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Sodium in PDB 1o00: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations

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

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations, PDB code: 1o00 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) 29.81 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.911, 150.671, 177.133, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.2

Other elements in 1o00:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations 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 Nad+ and MG2+ Showing Dual Nad(H) Conformations (pdb code 1o00). 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 Nad+ and MG2+ Showing Dual Nad(H) Conformations, PDB code: 1o00:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1o00

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Sodium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2701

b:34.7
occ:1.00
 O A:VAL40 2.2 20.1 1.0
OD1 A:ASP109 2.3 20.2 1.0
O A:ASP109 2.4 12.6 1.0
O A:GLN196 2.6 21.4 1.0
CG A:ASP109 3.4 17.6 1.0
C A:VAL40 3.4 20.7 1.0
C A:ASP109 3.4 13.6 1.0
OG1 A:THR39 3.7 23.1 1.0
C A:GLN196 3.8 19.2 1.0
CA A:ASP109 3.8 14.2 1.0
N A:VAL40 3.9 21.9 1.0
CD A:PRO42 4.1 25.0 1.0
CA A:VAL40 4.2 20.8 1.0
CB A:ASP109 4.2 15.4 1.0
CG A:PRO42 4.2 25.9 1.0
OD2 A:ASP109 4.2 18.4 1.0
CG2 A:THR197 4.4 21.1 1.0
N A:ASN41 4.5 20.9 1.0
CA A:GLN196 4.5 18.4 1.0
O A:VAL345 4.5 25.2 1.0
C A:THR39 4.6 22.8 1.0
N A:ASN110 4.6 14.3 1.0
CA A:ASN41 4.7 21.1 1.0
N A:THR197 4.8 18.5 1.0
CB A:GLN196 4.8 18.3 1.0
CA A:THR197 4.9 19.0 1.0
CB A:VAL40 4.9 20.6 1.0
N A:PRO42 4.9 24.7 1.0
CB A:THR39 4.9 24.5 1.0

Sodium binding site 2 out of 8 in 1o00

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Sodium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2702

b:32.8
occ:1.00
 OD1 B:ASP109 2.2 13.3 1.0
O B:VAL40 2.4 19.7 1.0
O B:GLN196 2.4 15.8 1.0
O B:ASP109 2.5 12.5 1.0
O B:HOH2859 3.1 19.3 1.0
CG B:ASP109 3.4 13.3 1.0
C B:ASP109 3.5 12.7 1.0
OG1 B:THR39 3.5 18.8 1.0
C B:VAL40 3.5 17.8 1.0
C B:GLN196 3.6 14.9 1.0
N B:VAL40 3.9 15.5 1.0
CA B:ASP109 3.9 11.6 1.0
CA B:VAL40 4.2 16.3 1.0
CD B:PRO42 4.2 18.0 1.0
CB B:ASP109 4.3 11.3 1.0
OD2 B:ASP109 4.3 12.0 1.0
CG2 B:THR197 4.3 14.0 1.0
CA B:GLN196 4.4 14.7 1.0
O B:VAL345 4.5 19.4 1.0
C B:THR39 4.6 16.0 1.0
N B:THR197 4.6 14.7 1.0
N B:ASN41 4.6 18.1 1.0
N B:ASN110 4.7 12.9 1.0
CB B:GLN196 4.7 15.2 1.0
CA B:THR197 4.8 14.5 1.0
CB B:THR39 4.8 17.8 1.0
CB B:VAL40 4.9 15.3 1.0
CA B:ASN41 4.9 19.3 1.0
CA B:THR39 4.9 16.1 1.0
CG2 B:VAL345 5.0 17.1 1.0

Sodium binding site 3 out of 8 in 1o00

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Sodium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na2703

b:45.8
occ:1.00
 O C:ASP109 2.4 14.7 1.0
O C:VAL40 2.4 12.5 1.0
O C:GLN196 2.5 15.0 1.0
OD1 C:ASP109 2.8 19.8 1.0
C C:ASP109 3.5 13.6 1.0
C C:VAL40 3.6 12.2 1.0
C C:GLN196 3.7 14.0 1.0
CG C:ASP109 3.8 17.8 1.0
O C:HOH3571 3.9 38.9 1.0
CD C:PRO42 3.9 11.2 1.0
OG1 C:THR39 4.1 15.4 1.0
O C:VAL345 4.1 16.9 1.0
O C:HOH3570 4.1 29.0 1.0
CA C:ASP109 4.1 14.7 1.0
N C:VAL40 4.2 11.2 1.0
CG2 C:THR197 4.3 11.1 1.0
CA C:GLN196 4.3 13.6 1.0
CA C:VAL40 4.4 11.8 1.0
CB C:GLN196 4.5 13.5 1.0
CB C:ASP109 4.6 15.0 1.0
N C:ASN110 4.6 12.7 1.0
CG2 C:VAL345 4.7 7.6 1.0
N C:ASN41 4.7 11.9 1.0
N C:THR197 4.7 13.9 1.0
OD2 C:ASP109 4.7 14.1 1.0
CG C:PRO42 4.8 12.3 1.0
N C:PRO42 4.8 11.8 1.0
CA C:ASN110 4.9 12.8 1.0
CA C:THR197 4.9 12.6 1.0
CB C:VAL40 4.9 12.1 1.0
CA C:ASN41 4.9 10.8 1.0
C C:THR39 5.0 11.7 1.0

Sodium binding site 4 out of 8 in 1o00

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Sodium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na2704

b:44.3
occ:1.00
 O D:VAL40 2.4 19.3 1.0
OD1 D:ASP109 2.4 19.2 1.0
O D:GLN196 2.4 19.6 1.0
O D:ASP109 2.6 9.7 1.0
OG1 D:THR39 3.5 20.6 1.0
C D:VAL40 3.5 18.2 1.0
CG D:ASP109 3.6 16.3 1.0
C D:GLN196 3.6 17.5 1.0
C D:ASP109 3.7 12.8 1.0
N D:VAL40 3.8 18.4 1.0
CA D:ASP109 4.1 13.0 1.0
CA D:VAL40 4.1 18.6 1.0
CD D:PRO42 4.3 21.2 1.0
CA D:GLN196 4.3 17.0 1.0
OD2 D:ASP109 4.4 16.3 1.0
CB D:ASP109 4.4 13.5 1.0
CG2 D:THR197 4.4 18.1 1.0
O D:VAL345 4.5 19.8 1.0
C D:THR39 4.5 18.6 1.0
N D:ASN41 4.6 18.8 1.0
CB D:GLN196 4.6 17.1 1.0
N D:THR197 4.6 18.3 1.0
CB D:THR39 4.7 20.0 1.0
CB D:VAL40 4.7 19.0 1.0
CA D:THR197 4.8 19.1 1.0
N D:ASN110 4.8 13.4 1.0
CA D:THR39 4.9 19.8 1.0
CA D:ASN41 5.0 19.7 1.0

Sodium binding site 5 out of 8 in 1o00

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Sodium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na2705

b:30.3
occ:1.00
 O E:ASP109 2.3 10.2 1.0
OD1 E:ASP109 2.4 12.4 1.0
O E:GLN196 2.4 17.7 1.0
O E:VAL40 2.5 18.1 1.0
C E:ASP109 3.4 11.7 1.0
O E:HOH845 3.4 18.5 1.0
CG E:ASP109 3.5 11.0 1.0
C E:GLN196 3.6 16.9 1.0
C E:VAL40 3.7 17.2 1.0
OG1 E:THR39 3.8 15.6 1.0
CA E:ASP109 3.9 11.9 1.0
CD E:PRO42 4.1 16.3 1.0
N E:VAL40 4.2 18.5 1.0
CG2 E:THR197 4.2 20.1 1.0
O E:VAL345 4.2 20.9 1.0
CB E:ASP109 4.3 12.3 1.0
CA E:GLN196 4.4 16.9 1.0
OD2 E:ASP109 4.4 9.6 1.0
CA E:VAL40 4.4 17.9 1.0
N E:ASN110 4.5 11.7 1.0
CB E:GLN196 4.6 16.2 1.0
N E:THR197 4.6 17.9 1.0
CG2 E:VAL345 4.7 17.2 1.0
CA E:THR197 4.8 18.1 1.0
N E:ASN41 4.8 17.1 1.0
CA E:ASN110 4.9 12.7 1.0
C E:THR39 4.9 18.9 1.0
N E:PRO42 4.9 17.4 1.0
CG E:PRO42 5.0 16.8 1.0

Sodium binding site 6 out of 8 in 1o00

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Sodium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na2706

b:38.4
occ:1.00
 O F:VAL40 2.2 15.6 1.0
O F:GLN196 2.4 12.3 1.0
OD1 F:ASP109 2.5 17.6 1.0
O F:ASP109 2.8 14.8 1.0
O F:HOH1489 3.2 48.5 1.0
C F:VAL40 3.3 15.6 1.0
OG1 F:THR39 3.4 15.4 1.0
N F:VAL40 3.6 16.6 1.0
C F:GLN196 3.6 10.1 1.0
CG F:ASP109 3.7 17.7 1.0
C F:ASP109 3.9 14.1 1.0
CA F:VAL40 3.9 16.6 1.0
O F:HOH1333 4.1 27.5 1.0
CA F:ASP109 4.2 14.3 1.0
CA F:GLN196 4.3 9.1 1.0
C F:THR39 4.3 14.5 1.0
CD F:PRO42 4.4 13.3 1.0
OD2 F:ASP109 4.5 14.1 1.0
N F:ASN41 4.5 15.4 1.0
CG F:PRO42 4.5 15.7 1.0
CB F:ASP109 4.5 15.7 1.0
CB F:THR39 4.6 14.5 1.0
CB F:VAL40 4.6 15.7 1.0
CG2 F:THR197 4.6 9.4 1.0
CB F:GLN196 4.6 8.9 1.0
O F:VAL345 4.6 16.3 1.0
N F:THR197 4.7 10.4 1.0
CA F:THR39 4.7 14.0 1.0
O F:HOH1032 4.9 21.2 1.0
CA F:THR197 4.9 9.8 1.0
CA F:ASN41 4.9 14.6 1.0

Sodium binding site 7 out of 8 in 1o00

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Sodium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na2707

b:26.3
occ:1.00
 O G:VAL40 2.3 17.1 1.0
OD1 G:ASP109 2.3 18.8 1.0
O G:GLN196 2.4 15.6 1.0
O G:ASP109 2.7 18.2 1.0
OG1 G:THR39 3.4 20.2 1.0
C G:VAL40 3.4 17.7 1.0
CG G:ASP109 3.5 18.0 1.0
C G:GLN196 3.6 14.8 1.0
N G:VAL40 3.7 19.0 1.0
C G:ASP109 3.7 17.2 1.0
CA G:VAL40 4.0 18.0 1.0
CA G:ASP109 4.1 17.8 1.0
OD2 G:ASP109 4.3 18.4 1.0
CA G:GLN196 4.4 14.4 1.0
CB G:ASP109 4.4 16.2 1.0
C G:THR39 4.4 19.0 1.0
CG2 G:THR197 4.5 13.7 1.0
N G:ASN41 4.5 16.9 1.0
CD G:PRO42 4.6 17.2 1.0
CB G:THR39 4.6 21.2 1.0
N G:THR197 4.6 15.5 1.0
O G:VAL345 4.7 22.2 1.0
CB G:VAL40 4.7 18.3 1.0
CA G:THR39 4.7 20.1 1.0
CB G:GLN196 4.8 15.1 1.0
CA G:THR197 4.8 16.2 1.0
N G:ASN110 4.9 17.0 1.0
CA G:ASN41 4.9 16.4 1.0
CD1 G:ILE48 5.0 16.1 1.0

Sodium binding site 8 out of 8 in 1o00

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Sodium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


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 Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na2708

b:46.1
occ:1.00
 O H:VAL40 2.2 23.3 1.0
OD1 H:ASP109 2.4 14.4 1.0
O H:ASP109 2.5 15.2 1.0
O H:GLN196 2.5 19.2 1.0
C H:VAL40 3.4 21.8 1.0
CG H:ASP109 3.5 15.0 1.0
C H:ASP109 3.5 14.8 1.0
OG1 H:THR39 3.6 21.5 1.0
C H:GLN196 3.7 17.3 1.0
N H:VAL40 3.8 22.0 1.0
CA H:ASP109 4.0 15.5 1.0
CA H:VAL40 4.1 22.0 1.0
CD H:PRO42 4.2 20.5 1.0
CG H:PRO42 4.3 22.9 1.0
CB H:ASP109 4.4 13.7 1.0
OD2 H:ASP109 4.4 15.2 1.0
O H:VAL345 4.4 19.8 1.0
CA H:GLN196 4.5 16.7 1.0
CG2 H:THR197 4.5 13.4 1.0
N H:ASN41 4.5 21.9 1.0
C H:THR39 4.5 20.6 1.0
CB H:VAL40 4.7 21.7 1.0
N H:ASN110 4.7 14.7 1.0
N H:THR197 4.8 17.1 1.0
CB H:GLN196 4.8 16.9 1.0
CA H:ASN41 4.8 21.0 1.0
CB H:THR39 4.9 20.5 1.0
CA H:THR197 4.9 15.2 1.0
N H:PRO42 4.9 21.3 1.0
CG2 H:VAL345 4.9 18.2 1.0
CA H:THR39 5.0 20.5 1.0
O H:HOH8679 5.0 29.1 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: Tue Dec 15 05:31:53 2020

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