Atomistry » Sodium » PDB 4khu-4kxx » 4kwf
Atomistry »
  Sodium »
    PDB 4khu-4kxx »
      4kwf »

Sodium in PDB 4kwf: Crystal Structure Analysis of ALDH2+ALDIB33

Enzymatic activity of Crystal Structure Analysis of ALDH2+ALDIB33

All present enzymatic activity of Crystal Structure Analysis of ALDH2+ALDIB33:
1.2.1.3;

Protein crystallography data

The structure of Crystal Structure Analysis of ALDH2+ALDIB33, PDB code: 4kwf 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) 49.12 / 2.31
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.293, 177.092, 102.551, 90.00, 94.39, 90.00
R / Rfree (%) 23.9 / 29.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure Analysis of ALDH2+ALDIB33 (pdb code 4kwf). 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+ALDIB33, PDB code: 4kwf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 1 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:91.1
occ:1.00
 O A:VAL345 3.0 43.7 1.0
O A:VAL40 3.3 58.0 1.0
O A:GLN196 3.6 53.9 1.0
O A:ASP109 4.0 46.6 1.0
C A:VAL345 4.0 43.7 1.0
C A:VAL40 4.1 54.7 1.0
CB A:ASP346 4.2 47.8 1.0
C A:GLN196 4.3 54.2 1.0
CD A:PRO42 4.3 52.6 1.0
CA A:GLN196 4.4 54.5 1.0
N A:VAL40 4.4 57.4 1.0
CA A:ASP346 4.4 48.8 1.0
CB A:VAL40 4.4 58.7 1.0
CB A:GLN196 4.4 54.5 1.0
OD1 A:ASP109 4.4 59.0 1.0
CA A:VAL40 4.5 57.5 1.0
CG2 A:VAL345 4.6 42.3 1.0
N A:ASP346 4.6 44.1 1.0
CG A:PRO42 4.8 52.7 1.0
CG A:GLN196 4.9 54.1 1.0
N A:PRO42 5.0 54.4 1.0

Sodium binding site 2 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 2 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:93.8
occ:1.00
 ND2 B:ASN41 3.4 69.7 1.0
OD1 B:ASN41 3.6 68.2 1.0
CG B:ASN41 3.9 71.4 1.0
CB B:SER43 4.0 73.3 1.0
CE1 B:PHE335 4.0 83.6 1.0
CD1 B:PHE335 4.0 82.1 1.0
CG B:PRO334 4.1 73.1 1.0
NE2 B:GLN14 4.2 89.0 1.0
OG B:SER43 4.3 73.8 1.0
CD B:PRO334 4.5 73.2 1.0
OD1 B:ASN333 4.6 64.7 1.0
CD1 B:LEU108 4.6 73.9 1.0
CG2 B:THR44 4.8 75.0 1.0
O B:GLN13 4.9 82.2 1.0

Sodium binding site 3 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 3 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:88.0
occ:1.00
 O C:VAL40 2.5 64.0 1.0
O C:GLN196 2.7 62.1 1.0
O C:ASP109 2.9 54.5 1.0
OD1 C:ASP109 3.3 59.8 1.0
C C:VAL40 3.6 62.4 1.0
O C:VAL345 3.7 61.5 1.0
C C:GLN196 3.7 62.2 1.0
CB C:GLN196 4.1 58.8 1.0
CA C:GLN196 4.1 58.1 1.0
C C:ASP109 4.1 55.5 1.0
N C:VAL40 4.1 66.3 1.0
CD C:PRO42 4.2 58.3 1.0
CA C:VAL40 4.3 64.2 1.0
OG1 C:THR39 4.3 61.7 1.0
CG C:ASP109 4.4 56.9 1.0
CG2 C:VAL345 4.5 61.6 1.0
CB C:VAL40 4.6 64.3 1.0
N C:ASN41 4.7 62.9 1.0
CG C:PRO42 4.8 58.3 1.0
N C:PRO42 4.8 60.1 1.0
CG2 C:THR197 4.8 73.4 1.0
C C:VAL345 4.8 57.5 1.0
CA C:ASP109 4.8 54.4 1.0
N C:THR197 4.9 61.5 1.0
CA C:ASN41 5.0 57.6 1.0

Sodium binding site 4 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 4 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:64.0
occ:1.00
 O D:ASP109 2.4 46.8 1.0
O D:GLN196 2.5 46.5 1.0
O D:VAL40 2.7 47.5 1.0
C D:ASP109 3.5 43.1 1.0
C D:GLN196 3.6 43.3 1.0
OD1 D:ASP109 3.6 47.5 1.0
C D:VAL40 3.8 45.7 1.0
OG1 D:THR39 4.0 39.3 1.0
CD D:PRO42 4.0 38.9 1.0
O D:VAL345 4.1 34.5 1.0
N D:VAL40 4.1 46.3 1.0
CA D:GLN196 4.1 41.2 1.0
CA D:ASP109 4.2 42.3 1.0
CB D:GLN196 4.4 41.6 1.0
CG D:ASP109 4.4 46.5 1.0
CA D:VAL40 4.5 45.6 1.0
CG2 D:THR197 4.6 36.6 1.0
N D:ASN110 4.6 42.5 1.0
CG D:PRO42 4.7 37.8 1.0
N D:THR197 4.7 39.5 1.0
CG2 D:VAL345 4.8 39.6 1.0
CB D:VAL40 4.8 46.3 1.0
N D:ASN41 4.9 46.8 1.0
CB D:ASP109 4.9 43.8 1.0
CA D:ASN110 4.9 42.8 1.0
N D:PRO42 5.0 40.0 1.0

Sodium binding site 5 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 5 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na602

b:73.6
occ:1.00
 O E:HOH701 2.4 50.1 1.0
O E:VAL40 3.0 56.5 1.0
O E:GLN196 3.0 56.0 1.0
O E:ASP109 3.1 46.6 1.0
O E:VAL345 3.2 45.0 1.0
C E:GLN196 3.8 53.1 1.0
C E:VAL40 3.9 52.6 1.0
CA E:GLN196 4.0 52.7 1.0
N E:VAL40 4.0 54.0 1.0
CB E:GLN196 4.1 50.6 1.0
OD1 E:ASP109 4.2 50.9 1.0
CB E:VAL40 4.2 54.3 1.0
CA E:VAL40 4.3 54.7 1.0
C E:ASP109 4.3 46.6 1.0
CG2 E:VAL345 4.3 43.8 1.0
CD E:PRO42 4.4 46.3 1.0
C E:VAL345 4.4 44.1 1.0
O E:HOH720 4.4 49.8 1.0
OG1 E:THR39 4.5 51.5 1.0
CG E:GLN196 4.5 50.5 1.0
CG E:PRO42 4.8 44.9 1.0
N E:PRO42 4.9 49.3 1.0
CB E:PRO42 4.9 46.3 1.0
CG1 E:VAL40 5.0 56.2 1.0

Sodium binding site 6 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 6 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:84.5
occ:1.00
 O F:VAL345 2.7 79.1 1.0
O F:ASP109 2.7 78.4 1.0
O F:VAL40 2.9 74.7 1.0
O F:GLN196 2.9 56.8 1.0
OD1 F:ASP109 3.8 75.8 1.0
C F:GLN196 3.9 59.3 1.0
C F:VAL345 3.9 78.8 1.0
CB F:PRO42 3.9 77.3 1.0
C F:ASP109 3.9 75.6 1.0
CG F:PRO42 3.9 78.5 1.0
CD F:PRO42 4.0 77.3 1.0
CB F:GLN196 4.0 58.6 1.0
C F:VAL40 4.0 75.2 1.0
CG2 F:VAL345 4.1 76.7 1.0
CA F:GLN196 4.2 56.5 1.0
N F:PRO42 4.4 75.2 1.0
CA F:PRO42 4.6 75.5 1.0
CA F:VAL345 4.6 76.8 1.0
CA F:ASP109 4.7 75.3 1.0
CB F:VAL40 4.8 77.5 1.0
CG F:ASP109 4.8 75.0 1.0
CA F:VAL40 4.8 75.4 1.0
CG2 F:THR197 4.8 66.0 1.0
CB F:ASP346 4.8 81.1 1.0
N F:VAL40 4.8 75.5 1.0
N F:ASP346 4.8 79.8 1.0
N F:ASN110 4.9 72.2 1.0
CA F:ASN110 4.9 69.7 1.0
C F:ASN41 5.0 75.6 1.0
CA F:ASP346 5.0 81.4 1.0
CB F:VAL345 5.0 75.8 1.0
N F:THR197 5.0 63.3 1.0

Sodium binding site 7 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 7 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:83.4
occ:1.00
 OD1 G:ASP109 2.7 60.4 1.0
O G:GLN196 2.7 55.3 1.0
O G:VAL40 2.8 62.6 1.0
O G:ASP109 2.9 55.2 1.0
OG1 G:THR39 3.5 62.9 1.0
C G:GLN196 3.7 59.2 1.0
N G:VAL40 3.7 58.3 1.0
C G:VAL40 3.8 60.5 1.0
CA G:GLN196 3.9 56.7 1.0
CG G:ASP109 3.9 58.3 1.0
C G:ASP109 4.0 55.9 1.0
CB G:GLN196 4.1 61.4 1.0
O G:VAL345 4.2 61.5 1.0
CA G:VAL40 4.2 60.0 1.0
CD G:PRO42 4.4 66.3 1.0
C G:THR39 4.5 60.7 1.0
CA G:ASP109 4.5 55.2 1.0
CB G:THR39 4.7 67.0 1.0
CB G:VAL40 4.7 61.2 1.0
OD2 G:ASP109 4.8 60.0 1.0
CB G:ASP109 4.8 56.4 1.0
CA G:THR39 4.8 63.6 1.0
CG G:GLN196 4.9 61.9 1.0
N G:THR197 4.9 59.7 1.0

Sodium binding site 8 out of 8 in 4kwf

Go back to Sodium Binding Sites List in 4kwf
Sodium binding site 8 out of 8 in the Crystal Structure Analysis of ALDH2+ALDIB33


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+ALDIB33 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na602

b:65.4
occ:1.00
 O H:GLN196 2.4 44.8 1.0
O H:VAL40 2.4 44.0 1.0
O H:ASP109 2.5 43.9 1.0
OD1 H:ASP109 3.0 53.8 1.0
C H:GLN196 3.5 41.7 1.0
OG1 H:THR39 3.5 45.3 1.0
C H:VAL40 3.6 42.4 1.0
C H:ASP109 3.6 42.1 1.0
O H:HOH706 3.8 56.4 1.0
N H:VAL40 3.8 42.6 1.0
CG H:ASP109 3.9 50.3 1.0
CA H:GLN196 4.0 39.5 1.0
CA H:ASP109 4.1 43.0 1.0
CD H:PRO42 4.2 39.4 1.0
CA H:VAL40 4.2 44.0 1.0
O H:VAL345 4.5 37.1 1.0
CB H:ASP109 4.5 45.9 1.0
CB H:GLN196 4.5 40.6 1.0
N H:ASN41 4.6 42.9 1.0
N H:THR197 4.6 41.0 1.0
N H:ASN110 4.7 40.6 1.0
C H:THR39 4.7 40.6 1.0
CB H:VAL40 4.7 42.9 1.0
CB H:THR39 4.8 42.1 1.0
OD2 H:ASP109 4.8 47.8 1.0
CG H:PRO42 4.9 39.5 1.0
CG2 H:THR197 4.9 42.3 1.0
CA H:ASN41 4.9 40.2 1.0
N H:PRO42 4.9 41.0 1.0
CA H:THR197 5.0 40.0 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: Sun Aug 17 20:19:17 2025

Last articles

Na in 6CSE
Na in 6CSF
Na in 6CRH
Na in 6CRB
Na in 6CRC
Na in 6CS8
Na in 6CR9
Na in 6CR8
Na in 6CR7
Na in 6CQP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy