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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 16:37:02 2024

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