Atomistry » Sodium » PDB 1nnh-1oan » 1o01
Atomistry »
  Sodium »
    PDB 1nnh-1oan »
      1o01 »

Sodium in PDB 1o01: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+, PDB code: 1o01 was solved by S.J.Perez-Miller, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.133, 150.571, 176.782, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Other elements in 1o01:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+ (pdb code 1o01). 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 Crotonaldehyde, Nad(H) and MG2+, PDB code: 1o01:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na4701

b:31.4
occ:1.00
 OD1 A:ASP109 2.3 20.3 1.0
O A:GLN196 2.4 20.1 1.0
O A:VAL40 2.5 21.4 1.0
O A:ASP109 2.6 17.3 1.0
O A:HOH5531 2.8 33.7 1.0
OG1 A:THR39 2.9 23.9 1.0
CG A:ASP109 3.2 20.1 1.0
O A:HOH5532 3.3 28.0 1.0
C A:VAL40 3.5 21.0 1.0
C A:ASP109 3.6 17.4 1.0
C A:GLN196 3.6 19.8 1.0
N A:VAL40 3.6 21.7 1.0
CA A:ASP109 3.8 17.8 1.0
OD2 A:ASP109 4.0 21.3 1.0
CA A:VAL40 4.1 20.7 1.0
CB A:ASP109 4.1 19.0 1.0
C A:THR39 4.2 22.2 1.0
CB A:THR39 4.2 24.4 1.0
CA A:GLN196 4.4 19.8 1.0
CD A:PRO42 4.4 23.3 1.0
CA A:THR39 4.5 23.2 1.0
N A:THR197 4.5 18.6 1.0
CG2 A:THR197 4.6 17.7 1.0
CA A:THR197 4.6 19.8 1.0
N A:ASN41 4.7 21.3 1.0
CD1 A:ILE48 4.7 24.9 1.0
N A:ASN110 4.8 17.7 1.0
CB A:VAL40 4.9 19.8 1.0
CB A:GLN196 4.9 20.9 1.0
CG2 A:THR39 4.9 25.4 1.0

Sodium binding site 2 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4702

b:18.3
occ:1.00
 OD1 B:ASP109 2.2 17.6 1.0
O B:GLN196 2.4 14.4 1.0
O B:VAL40 2.5 16.4 1.0
O B:ASP109 2.6 15.6 1.0
O B:HOH5982 2.8 26.9 1.0
OG1 B:THR39 2.9 16.6 1.0
CG B:ASP109 3.2 17.1 1.0
O B:HOH5981 3.3 16.2 1.0
C B:ASP109 3.5 15.4 1.0
C B:VAL40 3.6 16.4 1.0
C B:GLN196 3.6 15.1 1.0
N B:VAL40 3.6 16.9 1.0
CA B:ASP109 3.8 15.0 1.0
OD2 B:ASP109 4.0 17.6 1.0
CB B:ASP109 4.1 15.6 1.0
CA B:VAL40 4.1 15.9 1.0
CB B:THR39 4.2 17.9 1.0
C B:THR39 4.2 17.9 1.0
CA B:THR39 4.5 17.7 1.0
CA B:GLN196 4.5 14.7 1.0
CG2 B:THR197 4.5 13.7 1.0
N B:THR197 4.5 14.5 1.0
CD1 B:ILE48 4.6 18.0 1.0
CD B:PRO42 4.6 17.6 1.0
CA B:THR197 4.6 14.2 1.0
N B:ASN41 4.7 16.2 1.0
N B:ASN110 4.7 15.7 1.0
CG2 B:THR39 4.9 15.3 1.0
O B:THR39 5.0 18.2 1.0
CB B:VAL40 5.0 14.3 1.0

Sodium binding site 3 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na4703

b:19.0
occ:1.00
 O C:GLN196 2.3 16.1 1.0
O C:VAL40 2.5 17.1 1.0
OD1 C:ASP109 2.5 14.1 1.0
O C:HOH5665 2.5 29.6 1.0
O C:ASP109 2.6 14.8 1.0
O C:HOH5666 2.9 23.5 1.0
OG1 C:THR39 3.0 15.3 1.0
CG C:ASP109 3.5 13.2 1.0
C C:ASP109 3.5 14.0 1.0
C C:GLN196 3.5 16.1 1.0
C C:VAL40 3.6 16.6 1.0
N C:VAL40 3.7 15.4 1.0
CA C:ASP109 3.9 13.7 1.0
CA C:VAL40 4.2 15.0 1.0
CB C:ASP109 4.2 13.5 1.0
CB C:THR39 4.3 15.0 1.0
OD2 C:ASP109 4.3 12.9 1.0
CA C:GLN196 4.4 16.9 1.0
C C:THR39 4.4 15.0 1.0
CD C:PRO42 4.4 13.7 1.0
N C:THR197 4.5 15.6 1.0
CG2 C:THR197 4.5 16.3 1.0
CA C:THR197 4.6 14.8 1.0
CA C:THR39 4.6 15.0 1.0
O C:HOH5669 4.7 27.2 1.0
N C:ASN41 4.7 15.9 1.0
N C:ASN110 4.8 14.7 1.0
CD1 C:ILE48 4.8 12.9 1.0
CB C:GLN196 4.8 15.4 1.0
CB C:VAL40 4.9 15.0 1.0
CG2 C:THR39 5.0 16.5 1.0

Sodium binding site 4 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na4704

b:24.1
occ:1.00
 O D:VAL40 2.3 19.4 1.0
OD1 D:ASP109 2.5 15.7 1.0
O D:ASP109 2.5 11.4 1.0
O D:GLN196 2.5 16.4 1.0
O D:HOH5704 2.6 24.7 1.0
O D:HOH5703 3.1 28.0 1.0
OG1 D:THR39 3.2 17.6 1.0
C D:VAL40 3.4 18.7 1.0
C D:ASP109 3.5 14.2 1.0
CG D:ASP109 3.5 15.6 1.0
N D:VAL40 3.6 17.4 1.0
C D:GLN196 3.8 14.5 1.0
CA D:ASP109 3.8 13.2 1.0
CA D:VAL40 4.0 17.8 1.0
CB D:ASP109 4.2 14.4 1.0
CD D:PRO42 4.2 17.5 1.0
C D:THR39 4.3 16.0 1.0
OD2 D:ASP109 4.3 17.9 1.0
CB D:THR39 4.5 16.4 1.0
N D:ASN41 4.5 17.7 1.0
CA D:GLN196 4.6 15.7 1.0
CD1 D:ILE48 4.6 15.1 1.0
CG2 D:THR197 4.7 11.8 1.0
N D:ASN110 4.7 13.6 1.0
CA D:THR39 4.7 17.0 1.0
N D:THR197 4.7 12.5 1.0
CB D:VAL40 4.8 18.2 1.0
CA D:THR197 4.8 12.4 1.0
CA D:ASN41 4.9 17.6 1.0
O D:VAL345 5.0 18.0 1.0

Sodium binding site 5 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na4705

b:27.2
occ:1.00
 O E:VAL40 2.3 18.2 1.0
OD1 E:ASP109 2.4 15.8 1.0
O E:ASP109 2.5 16.6 1.0
O E:GLN196 2.6 17.2 1.0
O E:HOH5685 2.8 28.0 1.0
OG1 E:THR39 3.0 19.6 1.0
O E:HOH5683 3.2 16.5 1.0
C E:VAL40 3.4 19.2 1.0
CG E:ASP109 3.4 14.8 1.0
C E:ASP109 3.5 17.7 1.0
N E:VAL40 3.6 19.6 1.0
CA E:ASP109 3.7 16.7 1.0
C E:GLN196 3.8 16.0 1.0
CA E:VAL40 4.0 19.2 1.0
CB E:ASP109 4.1 15.2 1.0
C E:THR39 4.2 19.8 1.0
OD2 E:ASP109 4.3 15.6 1.0
CD E:PRO42 4.3 17.9 1.0
CB E:THR39 4.3 20.5 1.0
N E:ASN41 4.5 18.2 1.0
CA E:THR39 4.5 19.5 1.0
CD1 E:ILE48 4.6 16.5 1.0
CA E:GLN196 4.7 15.5 1.0
N E:ASN110 4.7 17.8 1.0
N E:THR197 4.8 16.1 1.0
CG2 E:THR197 4.8 15.9 1.0
CB E:VAL40 4.8 20.1 1.0
CA E:ASN41 4.9 17.4 1.0
CA E:THR197 4.9 17.1 1.0

Sodium binding site 6 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na4706

b:21.1
occ:1.00
 O F:VAL40 2.4 16.7 1.0
OD1 F:ASP109 2.4 13.3 1.0
O F:GLN196 2.5 13.7 1.0
O F:ASP109 2.5 13.1 1.0
O F:HOH2342 2.6 27.7 1.0
OG1 F:THR39 3.1 16.8 1.0
O F:HOH2346 3.3 25.1 1.0
C F:ASP109 3.4 14.8 1.0
CG F:ASP109 3.4 11.3 1.0
C F:VAL40 3.5 17.5 1.0
C F:GLN196 3.7 12.1 1.0
N F:VAL40 3.7 16.4 1.0
CA F:ASP109 3.8 12.4 1.0
CA F:VAL40 4.2 16.6 1.0
CB F:ASP109 4.2 9.4 1.0
CD F:PRO42 4.3 11.4 1.0
OD2 F:ASP109 4.3 10.6 1.0
CB F:THR39 4.4 14.8 1.0
C F:THR39 4.4 16.1 1.0
CG2 F:THR197 4.5 11.4 1.0
CA F:GLN196 4.5 13.4 1.0
N F:THR197 4.6 11.2 1.0
N F:ASN41 4.6 15.9 1.0
N F:ASN110 4.7 15.0 1.0
CA F:THR197 4.7 11.8 1.0
CA F:THR39 4.7 14.6 1.0
O F:HOH2343 4.7 28.3 1.0
CD1 F:ILE48 4.8 8.9 1.0
CB F:VAL40 4.9 16.2 1.0
CG2 F:THR39 4.9 14.1 1.0
CB F:GLN196 5.0 14.0 1.0
CA F:ASN41 5.0 14.3 1.0

Sodium binding site 7 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na4707

b:19.2
occ:1.00
 O G:VAL40 2.3 18.9 1.0
OD1 G:ASP109 2.3 23.8 1.0
O G:ASP109 2.5 18.7 1.0
O G:GLN196 2.6 20.5 1.0
O G:HOH1792 3.1 26.4 1.0
OG1 G:THR39 3.4 20.5 1.0
C G:VAL40 3.4 20.9 1.0
CG G:ASP109 3.4 22.9 1.0
C G:ASP109 3.5 18.5 1.0
N G:VAL40 3.7 19.7 1.0
C G:GLN196 3.8 21.2 1.0
CA G:ASP109 3.9 19.2 1.0
CA G:VAL40 4.0 19.7 1.0
CD G:PRO42 4.2 21.6 1.0
CB G:ASP109 4.2 20.2 1.0
OD2 G:ASP109 4.3 23.8 1.0
C G:THR39 4.4 19.5 1.0
N G:ASN41 4.5 19.4 1.0
CA G:GLN196 4.6 21.0 1.0
CB G:THR39 4.6 20.4 1.0
CG2 G:THR197 4.7 19.7 1.0
N G:ASN110 4.7 17.8 1.0
CA G:THR39 4.8 20.3 1.0
N G:THR197 4.8 20.2 1.0
CB G:VAL40 4.8 21.7 1.0
CD1 G:ILE48 4.8 24.0 1.0
O G:VAL345 4.9 17.3 1.0
CA G:THR197 4.9 18.9 1.0
CA G:ASN41 4.9 19.9 1.0
CB G:GLN196 5.0 21.4 1.0

Sodium binding site 8 out of 8 in 1o01

Go back to Sodium Binding Sites List in 1o01
Sodium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na4708

b:27.7
occ:1.00
 OD1 H:ASP109 2.3 21.1 1.0
O H:GLN196 2.4 24.9 1.0
O H:ASP109 2.5 20.5 1.0
O H:VAL40 2.5 23.6 1.0
O H:HOH1836 2.7 37.3 1.0
OG1 H:THR39 3.1 26.2 1.0
O H:HOH1834 3.2 27.5 1.0
CG H:ASP109 3.3 22.3 1.0
C H:ASP109 3.4 19.6 1.0
C H:GLN196 3.6 23.8 1.0
C H:VAL40 3.6 24.7 1.0
CA H:ASP109 3.8 19.2 1.0
N H:VAL40 3.9 23.4 1.0
CB H:ASP109 4.1 19.0 1.0
OD2 H:ASP109 4.1 19.8 1.0
CA H:VAL40 4.3 23.4 1.0
CD H:PRO42 4.3 24.7 1.0
CA H:GLN196 4.4 23.4 1.0
C H:THR39 4.4 23.8 1.0
CB H:THR39 4.4 24.4 1.0
CG2 H:THR197 4.5 17.9 1.0
N H:THR197 4.5 22.8 1.0
CA H:THR197 4.6 22.4 1.0
N H:ASN110 4.6 20.3 1.0
N H:ASN41 4.7 23.9 1.0
CA H:THR39 4.7 24.7 1.0
CD1 H:ILE48 4.8 28.2 1.0
CB H:GLN196 4.8 20.8 1.0

Reference:

S.J.Perez-Miller, T.D.Hurley. Coenzyme Isomerization Is Integral to Catalysis in Aldehyde Dehydrogenase Biochemistry V. 42 7100 2003.
ISSN: ISSN 0006-2960
PubMed: 12795606
DOI: 10.1021/BI034182W
Page generated: Sun Oct 6 21:02:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy