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Sodium in PDB 4kwg: Crystal Structure Analysis of ALDH2+ALDIB13

Enzymatic activity of Crystal Structure Analysis of ALDH2+ALDIB13

All present enzymatic activity of Crystal Structure Analysis of ALDH2+ALDIB13:
1.2.1.3;

Protein crystallography data

The structure of Crystal Structure Analysis of ALDH2+ALDIB13, PDB code: 4kwg was solved by T.D.Hurley, A.C.Kimble-Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.39 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.506, 176.193, 101.546, 90.00, 94.92, 90.00
R / Rfree (%) 19.3 / 22.9

Other elements in 4kwg:

The structure of Crystal Structure Analysis of ALDH2+ALDIB13 also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of ALDH2+ALDIB13 (pdb code 4kwg). 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 Analysis of ALDH2+ALDIB13, PDB code: 4kwg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4kwg

Go back to Sodium Binding Sites List in 4kwg
Sodium binding site 1 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:39.0
occ:1.00
 O A:GLN196 2.3 22.8 1.0
O A:VAL40 2.5 23.6 1.0
O A:ASP109 2.6 22.4 1.0
OD1 A:ASP109 2.7 23.8 1.0
OG1 A:THR39 3.5 23.0 1.0
C A:GLN196 3.5 23.3 1.0
C A:VAL40 3.6 23.9 1.0
C A:ASP109 3.7 22.5 1.0
N A:VAL40 3.7 24.0 1.0
CG A:ASP109 3.8 23.3 1.0
CA A:GLN196 4.1 23.5 1.0
CA A:ASP109 4.2 22.5 1.0
CA A:VAL40 4.2 24.2 1.0
CD A:PRO42 4.3 24.4 1.0
O A:VAL345 4.5 20.7 1.0
CB A:GLN196 4.5 24.2 1.0
CB A:ASP109 4.6 22.9 1.0
CG2 A:THR197 4.6 23.4 1.0
N A:THR197 4.6 23.2 1.0
OD2 A:ASP109 4.6 23.0 1.0
C A:THR39 4.6 23.7 1.0
N A:ASN41 4.7 23.2 1.0
CB A:THR39 4.8 23.0 1.0
CB A:VAL40 4.8 24.3 1.0
N A:ASN110 4.8 22.0 1.0
CA A:THR197 4.9 22.9 1.0
CG2 A:VAL345 4.9 20.1 1.0
CG A:PRO42 4.9 24.4 1.0
CA A:THR39 5.0 23.5 1.0

Sodium binding site 2 out of 8 in 4kwg

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Sodium binding site 2 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:44.3
occ:1.00
 O B:HOH812 2.9 42.2 1.0
O B:GLN13 3.1 33.2 1.0
NE2 B:GLN14 3.4 35.9 1.0
CE1 B:PHE335 3.7 26.9 1.0
CD1 B:PHE335 3.8 27.1 1.0
CD B:GLN14 3.9 35.4 1.0
OE1 B:GLN14 4.1 35.0 1.0
OD1 B:ASN41 4.2 26.9 1.0
C B:GLN13 4.2 33.2 1.0
CD1 B:LEU108 4.4 24.9 1.0
CB B:GLN13 4.5 34.6 1.0
CG B:GLN14 4.8 34.6 1.0
CA B:GLN13 4.9 33.7 1.0
CZ B:PHE335 4.9 26.6 1.0
NE2 B:GLN13 5.0 35.7 1.0

Sodium binding site 3 out of 8 in 4kwg

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Sodium binding site 3 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:58.8
occ:1.00
 O C:VAL345 2.9 22.7 1.0
O C:VAL40 2.9 26.5 1.0
O C:ASP109 3.0 23.1 1.0
O C:GLN196 3.0 24.2 1.0
C C:VAL40 3.9 26.1 1.0
CD C:PRO42 3.9 25.2 1.0
C C:GLN196 4.0 24.3 1.0
CB C:GLN196 4.0 24.6 1.0
C C:VAL345 4.1 23.4 1.0
CG2 C:VAL345 4.1 23.5 1.0
CG C:PRO42 4.1 25.2 1.0
CA C:GLN196 4.2 24.1 1.0
C C:ASP109 4.2 22.4 1.0
N C:VAL40 4.3 25.8 1.0
OD1 C:ASP109 4.3 24.7 1.0
CB C:PRO42 4.3 25.4 1.0
CB C:VAL40 4.4 26.2 1.0
CA C:VAL40 4.4 26.1 1.0
N C:PRO42 4.5 25.3 1.0
OG1 C:THR39 4.7 25.9 1.0
CG C:GLN196 4.7 25.2 1.0
CA C:VAL345 4.8 23.2 1.0
CA C:PRO42 4.9 25.4 1.0
CG2 C:THR197 5.0 25.4 1.0

Sodium binding site 4 out of 8 in 4kwg

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Sodium binding site 4 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:40.5
occ:1.00
 O D:GLN196 2.3 20.2 1.0
O D:VAL40 2.5 18.6 1.0
O D:ASP109 2.5 18.1 1.0
OD1 D:ASP109 3.3 19.6 1.0
C D:GLN196 3.4 20.0 1.0
C D:VAL40 3.6 18.7 1.0
OG1 D:THR39 3.6 20.4 1.0
C D:ASP109 3.6 18.1 1.0
N D:VAL40 3.9 19.1 1.0
CD D:PRO42 4.0 17.4 1.0
CA D:GLN196 4.0 19.8 1.0
CG D:ASP109 4.1 19.6 1.0
CA D:ASP109 4.2 18.4 1.0
CA D:VAL40 4.2 19.0 1.0
O D:VAL345 4.3 17.1 1.0
CB D:GLN196 4.3 20.1 1.0
N D:THR197 4.6 19.8 1.0
CG2 D:THR197 4.6 19.8 1.0
CB D:VAL40 4.7 19.2 1.0
CB D:ASP109 4.7 18.9 1.0
CG D:PRO42 4.7 17.5 1.0
N D:ASN41 4.7 18.5 1.0
N D:ASN110 4.8 18.2 1.0
OD2 D:ASP109 4.8 20.7 1.0
C D:THR39 4.8 19.3 1.0
CA D:THR197 4.9 19.8 1.0
N D:PRO42 4.9 17.5 1.0
CG2 D:VAL345 4.9 17.9 1.0
CB D:THR39 5.0 19.9 1.0

Sodium binding site 5 out of 8 in 4kwg

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Sodium binding site 5 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:33.1
occ:1.00
 O E:GLN196 2.3 21.6 1.0
O E:VAL40 2.5 24.6 1.0
O E:ASP109 2.5 20.4 1.0
OD1 E:ASP109 2.8 21.1 1.0
O E:HOH784 3.1 31.6 1.0
OG1 E:THR39 3.4 23.8 1.0
C E:GLN196 3.5 22.6 1.0
C E:ASP109 3.5 20.1 1.0
C E:VAL40 3.6 24.6 1.0
CG E:ASP109 3.7 21.1 1.0
N E:VAL40 3.8 25.3 1.0
CA E:ASP109 4.0 20.3 1.0
CA E:VAL40 4.2 25.4 1.0
CA E:GLN196 4.3 23.2 1.0
CD E:PRO42 4.3 22.8 1.0
CB E:ASP109 4.4 20.5 1.0
OD2 E:ASP109 4.5 21.3 1.0
CG2 E:THR197 4.5 21.4 1.0
C E:THR39 4.6 25.1 1.0
N E:THR197 4.6 22.0 1.0
O E:VAL345 4.6 20.5 1.0
CB E:THR39 4.7 24.7 1.0
N E:ASN41 4.7 24.1 1.0
CB E:GLN196 4.7 24.0 1.0
N E:ASN110 4.7 19.8 1.0
CB E:VAL40 4.8 25.5 1.0
CA E:THR197 4.8 21.5 1.0
CA E:THR39 4.9 24.8 1.0

Sodium binding site 6 out of 8 in 4kwg

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Sodium binding site 6 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:59.9
occ:1.00
 O F:VAL40 2.9 26.2 1.0
O F:GLN196 3.1 23.0 1.0
O F:VAL345 3.2 24.3 1.0
O F:ASP109 3.5 21.7 1.0
C F:VAL40 3.9 26.1 1.0
C F:GLN196 3.9 23.3 1.0
CB F:GLN196 4.0 24.0 1.0
CA F:GLN196 4.0 23.7 1.0
N F:VAL40 4.1 26.7 1.0
CD F:PRO42 4.2 24.9 1.0
CB F:VAL40 4.3 27.4 1.0
CA F:VAL40 4.4 27.1 1.0
CG2 F:VAL345 4.4 23.9 1.0
C F:VAL345 4.4 24.5 1.0
CG F:GLN196 4.4 24.0 1.0
CG F:PRO42 4.6 24.8 1.0
OD1 F:ASP109 4.6 23.3 1.0
OG1 F:THR39 4.6 27.1 1.0
C F:ASP109 4.7 22.3 1.0
CB F:PRO42 4.7 24.6 1.0
N F:PRO42 4.8 24.8 1.0
CB F:ASP346 4.9 25.8 1.0

Sodium binding site 7 out of 8 in 4kwg

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Sodium binding site 7 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:35.5
occ:1.00
 O G:GLN196 2.2 23.7 1.0
O G:VAL40 2.4 22.6 1.0
OD1 G:ASP109 2.6 23.1 1.0
O G:ASP109 2.6 22.0 1.0
OG1 G:THR39 2.9 24.0 1.0
C G:GLN196 3.4 23.6 1.0
C G:VAL40 3.5 23.8 1.0
N G:VAL40 3.5 24.3 1.0
CG G:ASP109 3.5 23.3 1.0
C G:ASP109 3.6 22.2 1.0
CA G:ASP109 3.9 22.4 1.0
CA G:VAL40 4.0 24.1 1.0
C G:THR39 4.2 24.5 1.0
CA G:GLN196 4.2 23.8 1.0
CB G:THR39 4.2 24.4 1.0
CB G:ASP109 4.3 22.8 1.0
OD2 G:ASP109 4.3 24.4 1.0
CD G:PRO42 4.3 24.0 1.0
N G:THR197 4.5 23.2 1.0
CA G:THR39 4.5 24.7 1.0
CG2 G:THR197 4.6 23.0 1.0
N G:ASN41 4.6 23.4 1.0
CA G:THR197 4.6 22.9 1.0
CB G:GLN196 4.8 24.5 1.0
N G:ASN110 4.8 21.9 1.0
CB G:VAL40 4.8 24.2 1.0
CD1 G:ILE48 4.8 28.3 1.0
O G:THR39 4.9 25.2 1.0

Sodium binding site 8 out of 8 in 4kwg

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Sodium binding site 8 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB13


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure Analysis of ALDH2+ALDIB13 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na602

b:29.3
occ:1.00
 O H:GLN196 2.3 20.2 1.0
O H:VAL40 2.6 20.2 1.0
O H:ASP109 2.6 18.3 1.0
OD1 H:ASP109 2.7 19.8 1.0
O H:HOH791 3.0 30.6 1.0
OG1 H:THR39 3.3 19.9 1.0
C H:GLN196 3.5 19.4 1.0
C H:ASP109 3.6 18.3 1.0
CG H:ASP109 3.6 19.2 1.0
C H:VAL40 3.7 19.9 1.0
N H:VAL40 3.8 20.4 1.0
CA H:ASP109 3.9 18.3 1.0
CA H:GLN196 4.2 19.3 1.0
CA H:VAL40 4.3 20.4 1.0
CB H:ASP109 4.3 18.7 1.0
CD H:PRO42 4.4 17.9 1.0
OD2 H:ASP109 4.5 19.1 1.0
CB H:THR39 4.5 19.8 1.0
N H:THR197 4.5 19.0 1.0
C H:THR39 4.6 20.0 1.0
CG2 H:THR197 4.6 18.3 1.0
CB H:GLN196 4.7 19.2 1.0
N H:ASN41 4.7 19.4 1.0
CA H:THR197 4.8 18.4 1.0
N H:ASN110 4.8 18.1 1.0
CD1 H:ILE48 4.8 21.0 1.0
O H:VAL345 4.8 17.5 1.0
CA H:THR39 4.9 19.9 1.0
CB H:VAL40 5.0 20.5 1.0

Reference:

A.C.Kimble-Hill, B.Parajuli, C.H.Chen, D.Mochly-Rosen, T.D.Hurley. Development of Selective Inhibitors For Aldehyde Dehydrogenases Based on Substituted Indole-2,3-Diones. J.Med.Chem. V. 57 714 2014.
ISSN: ISSN 0022-2623
PubMed: 24444054
DOI: 10.1021/JM401377V
Page generated: Mon Oct 7 16:37:36 2024

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