3sz9
Sodium binding site 3 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:22.3
occ:1.00
 O C:HOH1793 2.2 40.3 1.0
O C:GLN196 2.3 17.9 1.0
O C:VAL40 2.4 19.6 1.0
OD1 C:ASP109 2.5 21.7 1.0
O C:ASP109 2.7 16.6 1.0
OG1 C:THR39 2.9 19.9 1.0
O C:HOH783 2.9 26.8 1.0
C C:VAL40 3.5 21.4 1.0
CG C:ASP109 3.5 21.5 1.0
C C:GLN196 3.5 18.9 1.0
N C:VAL40 3.6 21.0 1.0
C C:ASP109 3.7 18.1 1.0
CA C:ASP109 4.0 18.8 1.0
CA C:VAL40 4.1 21.8 1.0
CA C:GLN196 4.2 19.7 1.0
CB C:THR39 4.2 17.9 1.0
OD2 C:ASP109 4.3 21.4 1.0
CB C:ASP109 4.3 17.8 1.0
CD C:PRO42 4.3 20.2 1.0
C C:THR39 4.4 18.4 1.0
N C:THR197 4.5 17.7 1.0
N C:ASN41 4.5 19.7 1.0
CA C:THR197 4.7 18.0 1.0
CB C:GLN196 4.7 20.1 1.0
CA C:THR39 4.7 18.4 1.0
CD1 C:ILE48 4.8 21.2 1.0
CB C:VAL40 4.8 22.2 1.0
CG2 C:THR197 4.8 13.8 1.0
N C:ASN110 4.9 16.9 1.0
CA C:ASN41 4.9 19.0 1.0
CG2 C:THR39 4.9 17.5 1.0
O C:VAL345 5.0 14.0 1.0

Sodium binding site 4 out of 8 in 3sz9

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Sodium binding site 4 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:36.9
occ:1.00
 O D:ASP109 2.2 33.9 1.0
OD1 D:ASP109 2.4 32.9 1.0
O D:GLN196 2.4 37.9 1.0
O D:VAL40 2.8 35.2 1.0
OG1 D:THR39 3.0 35.4 1.0
C D:ASP109 3.3 33.8 1.0
CG D:ASP109 3.3 32.4 1.0
C D:GLN196 3.6 39.6 1.0
CA D:ASP109 3.8 34.3 1.0
N D:VAL40 3.8 36.1 1.0
C D:VAL40 3.8 35.5 1.0
OD2 D:ASP109 4.1 37.0 1.0
CB D:ASP109 4.1 34.3 1.0
CB D:THR39 4.4 38.8 1.0
CA D:VAL40 4.4 35.5 1.0
CD D:PRO42 4.4 36.1 1.0
N D:ASN110 4.4 33.6 1.0
CA D:GLN196 4.4 39.2 1.0
C D:THR39 4.5 37.8 1.0
N D:THR197 4.5 39.5 1.0
CG2 D:THR197 4.6 39.8 1.0
CA D:THR197 4.6 39.1 1.0
CA D:ASN110 4.8 32.4 1.0
CA D:THR39 4.9 38.3 1.0
N D:ASN41 4.9 34.4 1.0
O D:VAL345 4.9 35.6 1.0
CB D:GLN196 4.9 39.9 1.0
CD1 D:ILE48 5.0 43.8 1.0

Sodium binding site 5 out of 8 in 3sz9

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Sodium binding site 5 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:33.6
occ:1.00
 O E:GLN196 2.3 25.9 1.0
OD1 E:ASP109 2.4 20.9 1.0
O E:VAL40 2.5 29.6 1.0
O E:HOH2549 2.5 35.0 1.0
O E:ASP109 2.5 20.3 1.0
OG1 E:THR39 2.9 31.6 1.0
O E:HOH1090 3.2 33.8 1.0
CG E:ASP109 3.4 24.3 1.0
C E:GLN196 3.5 26.1 1.0
C E:ASP109 3.5 20.9 1.0
C E:VAL40 3.6 29.5 1.0
N E:VAL40 3.6 29.4 1.0
CA E:ASP109 3.9 20.4 1.0
OD2 E:ASP109 4.1 26.0 1.0
CB E:ASP109 4.2 22.0 1.0
CA E:VAL40 4.2 29.1 1.0
CB E:THR39 4.2 30.7 1.0
CA E:GLN196 4.3 25.7 1.0
C E:THR39 4.4 29.5 1.0
CD E:PRO42 4.4 28.5 1.0
N E:THR197 4.5 24.3 1.0
CG2 E:THR197 4.6 25.0 1.0
CA E:THR197 4.6 25.6 1.0
N E:ASN41 4.6 29.0 1.0
CA E:THR39 4.7 29.7 1.0
N E:ASN110 4.7 19.6 1.0
CB E:GLN196 4.8 26.6 1.0
CD1 E:ILE48 4.9 31.1 1.0
CB E:VAL40 4.9 29.4 1.0
CG2 E:THR39 5.0 30.6 1.0

Sodium binding site 6 out of 8 in 3sz9

Go back to Sodium Binding Sites List in 3sz9
Sodium binding site 6 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:23.3
occ:1.00
 O F:HOH591 2.3 24.8 1.0
O F:GLN196 2.4 13.3 1.0
O F:VAL40 2.4 19.9 1.0
OD1 F:ASP109 2.4 22.1 1.0
O F:ASP109 2.6 17.2 1.0
OG1 F:THR39 3.0 21.6 1.0
CG F:ASP109 3.4 21.6 1.0
O F:HOH1490 3.4 33.7 1.0
C F:ASP109 3.5 17.6 1.0
C F:VAL40 3.5 20.2 1.0
C F:GLN196 3.6 16.6 1.0
N F:VAL40 3.7 18.9 1.0
CA F:ASP109 3.7 16.6 1.0
CB F:ASP109 4.1 16.5 1.0
CA F:VAL40 4.2 19.6 1.0
OD2 F:ASP109 4.3 18.4 1.0
CD F:PRO42 4.3 16.5 1.0
CB F:THR39 4.4 17.3 1.0
CA F:GLN196 4.4 16.6 1.0
C F:THR39 4.4 17.3 1.0
CD1 F:ILE48 4.5 19.5 1.0
N F:THR197 4.6 14.2 1.0
N F:ASN41 4.6 19.5 1.0
CA F:THR197 4.7 15.6 1.0
CG2 F:THR197 4.7 17.3 1.0
N F:ASN110 4.7 17.8 1.0
CA F:THR39 4.8 16.5 1.0
CB F:VAL40 4.9 19.3 1.0
CB F:GLN196 4.9 17.5 1.0
CA F:ASN41 5.0 18.6 1.0

Sodium binding site 7 out of 8 in 3sz9

Go back to Sodium Binding Sites List in 3sz9
Sodium binding site 7 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:26.4
occ:1.00
 O G:GLN196 2.3 21.6 1.0
O G:HOH1885 2.3 33.9 1.0
OD1 G:ASP109 2.4 19.5 1.0
O G:VAL40 2.5 20.9 1.0
O G:ASP109 2.5 20.1 1.0
O G:HOH528 2.8 27.9 1.0
OG1 G:THR39 3.0 25.7 1.0
CG G:ASP109 3.4 21.6 1.0
C G:ASP109 3.5 18.1 1.0
C G:GLN196 3.5 21.8 1.0
N G:VAL40 3.5 23.2 1.0
C G:VAL40 3.5 21.0 1.0
CA G:ASP109 3.8 17.9 1.0
CA G:VAL40 4.1 22.5 1.0
CB G:ASP109 4.2 18.5 1.0
OD2 G:ASP109 4.2 23.6 1.0
CA G:GLN196 4.2 22.1 1.0
CB G:THR39 4.3 23.5 1.0
C G:THR39 4.3 23.3 1.0
CD G:PRO42 4.4 20.4 1.0
N G:THR197 4.5 22.1 1.0
N G:ASN41 4.7 18.3 1.0
CD1 G:ILE48 4.7 21.0 1.0
N G:ASN110 4.7 18.9 1.0
CA G:THR39 4.7 22.9 1.0
CA G:THR197 4.7 22.4 1.0
CG2 G:THR197 4.7 21.7 1.0
CB G:VAL40 4.7 22.7 1.0
CB G:GLN196 4.8 21.8 1.0
O G:VAL345 5.0 19.4 1.0

Sodium binding site 8 out of 8 in 3sz9

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Sodium binding site 8 out of 8 in the Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human ALDH2 Modified with the Beta-Elimination Product of Aldi-3; 1-(4-Ethylbenzene)Prop-2-En-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:32.0
occ:1.00
 O H:GLN196 2.4 28.4 1.0
O H:ASP109 2.4 31.2 1.0
OD1 H:ASP109 2.5 34.4 1.0
O H:VAL40 2.6 36.7 1.0
OG1 H:THR39 3.0 36.0 1.0
C H:ASP109 3.4 29.8 1.0
CG H:ASP109 3.4 33.5 1.0
C H:VAL40 3.5 35.8 1.0
C H:GLN196 3.6 28.9 1.0
CA H:ASP109 3.8 30.2 1.0
N H:VAL40 3.8 34.4 1.0
CB H:ASP109 4.1 30.4 1.0
CD H:PRO42 4.2 34.7 1.0
CA H:VAL40 4.2 35.7 1.0
OD2 H:ASP109 4.3 35.8 1.0
CA H:GLN196 4.3 28.4 1.0
N H:ASN41 4.4 35.5 1.0
CB H:THR39 4.4 35.2 1.0
CG2 H:THR197 4.5 26.4 1.0
C H:THR39 4.6 34.9 1.0
N H:THR197 4.6 27.2 1.0
N H:ASN110 4.6 28.2 1.0
CB H:GLN196 4.7 28.0 1.0
CA H:THR197 4.7 28.2 1.0
CD1 H:ILE48 4.7 31.8 1.0
CA H:ASN41 4.9 34.9 1.0
CA H:THR39 4.9 35.7 1.0
O H:VAL345 5.0 27.9 1.0
CB H:VAL40 5.0 36.3 1.0

Reference:

M.Khanna, C.H.Chen, A.Kimble-Hill, B.Parajuli, S.Perez-Miller, S.Baskaran, J.Kim, K.Dria, V.Vasiliou, D.Mochly-Rosen, T.D.Hurley. Discovery of A Novel Class of Covalent Inhibitor For Aldehyde Dehydrogenases. J.Biol.Chem. V. 286 43486 2011.
ISSN: ISSN 0021-9258
PubMed: 22021038
DOI: 10.1074/JBC.M111.293597
Page generated: Mon Oct 7 13:02:33 2024

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