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Sodium in PDB 3inj: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1, PDB code: 3inj 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) 46.36 / 1.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.916, 176.839, 102.464, 90.00, 94.52, 90.00
R / Rfree (%) 17.9 / 20

Other elements in 3inj:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 (pdb code 3inj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1, PDB code: 3inj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3inj

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Sodium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:17.4
occ:1.00
 O A:GLN196 2.4 18.8 1.0
O A:ASP109 2.4 17.1 1.0
OD1 A:ASP109 2.4 19.0 1.0
O A:VAL40 2.4 19.4 1.0
O A:HOH4009 2.4 29.8 1.0
OG1 A:THR39 3.1 19.4 1.0
C A:ASP109 3.4 17.5 1.0
CG A:ASP109 3.4 18.2 1.0
C A:VAL40 3.5 19.8 1.0
C A:GLN196 3.6 18.2 1.0
N A:VAL40 3.7 21.0 1.0
O A:HOH2332 3.7 23.9 1.0
CA A:ASP109 3.8 16.1 1.0
CD A:PRO42 4.1 17.7 1.0
CA A:VAL40 4.2 20.8 1.0
CB A:ASP109 4.2 16.4 1.0
OD2 A:ASP109 4.2 19.3 1.0
CA A:GLN196 4.3 18.4 1.0
O A:HOH2194 4.3 22.6 1.0
CB A:THR39 4.4 20.7 1.0
C A:THR39 4.4 21.8 1.0
N A:THR197 4.6 18.6 1.0
N A:ASN41 4.6 19.3 1.0
CG2 A:THR197 4.6 17.7 1.0
N A:ASN110 4.6 16.5 1.0
CA A:THR39 4.7 20.4 1.0
CD1 A:ILE48 4.8 19.5 1.0
CA A:THR197 4.8 17.8 1.0
CB A:GLN196 4.8 18.2 1.0
CA A:ASN41 4.9 18.7 1.0
CB A:VAL40 5.0 21.9 1.0
O A:VAL345 5.0 16.7 1.0

Sodium binding site 2 out of 8 in 3inj

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Sodium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na601

b:21.5
occ:1.00
 O B:GLN196 2.4 21.3 1.0
OD1 B:ASP109 2.4 19.4 1.0
O B:ASP109 2.4 19.6 1.0
O B:VAL40 2.4 22.2 1.0
O B:HOH2258 2.6 25.1 1.0
OG1 B:THR39 3.0 20.7 1.0
CG B:ASP109 3.3 19.1 1.0
C B:ASP109 3.4 19.1 1.0
C B:VAL40 3.5 23.2 1.0
C B:GLN196 3.5 20.4 1.0
N B:VAL40 3.6 23.1 1.0
O B:HOH1913 3.7 23.2 1.0
CA B:ASP109 3.7 18.5 1.0
CB B:ASP109 4.0 18.9 1.0
CA B:VAL40 4.1 22.7 1.0
OD2 B:ASP109 4.2 20.2 1.0
CB B:THR39 4.3 21.5 1.0
CA B:GLN196 4.3 20.0 1.0
C B:THR39 4.3 22.2 1.0
CD B:PRO42 4.4 21.4 1.0
N B:THR197 4.5 19.6 1.0
CG2 B:THR197 4.6 17.9 1.0
N B:ASN110 4.6 17.8 1.0
N B:ASN41 4.6 22.2 1.0
CA B:THR39 4.7 22.0 1.0
CA B:THR197 4.7 18.4 1.0
CB B:GLN196 4.9 20.2 1.0
CA B:ASN41 5.0 22.3 1.0

Sodium binding site 3 out of 8 in 3inj

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Sodium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:21.4
occ:1.00
 O C:GLN196 2.4 20.4 1.0
O C:ASP109 2.4 19.2 1.0
OD1 C:ASP109 2.4 22.1 1.0
O C:VAL40 2.4 23.6 1.0
OG1 C:THR39 3.0 22.9 1.0
C C:ASP109 3.4 19.4 1.0
CG C:ASP109 3.4 21.1 1.0
C C:GLN196 3.5 21.3 1.0
C C:VAL40 3.5 24.3 1.0
N C:VAL40 3.6 23.6 1.0
O C:HOH3384 3.7 25.7 1.0
CA C:ASP109 3.7 19.9 1.0
CB C:ASP109 4.1 20.1 1.0
CA C:VAL40 4.2 23.7 1.0
CD C:PRO42 4.2 22.0 1.0
CA C:GLN196 4.3 22.6 1.0
OD2 C:ASP109 4.3 20.6 1.0
CB C:THR39 4.4 23.6 1.0
C C:THR39 4.4 24.7 1.0
CG C:PRO42 4.5 20.5 1.0
N C:THR197 4.5 21.2 1.0
N C:ASN110 4.6 19.4 1.0
CG2 C:THR197 4.6 19.7 1.0
N C:ASN41 4.6 24.3 1.0
CA C:THR197 4.7 20.3 1.0
CA C:THR39 4.7 23.5 1.0
CD1 C:ILE48 4.7 21.8 1.0
CB C:GLN196 4.9 22.5 1.0
CB C:VAL40 4.9 24.7 1.0
CA C:ASN41 5.0 23.8 1.0
O C:VAL345 5.0 20.2 1.0

Sodium binding site 4 out of 8 in 3inj

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Sodium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:17.8
occ:1.00
 O D:GLN196 2.3 15.6 1.0
OD1 D:ASP109 2.4 15.9 1.0
O D:VAL40 2.4 17.2 1.0
O D:HOH4002 2.4 29.8 1.0
O D:ASP109 2.4 15.8 1.0
OG1 D:THR39 3.0 18.3 1.0
O D:HOH1225 3.3 18.1 1.0
CG D:ASP109 3.4 16.1 1.0
C D:ASP109 3.4 15.9 1.0
C D:VAL40 3.5 16.7 1.0
C D:GLN196 3.5 16.0 1.0
N D:VAL40 3.7 17.1 1.0
CA D:ASP109 3.7 15.7 1.0
CB D:ASP109 4.1 15.4 1.0
CA D:VAL40 4.2 16.6 1.0
OD2 D:ASP109 4.3 16.0 1.0
CA D:GLN196 4.3 16.2 1.0
CB D:THR39 4.4 17.1 1.0
CD1 D:ILE48 4.5 16.4 1.0
C D:THR39 4.5 16.8 1.0
CD D:PRO42 4.5 16.2 1.0
N D:THR197 4.5 15.8 1.0
N D:ASN41 4.6 17.4 1.0
CG D:PRO42 4.6 16.2 1.0
N D:ASN110 4.6 15.0 1.0
CG2 D:THR197 4.7 14.7 1.0
CA D:THR197 4.7 15.9 1.0
CA D:THR39 4.8 16.9 1.0
CB D:VAL40 4.9 17.7 1.0
CB D:GLN196 4.9 16.0 1.0
CA D:ASN41 5.0 16.8 1.0
O D:VAL345 5.0 15.0 1.0

Sodium binding site 5 out of 8 in 3inj

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Sodium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na601

b:19.4
occ:1.00
 OD1 E:ASP109 2.4 21.3 1.0
O E:ASP109 2.4 19.0 1.0
O E:GLN196 2.4 21.4 1.0
O E:VAL40 2.4 22.3 1.0
O E:HOH1210 2.6 24.4 1.0
OG1 E:THR39 3.0 21.8 1.0
CG E:ASP109 3.3 20.5 1.0
O E:HOH818 3.3 23.9 1.0
C E:ASP109 3.4 18.8 1.0
C E:VAL40 3.5 22.1 1.0
C E:GLN196 3.6 21.3 1.0
N E:VAL40 3.6 23.6 1.0
CA E:ASP109 3.7 19.2 1.0
CB E:ASP109 4.0 19.1 1.0
OD2 E:ASP109 4.1 21.2 1.0
CA E:VAL40 4.1 23.1 1.0
CB E:THR39 4.3 22.9 1.0
C E:THR39 4.3 23.0 1.0
CA E:GLN196 4.4 20.8 1.0
CG2 E:THR197 4.5 19.3 1.0
N E:THR197 4.5 20.2 1.0
N E:ASN110 4.6 18.4 1.0
N E:ASN41 4.6 23.0 1.0
CA E:THR197 4.6 20.7 1.0
CD E:PRO42 4.6 21.8 1.0
CA E:THR39 4.7 22.6 1.0
CD1 E:ILE48 4.7 22.0 1.0
CG E:PRO42 4.8 21.3 1.0
CB E:VAL40 4.9 25.6 1.0
CA E:ASN41 4.9 21.8 1.0
CG2 E:THR39 4.9 22.2 1.0

Sodium binding site 6 out of 8 in 3inj

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Sodium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na601

b:22.0
occ:1.00
 O F:GLN196 2.4 23.6 1.0
O F:VAL40 2.4 25.3 1.0
O F:ASP109 2.4 22.5 1.0
OD1 F:ASP109 2.5 22.8 1.0
OG1 F:THR39 3.0 24.6 1.0
C F:ASP109 3.4 21.7 1.0
CG F:ASP109 3.4 22.8 1.0
C F:VAL40 3.5 24.9 1.0
C F:GLN196 3.5 23.2 1.0
N F:VAL40 3.7 23.4 1.0
CA F:ASP109 3.8 22.2 1.0
CB F:ASP109 4.1 21.6 1.0
CA F:VAL40 4.2 25.0 1.0
CA F:GLN196 4.3 23.2 1.0
CD F:PRO42 4.3 23.7 1.0
OD2 F:ASP109 4.3 22.0 1.0
CB F:THR39 4.4 25.0 1.0
C F:THR39 4.4 25.1 1.0
CG2 F:THR197 4.6 20.8 1.0
N F:THR197 4.6 22.0 1.0
N F:ASN41 4.6 24.8 1.0
N F:ASN110 4.6 21.8 1.0
CB F:GLN196 4.7 23.7 1.0
CA F:THR197 4.8 20.9 1.0
CA F:THR39 4.8 27.1 1.0
CD1 F:ILE48 4.8 23.6 1.0
CB F:VAL40 4.9 24.6 1.0
CA F:ASN41 4.9 25.5 1.0

Sodium binding site 7 out of 8 in 3inj

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Sodium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na601

b:22.0
occ:1.00
 O G:GLN196 2.4 20.1 1.0
OD1 G:ASP109 2.4 20.2 1.0
O G:ASP109 2.4 16.7 1.0
O G:VAL40 2.4 21.2 1.0
OG1 G:THR39 3.0 22.1 1.0
CG G:ASP109 3.3 19.8 1.0
C G:ASP109 3.4 17.3 1.0
C G:VAL40 3.5 22.4 1.0
C G:GLN196 3.6 21.0 1.0
N G:VAL40 3.6 22.9 1.0
CA G:ASP109 3.7 18.0 1.0
CB G:ASP109 4.1 19.5 1.0
CA G:VAL40 4.1 22.3 1.0
OD2 G:ASP109 4.2 18.5 1.0
CD G:PRO42 4.3 18.1 1.0
O G:HOH3091 4.3 22.3 1.0
CB G:THR39 4.4 22.3 1.0
CA G:GLN196 4.4 21.4 1.0
C G:THR39 4.4 22.2 1.0
N G:ASN41 4.5 21.3 1.0
N G:THR197 4.6 19.7 1.0
N G:ASN110 4.6 17.4 1.0
CG2 G:THR197 4.6 18.2 1.0
CA G:THR197 4.7 19.2 1.0
CA G:THR39 4.7 23.1 1.0
CB G:GLN196 4.9 20.0 1.0
CA G:ASN41 4.9 19.8 1.0
CD1 G:ILE48 4.9 20.4 1.0
CB G:VAL40 5.0 23.1 1.0
CG2 G:THR39 5.0 20.9 1.0

Sodium binding site 8 out of 8 in 3inj

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Sodium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Agonist Alda-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na601

b:15.8
occ:1.00
 O H:GLN196 2.4 17.2 1.0
O H:VAL40 2.4 17.5 1.0
OD1 H:ASP109 2.4 16.1 1.0
O H:ASP109 2.5 17.7 1.0
OG1 H:THR39 3.0 18.4 1.0
O H:HOH2189 3.3 19.6 1.0
CG H:ASP109 3.5 17.3 1.0
C H:ASP109 3.5 17.1 1.0
C H:VAL40 3.5 17.2 1.0
C H:GLN196 3.6 16.3 1.0
N H:VAL40 3.8 17.0 1.0
CA H:ASP109 3.9 16.7 1.0
CA H:VAL40 4.2 17.3 1.0
CB H:ASP109 4.2 16.4 1.0
CD H:PRO42 4.3 16.1 1.0
OD2 H:ASP109 4.4 15.8 1.0
CB H:THR39 4.4 18.2 1.0
CA H:GLN196 4.4 16.7 1.0
C H:THR39 4.5 17.1 1.0
O H:HOH1692 4.5 22.4 1.0
N H:THR197 4.5 16.1 1.0
CD1 H:ILE48 4.6 16.9 1.0
N H:ASN41 4.6 17.1 1.0
CG2 H:THR197 4.7 15.6 1.0
CA H:THR197 4.7 15.8 1.0
N H:ASN110 4.7 15.9 1.0
CA H:THR39 4.8 17.0 1.0
O H:VAL345 4.9 16.7 1.0
CB H:VAL40 4.9 17.7 1.0
CA H:ASN41 5.0 17.3 1.0
CB H:GLN196 5.0 16.9 1.0

Reference:

S.Perez-Miller, H.Younus, R.Vanam, C.H.Chen, D.Mochly-Rosen, T.D.Hurley. Alda-1 Is An Agonist and Chemical Chaperone For the Common Human Aldehyde Dehydrogenase 2 Variant. Nat.Struct.Mol.Biol. V. 17 159 2010.
ISSN: ISSN 1545-9993
PubMed: 20062057
DOI: 10.1038/NSMB.1737
Page generated: Mon Oct 7 10:59:24 2024

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