Atomistry » Sodium » PDB 3icf-3ivu » 3inj
Atomistry »
  Sodium »
    PDB 3icf-3ivu »
      3inj »

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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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

Go back to Sodium Binding Sites List in 3inj
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: Tue Dec 15 06:15:07 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy