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Sodium in PDB 2j6l: Structure of Aminoadipate-Semialdehyde Dehydrogenase

Enzymatic activity of Structure of Aminoadipate-Semialdehyde Dehydrogenase

All present enzymatic activity of Structure of Aminoadipate-Semialdehyde Dehydrogenase:
1.2.1.3;

Protein crystallography data

The structure of Structure of Aminoadipate-Semialdehyde Dehydrogenase, PDB code: 2j6l was solved by G.Bunkoczi, K.Guo, J.E.Debreczeni, C.Smee, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, F.Von Delft, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.3
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 155.289, 162.326, 159.016, 90.00, 94.17, 90.00
R / Rfree (%) 13.7 / 18.9

Other elements in 2j6l:

The structure of Structure of Aminoadipate-Semialdehyde Dehydrogenase also contains other interesting chemical elements:

Bromine (Br) 15 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Aminoadipate-Semialdehyde Dehydrogenase (pdb code 2j6l). 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 Aminoadipate-Semialdehyde Dehydrogenase, PDB code: 2j6l:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2j6l

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Sodium binding site 1 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1504

b:34.1
occ:1.00
 O A:HOH2498 2.1 24.5 1.0
O A:ARG377 2.1 17.2 1.0
O A:HOH2502 2.3 32.5 1.0
O A:GLY379 2.3 18.9 1.0
O A:HOH2505 2.4 25.2 1.0
O A:HOH2466 3.0 23.2 1.0
C A:ARG377 3.4 17.2 1.0
C A:GLY379 3.5 16.6 1.0
O A:MET375 3.7 18.2 1.0
C A:PRO378 3.8 14.4 1.0
N A:GLY379 3.8 16.4 1.0
N A:ARG377 4.1 20.5 1.0
O A:PRO378 4.1 17.3 1.0
O A:HOH2507 4.1 35.1 1.0
CA A:PRO378 4.2 16.2 1.0
O A:HOH2465 4.2 44.1 1.0
N A:PRO378 4.2 17.3 1.0
CA A:GLY379 4.3 16.4 1.0
N A:TYR381 4.3 13.4 1.0
CA A:ARG377 4.3 20.2 1.0
N A:ASN380 4.5 13.1 1.0
CG A:ARG377 4.6 16.6 1.0
CA A:ASN380 4.7 13.0 1.0
C A:MET375 4.8 17.9 1.0
O A:TYR381 4.9 11.3 1.0

Sodium binding site 2 out of 8 in 2j6l

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Sodium binding site 2 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1505

b:18.5
occ:1.00
 O B:HOH2478 2.2 19.4 1.0
O B:ARG377 2.3 15.1 1.0
O B:HOH2492 2.3 29.2 1.0
O B:GLY379 2.3 12.8 1.0
O B:HOH2477 2.5 28.0 1.0
O B:HOH2493 2.6 28.8 1.0
C B:ARG377 3.5 16.0 1.0
C B:GLY379 3.5 13.0 1.0
N B:GLY379 3.7 13.8 1.0
C B:PRO378 3.8 14.5 1.0
O B:MET375 4.0 17.1 1.0
CA B:PRO378 4.1 16.6 1.0
O B:HOH2108 4.1 31.1 1.0
CA B:GLY379 4.2 12.3 1.0
N B:PRO378 4.3 16.4 1.0
O B:PRO378 4.3 15.6 1.0
O B:HOH2494 4.3 22.9 1.0
N B:ARG377 4.4 17.3 1.0
N B:TYR381 4.4 10.1 1.0
CG1 B:VAL374 4.5 16.9 0.5
O B:HOH2038 4.5 56.7 1.0
CA B:ARG377 4.5 15.7 1.0
N B:ASN380 4.6 10.9 1.0
O B:HOH2248 4.7 35.1 1.0
CA B:ASN380 4.8 11.1 1.0
O B:HOH2483 4.8 36.9 1.0
O B:TYR381 4.9 11.7 1.0
CG B:ARG377 5.0 16.7 1.0

Sodium binding site 3 out of 8 in 2j6l

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Sodium binding site 3 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1503

b:42.6
occ:1.00
 O C:HOH2448 2.4 36.8 1.0
O C:HOH2441 2.4 47.5 1.0
O C:HOH2445 2.4 25.7 1.0
O C:ARG377 2.4 20.7 1.0
O C:GLY379 2.5 18.4 1.0
C C:ARG377 3.6 21.0 1.0
C C:GLY379 3.6 14.8 1.0
NZ C:LYS348 3.8 36.1 1.0
N C:GLY379 4.0 16.0 1.0
O C:MET375 4.0 24.3 1.0
C C:PRO378 4.0 17.5 1.0
CA C:PRO378 4.3 19.9 1.0
N C:ARG377 4.3 22.8 1.0
N C:PRO378 4.4 22.6 1.0
CA C:GLY379 4.4 14.2 1.0
O C:PRO378 4.4 18.1 1.0
CA C:ARG377 4.6 22.1 1.0
N C:ASN380 4.6 15.1 1.0
N C:TYR381 4.7 19.2 1.0
CG1 C:VAL374 4.8 31.8 1.0
CA C:ASN380 4.9 14.9 1.0
O C:HOH2112 4.9 23.5 1.0
CG C:ARG377 5.0 27.9 1.0

Sodium binding site 4 out of 8 in 2j6l

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Sodium binding site 4 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1503

b:42.8
occ:1.00
 O D:HOH2498 2.1 31.0 1.0
O D:HOH2500 2.1 34.5 1.0
O D:GLY379 2.3 23.4 1.0
O D:HOH2499 2.3 41.5 1.0
O D:ARG377 2.4 28.4 1.0
O D:HOH2502 2.6 30.7 1.0
C D:GLY379 3.5 21.8 1.0
C D:ARG377 3.6 28.2 1.0
N D:GLY379 3.8 24.0 1.0
O D:HOH2118 3.9 36.4 1.0
C D:PRO378 3.9 25.3 1.0
O D:MET375 3.9 27.0 1.0
CA D:PRO378 4.1 26.4 1.0
CA D:GLY379 4.2 23.0 1.0
O D:HOH2503 4.3 25.5 1.0
O D:PRO378 4.3 25.3 1.0
N D:PRO378 4.4 27.6 1.0
N D:TYR381 4.4 20.1 1.0
N D:ARG377 4.4 29.6 1.0
O D:HOH2272 4.5 31.7 1.0
N D:ASN380 4.5 21.5 1.0
CG1 D:VAL374 4.6 31.6 1.0
CA D:ARG377 4.6 28.8 1.0
CA D:ASN380 4.7 19.3 1.0
CG D:ARG377 4.9 28.7 1.0
O D:TYR381 4.9 20.1 1.0

Sodium binding site 5 out of 8 in 2j6l

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Sodium binding site 5 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1505

b:23.1
occ:1.00
 O E:HOH2490 2.1 21.3 1.0
O E:GLY379 2.3 14.9 1.0
O E:ARG377 2.3 15.7 1.0
O E:HOH2491 2.4 28.1 1.0
O E:HOH2500 2.5 27.2 1.0
O E:HOH2501 3.0 32.8 1.0
C E:GLY379 3.5 13.2 1.0
C E:ARG377 3.5 15.8 1.0
N E:GLY379 3.8 15.0 1.0
C E:PRO378 3.8 13.3 1.0
O E:MET375 3.9 18.4 1.0
O E:HOH2502 4.0 26.6 1.0
CA E:PRO378 4.2 15.2 1.0
CA E:GLY379 4.2 13.3 1.0
O E:PRO378 4.3 17.0 1.0
N E:ARG377 4.3 21.7 1.0
N E:PRO378 4.3 16.3 1.0
N E:TYR381 4.4 9.0 1.0
N E:ASN380 4.5 10.6 1.0
O E:HOH2459 4.5 29.7 1.0
O E:HOH2235 4.5 48.8 1.0
O E:HOH2493 4.5 37.5 1.0
CA E:ARG377 4.6 20.3 1.0
CA E:ASN380 4.7 9.6 1.0
CG1 E:VAL374 4.9 20.7 1.0
CG E:ARG377 4.9 20.2 1.0
O E:TYR381 5.0 10.6 1.0

Sodium binding site 6 out of 8 in 2j6l

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Sodium binding site 6 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1503

b:21.0
occ:1.00
 O F:ARG377 2.2 16.2 1.0
O F:HOH2490 2.2 19.8 1.0
O F:HOH2499 2.4 31.4 1.0
O F:GLY379 2.4 14.3 1.0
O F:HOH2491 2.5 27.6 1.0
O F:HOH2498 2.9 31.9 1.0
C F:ARG377 3.4 16.1 1.0
C F:GLY379 3.5 13.8 1.0
N F:GLY379 3.7 14.0 1.0
C F:PRO378 3.7 15.6 1.0
O F:MET375 3.9 17.2 1.0
CA F:PRO378 4.1 15.2 1.0
N F:PRO378 4.2 14.9 1.0
O F:PRO378 4.2 15.2 1.0
CA F:GLY379 4.2 13.8 1.0
N F:ARG377 4.3 17.9 1.0
O F:HOH2501 4.3 22.9 1.0
CA F:ARG377 4.4 15.8 1.0
N F:TYR381 4.6 11.8 1.0
N F:ASN380 4.6 12.9 1.0
CG1 F:VAL374 4.7 23.6 1.0
CG F:ARG377 4.8 15.7 1.0
O F:HOH2116 4.8 22.9 1.0
CA F:ASN380 4.9 14.2 1.0

Sodium binding site 7 out of 8 in 2j6l

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Sodium binding site 7 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1503

b:23.2
occ:1.00
 O G:HOH2522 2.1 25.9 1.0
O G:ARG377 2.2 17.3 1.0
O G:HOH2517 2.2 22.9 1.0
O G:GLY379 2.4 16.1 1.0
O G:HOH2516 2.5 28.8 1.0
O G:HOH2525 2.7 27.9 1.0
C G:ARG377 3.4 15.8 1.0
C G:GLY379 3.5 13.6 1.0
N G:GLY379 3.7 14.0 1.0
C G:PRO378 3.7 14.0 1.0
O G:MET375 4.0 17.3 1.0
CA G:PRO378 4.1 15.8 1.0
O G:PRO378 4.2 14.9 1.0
CA G:GLY379 4.2 13.9 1.0
N G:PRO378 4.2 15.8 1.0
N G:ARG377 4.3 16.7 1.0
O G:HOH2526 4.4 24.6 1.0
N G:TYR381 4.5 12.5 1.0
CA G:ARG377 4.5 15.7 1.0
N G:ASN380 4.6 11.6 1.0
CG1 G:VAL374 4.7 19.7 1.0
CA G:ASN380 4.8 13.2 1.0
CG G:ARG377 4.8 15.8 1.0
O G:HOH2122 4.9 29.9 1.0

Sodium binding site 8 out of 8 in 2j6l

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Sodium binding site 8 out of 8 in the Structure of Aminoadipate-Semialdehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Aminoadipate-Semialdehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1503

b:48.3
occ:1.00
 O H:ARG377 2.3 22.2 1.0
O H:GLY379 2.4 19.7 1.0
O H:HOH2498 2.5 22.8 1.0
O H:HOH2504 2.5 42.8 1.0
O H:HOH2505 2.9 29.6 1.0
C H:ARG377 3.5 21.8 1.0
C H:GLY379 3.6 16.3 1.0
N H:GLY379 3.7 18.4 1.0
C H:PRO378 3.8 17.9 1.0
O H:HOH2108 3.9 37.7 1.0
CA H:PRO378 4.0 20.0 1.0
O H:MET375 4.1 20.2 1.0
O H:HOH2506 4.2 25.4 1.0
N H:PRO378 4.3 20.1 1.0
O H:PRO378 4.3 21.0 1.0
CA H:GLY379 4.3 16.4 1.0
N H:ARG377 4.4 24.3 1.0
CA H:ARG377 4.6 22.1 1.0
O H:HOH2106 4.6 35.7 1.0
N H:ASN380 4.6 16.2 1.0
O H:HOH2273 4.7 39.2 1.0
N H:TYR381 4.7 15.8 1.0
CA H:ASN380 4.9 15.6 1.0

Reference:

C.Brocker, N.Lassen, T.Estey, A.Pappa, M.Cantore, V.V.Orlova, T.Chavakis, K.L.Kavanagh, U.Oppermann, V.Vasiliou. Aldehyde Dehydrogenase 7A1 (ALDH7A1) Is A Novel Enzyme Involved in Cellular Defense Against Hyperosmotic Stress. J.Biol.Chem. V. 285 18452 2010.
ISSN: ISSN 0021-9258
PubMed: 20207735
DOI: 10.1074/JBC.M109.077925
Page generated: Mon Oct 7 02:58:29 2024

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