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Sodium in PDB 2onm: Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+, PDB code: 2onm was solved by H.N.Larson, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.01 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 96.201, 104.854, 162.359, 78.99, 82.14, 88.55
R / Rfree (%) 23 / 27.1

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+ (pdb code 2onm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+, PDB code: 2onm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 2onm

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Sodium binding site 1 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:82.8
occ:1.00
 O A:GLN196 2.3 68.4 1.0
O A:VAL40 2.4 73.5 1.0
OD1 A:ASP109 2.5 72.9 1.0
O A:ASP109 2.7 67.9 1.0
OG1 A:THR39 3.1 69.0 1.0
C A:GLN196 3.5 67.3 1.0
C A:VAL40 3.5 72.8 1.0
CG A:ASP109 3.6 71.1 1.0
N A:VAL40 3.6 72.0 1.0
C A:ASP109 3.7 67.1 1.0
CA A:VAL40 4.0 72.7 1.0
CA A:ASP109 4.0 67.5 1.0
CA A:GLN196 4.2 66.9 1.0
C A:THR39 4.2 71.4 1.0
CD A:PRO42 4.3 74.1 1.0
CB A:ASP109 4.4 68.9 1.0
OD2 A:ASP109 4.4 70.1 1.0
CB A:THR39 4.4 71.1 1.0
N A:THR197 4.5 66.6 1.0
CA A:THR39 4.6 71.3 1.0
CG2 A:THR197 4.6 63.8 1.0
N A:ASN41 4.6 72.5 1.0
CB A:GLN196 4.6 68.0 1.0
CD1 A:ILE48 4.7 69.4 1.0
CA A:THR197 4.7 65.6 1.0
CB A:VAL40 4.7 73.0 1.0
N A:ASN110 4.9 66.7 1.0
O A:VAL345 4.9 79.1 1.0

Sodium binding site 2 out of 17 in 2onm

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Sodium binding site 2 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5003

b:55.5
occ:1.00
 O B:HOH2286 2.9 50.5 1.0
O B:GLY299 2.9 32.9 1.0
O B:GLY402 3.2 31.9 1.0
N B:GLY402 3.2 34.9 1.0
N B:PHE401 3.4 41.4 1.0
CA B:PHE401 3.4 39.6 1.0
C B:PHE401 3.7 37.0 1.0
C B:GLY299 3.8 31.6 1.0
CB B:ALA304 3.8 31.3 1.0
CA B:GLY299 4.0 31.8 1.0
O B:HOH1176 4.0 48.0 1.0
C B:GLY402 4.0 31.1 1.0
CA B:GLY402 4.2 32.5 1.0
C B:ILE400 4.5 43.1 1.0
CD1 B:LEU294 4.6 33.0 1.0
O B:LEU294 4.6 31.3 1.0
O B:PHE401 4.7 34.5 1.0
CB B:SER306 4.7 40.8 1.0
CG B:LEU294 4.8 33.7 1.0
CB B:PHE401 4.9 39.5 1.0
CB B:ILE400 4.9 43.1 1.0
N B:GLN300 5.0 30.5 1.0

Sodium binding site 3 out of 17 in 2onm

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Sodium binding site 3 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na602

b:40.1
occ:1.00
 O B:VAL40 2.3 37.8 1.0
O B:GLN196 2.4 40.6 1.0
OD1 B:ASP109 2.5 34.2 1.0
O B:HOH2722 2.6 47.4 1.0
O B:ASP109 2.6 27.7 1.0
OG1 B:THR39 3.4 39.2 1.0
C B:VAL40 3.4 37.2 1.0
C B:GLN196 3.5 38.8 1.0
CG B:ASP109 3.6 34.0 1.0
C B:ASP109 3.6 28.4 1.0
N B:VAL40 3.7 36.1 1.0
O B:HOH2167 3.7 43.1 1.0
CA B:ASP109 4.0 28.9 1.0
CA B:VAL40 4.1 37.5 1.0
CD B:PRO42 4.2 31.7 1.0
CA B:GLN196 4.2 39.0 1.0
C B:THR39 4.3 36.5 1.0
CB B:ASP109 4.4 30.7 1.0
OD2 B:ASP109 4.5 33.8 1.0
N B:ASN41 4.5 37.6 1.0
CG2 B:THR197 4.6 36.8 1.0
CB B:GLN196 4.6 36.2 1.0
CB B:THR39 4.6 35.8 1.0
N B:THR197 4.6 37.4 1.0
CA B:THR39 4.7 36.7 1.0
CD1 B:ILE48 4.8 30.7 1.0
CB B:VAL40 4.8 39.7 1.0
CA B:THR197 4.8 36.9 1.0
O B:VAL345 4.8 37.4 1.0
N B:ASN110 4.8 29.1 1.0
CA B:ASN41 4.9 35.8 1.0

Sodium binding site 4 out of 17 in 2onm

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Sodium binding site 4 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na5004

b:51.2
occ:1.00
 OG1 C:THR308 2.7 27.5 1.0
O C:ALA290 2.9 28.1 1.0
O C:GLY305 3.0 29.2 1.0
OD1 C:ASN275 3.4 36.0 1.0
C C:ALA290 3.6 30.4 1.0
CA C:ALA290 3.6 29.2 1.0
CB C:ALA290 3.7 26.7 1.0
CE C:MET405 3.7 37.3 1.0
CB C:THR308 3.7 28.0 1.0
CG2 C:THR308 3.8 26.2 1.0
CB C:ALA293 3.9 32.2 1.0
O C:HOH1060 3.9 27.1 1.0
C C:GLY305 4.0 31.9 1.0
CB C:ASN275 4.0 28.8 1.0
CB C:LEU294 4.1 30.1 1.0
CG C:ASN275 4.2 31.4 1.0
CA C:GLY305 4.3 31.9 1.0
N C:LEU294 4.3 32.5 1.0
CA C:THR308 4.4 29.9 1.0
C C:ALA293 4.7 31.2 1.0
N C:THR308 4.7 31.3 1.0
CA C:LEU294 4.8 30.3 1.0
CA C:ALA293 4.9 30.6 1.0
N C:HIS291 4.9 30.9 1.0

Sodium binding site 5 out of 17 in 2onm

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Sodium binding site 5 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na603

b:54.1
occ:1.00
 O C:VAL40 2.4 39.3 1.0
O C:GLN196 2.6 41.8 1.0
O C:ASP109 2.7 37.9 1.0
O C:HOH1247 3.0 64.3 1.0
OD1 C:ASP109 3.2 47.1 1.0
C C:VAL40 3.6 37.5 1.0
C C:GLN196 3.7 40.0 1.0
CD C:PRO42 3.8 35.3 1.0
C C:ASP109 3.8 36.0 1.0
O C:VAL345 3.9 35.8 1.0
N C:VAL40 4.0 36.9 1.0
OG1 C:THR39 4.0 36.1 1.0
CA C:GLN196 4.1 39.8 1.0
CA C:VAL40 4.2 36.7 1.0
CB C:GLN196 4.2 39.4 1.0
CG C:ASP109 4.3 43.2 1.0
CA C:ASP109 4.5 36.6 1.0
CG2 C:THR197 4.5 33.8 1.0
CB C:VAL40 4.6 35.6 1.0
N C:ASN41 4.7 38.8 1.0
N C:PRO42 4.7 37.7 1.0
CG2 C:VAL345 4.7 33.6 1.0
CG C:PRO42 4.7 35.9 1.0
N C:THR197 4.8 37.9 1.0
N C:ASN110 4.9 36.4 1.0
C C:THR39 4.9 38.4 1.0
CB C:ASP109 5.0 37.7 1.0

Sodium binding site 6 out of 17 in 2onm

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Sodium binding site 6 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na604

b:73.9
occ:1.00
 O D:VAL40 2.5 79.3 1.0
O D:GLN196 2.7 75.9 1.0
O D:ASP109 3.0 63.4 1.0
OD1 D:ASP109 3.3 64.9 1.0
C D:VAL40 3.6 78.8 1.0
O D:VAL345 3.7 78.7 1.0
C D:GLN196 3.7 75.0 1.0
CD D:PRO42 3.9 80.8 1.0
N D:VAL40 3.9 79.1 1.0
CA D:GLN196 4.1 74.5 1.0
CA D:VAL40 4.1 79.3 1.0
C D:ASP109 4.2 63.8 1.0
CB D:GLN196 4.2 75.8 1.0
OG1 D:THR39 4.2 79.5 1.0
O D:HOH1996 4.4 56.6 1.0
CG D:ASP109 4.4 66.1 1.0
CB D:VAL40 4.4 80.0 1.0
CG2 D:VAL345 4.6 81.2 1.0
N D:PRO42 4.7 80.4 1.0
CG2 D:THR197 4.7 75.0 1.0
N D:ASN41 4.7 78.1 1.0
CA D:ASP109 4.8 64.7 1.0
CG D:PRO42 4.8 81.1 1.0
C D:VAL345 4.8 78.4 1.0
N D:THR197 4.9 74.3 1.0
C D:THR39 4.9 79.8 1.0

Sodium binding site 7 out of 17 in 2onm

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Sodium binding site 7 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na605

b:37.2
occ:1.00
 O E:VAL40 2.3 41.2 1.0
O E:ASP109 2.4 40.5 1.0
OD1 E:ASP109 2.6 44.1 1.0
O E:GLN196 2.6 34.3 1.0
C E:ASP109 3.4 38.7 1.0
C E:VAL40 3.4 40.9 1.0
OG1 E:THR39 3.7 47.0 1.0
CG E:ASP109 3.7 43.6 1.0
C E:GLN196 3.8 36.3 1.0
CA E:ASP109 3.9 38.9 1.0
N E:VAL40 3.9 43.4 1.0
CD E:PRO42 3.9 38.9 1.0
CA E:VAL40 4.1 42.2 1.0
CB E:ASP109 4.4 39.0 1.0
CA E:GLN196 4.5 36.7 1.0
N E:ASN41 4.5 39.7 1.0
CG2 E:THR197 4.5 33.6 1.0
N E:ASN110 4.6 39.3 1.0
O E:VAL345 4.6 33.8 1.0
C E:THR39 4.6 43.5 1.0
OD2 E:ASP109 4.6 42.3 1.0
N E:PRO42 4.7 39.9 1.0
CA E:ASN41 4.7 38.2 1.0
CB E:GLN196 4.8 34.8 1.0
N E:THR197 4.8 35.5 1.0
CG E:PRO42 4.8 36.5 1.0
CB E:VAL40 4.8 43.0 1.0
CD1 E:ILE48 4.9 37.1 1.0
CB E:THR39 4.9 43.4 1.0
CA E:THR197 5.0 34.9 1.0
CA E:ASN110 5.0 36.9 1.0

Sodium binding site 8 out of 17 in 2onm

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Sodium binding site 8 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


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 Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na5007

b:54.9
occ:1.00
 O F:GLY299 2.8 32.7 1.0
O F:GLY402 3.1 37.7 1.0
N F:GLY402 3.1 34.9 1.0
O F:HOH1405 3.4 53.8 1.0
CA F:PHE401 3.5 36.1 1.0
N F:PHE401 3.6 37.6 1.0
C F:GLY299 3.6 33.4 1.0
C F:PHE401 3.7 36.3 1.0
CA F:GLY299 3.7 32.0 1.0
CB F:ALA304 3.9 35.2 1.0
C F:GLY402 3.9 37.3 1.0
CA F:GLY402 4.1 36.3 1.0
O F:HOH1592 4.1 45.6 1.0
CD1 F:LEU294 4.3 34.2 1.0
O F:LEU294 4.4 32.9 1.0
CG F:LEU294 4.7 37.4 1.0
C F:ILE400 4.7 37.7 1.0
O F:PHE401 4.7 38.4 1.0
N F:GLN300 4.8 34.2 1.0
CB F:SER306 4.9 38.7 1.0
O F:HOH2754 4.9 31.4 1.0
CB F:PHE401 5.0 35.3 1.0

Sodium binding site 9 out of 17 in 2onm

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Sodium binding site 9 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na606

b:32.3
occ:1.00
 O F:VAL40 2.3 30.6 1.0
O F:GLN196 2.4 36.9 1.0
O F:HOH2029 2.5 40.3 1.0
OD1 F:ASP109 2.6 39.5 1.0
O F:ASP109 2.7 36.7 1.0
OG1 F:THR39 2.9 34.9 1.0
C F:VAL40 3.4 28.7 1.0
CG F:ASP109 3.5 39.9 1.0
N F:VAL40 3.6 31.8 1.0
C F:GLN196 3.6 35.7 1.0
C F:ASP109 3.6 34.3 1.0
CA F:ASP109 3.9 34.0 1.0
CA F:VAL40 4.0 29.8 1.0
CB F:ASP109 4.2 37.5 1.0
CB F:THR39 4.3 34.5 1.0
C F:THR39 4.3 32.0 1.0
OD2 F:ASP109 4.3 39.9 1.0
CA F:GLN196 4.3 35.7 1.0
CD F:PRO42 4.4 27.9 1.0
N F:ASN41 4.5 30.6 1.0
CA F:THR39 4.6 33.2 1.0
N F:THR197 4.6 35.0 1.0
CD1 F:ILE48 4.6 31.7 1.0
CG2 F:THR197 4.7 33.6 1.0
CB F:VAL40 4.7 30.2 1.0
CA F:THR197 4.8 35.1 1.0
CB F:GLN196 4.8 31.7 1.0
N F:ASN110 4.8 33.4 1.0
CA F:ASN41 4.9 30.2 1.0
CG2 F:THR39 4.9 34.8 1.0

Sodium binding site 10 out of 17 in 2onm

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Sodium binding site 10 out of 17 in the Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Human Mitochondrial Aldehyde Dehydrogenase Asian Variant, ALDH2*2, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na5008

b:48.5
occ:1.00
 O G:GLY305 2.8 45.7 1.0
O G:ALA290 2.8 38.7 1.0
OG1 G:THR308 2.9 30.3 1.0
OD1 G:ASN275 3.4 37.3 1.0
CB G:ALA293 3.6 40.3 1.0
C G:ALA290 3.6 37.6 1.0
CA G:ALA290 3.7 37.6 1.0
C G:GLY305 3.8 46.4 1.0
CB G:ALA290 3.9 35.4 1.0
CB G:ASN275 4.0 33.9 1.0
CA G:GLY305 4.0 45.1 1.0
O G:HOH1002 4.1 39.3 1.0
CE G:MET405 4.1 43.7 1.0
CB G:LEU294 4.1 41.6 1.0
CG G:ASN275 4.1 35.5 1.0
CB G:THR308 4.1 33.1 1.0
N G:LEU294 4.1 39.3 1.0
CG2 G:THR308 4.4 34.3 1.0
C G:ALA293 4.5 39.7 1.0
CA G:ALA293 4.6 39.0 1.0
CA G:LEU294 4.7 39.7 1.0
CA G:THR308 4.7 34.2 1.0
N G:GLY305 4.9 46.0 1.0
N G:HIS291 4.9 38.6 1.0
N G:THR308 5.0 36.5 1.0

Reference:

H.N.Larson, J.Zhou, Z.Chen, J.S.Stamler, H.Weiner, T.D.Hurley. Structural and Functional Consequences of Coenzyme Binding to the Inactive Asian Variant of Mitochondrial Aldehyde Dehydrogenase: Roles of Residues 475 and 487. J.Biol.Chem. V. 282 12940 2007.
ISSN: ISSN 0021-9258
PubMed: 17327228
DOI: 10.1074/JBC.M607959200
Page generated: Mon Oct 7 03:13:44 2024

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