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Sodium in PDB 1o05: Apo Form of Human Mitochondrial Aldehyde Dehydrogenase

Enzymatic activity of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase

All present enzymatic activity of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase:
1.2.1.3;

Protein crystallography data

The structure of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase, PDB code: 1o05 was solved by T.D.Hurley, S.Perez-Miller, H.Breen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.96 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.180, 151.940, 177.120, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 21.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase (pdb code 1o05). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase, PDB code: 1o05:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1o05

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Sodium binding site 1 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na5001

b:31.1
occ:1.00
 O A:GLN196 2.3 21.5 1.0
O A:VAL40 2.4 21.4 1.0
O A:HOH5307 2.5 32.4 1.0
OD1 A:ASP109 2.6 20.1 1.0
O A:ASP109 2.7 17.8 1.0
O A:HOH5279 3.0 32.6 1.0
OG1 A:THR39 3.4 25.4 1.0
C A:GLN196 3.4 21.0 1.0
C A:VAL40 3.5 21.9 1.0
N A:VAL40 3.6 22.6 1.0
CG A:ASP109 3.6 19.2 1.0
C A:ASP109 3.8 17.9 1.0
CA A:VAL40 4.0 22.2 1.0
CA A:GLN196 4.1 20.2 1.0
CA A:ASP109 4.1 17.9 1.0
CD A:PRO42 4.2 20.8 1.0
C A:THR39 4.3 23.2 1.0
OD2 A:ASP109 4.4 17.2 1.0
CB A:ASP109 4.4 17.5 1.0
N A:THR197 4.5 20.4 1.0
CB A:THR39 4.6 24.3 1.0
CB A:GLN196 4.6 21.4 1.0
N A:ASN41 4.6 21.2 1.0
CA A:THR39 4.6 23.4 1.0
CG2 A:THR197 4.7 21.6 1.0
CB A:VAL40 4.8 22.6 1.0
CA A:THR197 4.8 19.8 1.0
O A:VAL345 4.8 26.3 1.0
N A:ASN110 5.0 16.6 1.0

Sodium binding site 2 out of 8 in 1o05

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Sodium binding site 2 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5002

b:18.6
occ:1.00
 O B:VAL40 2.3 14.9 1.0
O B:ASP109 2.4 13.6 1.0
O B:GLN196 2.4 13.9 1.0
OD1 B:ASP109 2.4 14.4 1.0
O B:HOH5298 2.5 37.5 1.0
O B:HOH5291 3.0 37.0 1.0
C B:ASP109 3.4 13.5 1.0
OG1 B:THR39 3.4 14.8 1.0
CG B:ASP109 3.5 14.6 1.0
C B:VAL40 3.5 14.6 1.0
C B:GLN196 3.6 14.0 1.0
CA B:ASP109 3.8 12.6 1.0
N B:VAL40 3.9 13.8 1.0
CD B:PRO42 4.1 16.1 1.0
CA B:VAL40 4.2 13.4 1.0
CB B:ASP109 4.2 12.4 1.0
OD2 B:ASP109 4.3 14.0 1.0
O B:HOH5376 4.4 33.5 1.0
CA B:GLN196 4.4 14.6 1.0
C B:THR39 4.5 13.3 1.0
N B:ASN41 4.6 13.9 1.0
N B:ASN110 4.6 13.7 1.0
N B:THR197 4.7 13.8 1.0
CB B:THR39 4.7 13.8 1.0
CG2 B:THR197 4.7 12.3 1.0
CA B:THR39 4.8 13.1 1.0
CA B:THR197 4.8 12.6 1.0
O B:VAL345 4.9 14.3 1.0
CD1 B:ILE48 4.9 11.5 1.0
CA B:ASN41 4.9 14.9 1.0
CB B:GLN196 4.9 15.9 1.0
CB B:VAL40 5.0 13.8 1.0
N B:PRO42 5.0 16.0 1.0

Sodium binding site 3 out of 8 in 1o05

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Sodium binding site 3 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5003

b:24.7
occ:1.00
 O B:HOH5242 2.6 18.9 1.0
O B:HOH5241 2.7 19.0 1.0
O B:GLY299 2.8 10.9 1.0
O B:GLY402 3.1 12.5 1.0
CB B:ALA304 3.6 11.6 1.0
C B:GLY299 3.6 13.0 1.0
N B:GLY402 3.7 14.9 1.0
CA B:GLY299 3.7 11.6 1.0
O B:LEU294 3.8 8.8 1.0
N B:PHE401 4.1 13.6 1.0
C B:GLY402 4.1 12.8 1.0
CA B:PHE401 4.1 14.8 1.0
CG B:LEU294 4.2 12.1 1.0
C B:PHE401 4.2 14.3 1.0
O B:HOH5101 4.3 10.2 1.0
CD1 B:LEU294 4.3 11.5 1.0
CA B:GLY402 4.5 13.1 1.0
O B:HOH5116 4.5 4.3 1.0
C B:LEU294 4.8 9.8 1.0
CB B:SER306 4.8 12.6 1.0
O B:VAL404 4.9 10.1 1.0
CD2 B:LEU294 4.9 10.2 1.0
N B:GLN300 4.9 12.7 1.0
O B:HOH5243 4.9 13.8 1.0

Sodium binding site 4 out of 8 in 1o05

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Sodium binding site 4 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na5004

b:21.7
occ:1.00
 O C:ALA290 2.7 16.3 1.0
OG1 C:THR308 2.8 10.9 1.0
O C:GLY305 3.1 11.0 1.0
C C:ALA290 3.4 14.8 1.0
OD1 C:ASN275 3.5 13.4 1.0
CA C:ALA290 3.5 13.7 1.0
CB C:ALA290 3.7 13.9 1.0
CE C:MET405 3.7 23.0 1.0
CB C:ALA293 3.8 11.5 1.0
CB C:THR308 4.0 10.7 1.0
C C:GLY305 4.0 12.6 1.0
CG2 C:THR308 4.0 10.9 1.0
CB C:ASN275 4.1 10.6 1.0
O C:HOH5150 4.2 8.5 1.0
CG C:ASN275 4.2 12.3 1.0
CB C:LEU294 4.2 15.9 1.0
N C:LEU294 4.2 14.9 1.0
CA C:GLY305 4.3 12.1 1.0
C C:ALA293 4.6 15.0 1.0
N C:HIS291 4.7 14.6 1.0
CA C:THR308 4.7 11.4 1.0
CA C:ALA293 4.7 14.5 1.0
CA C:LEU294 4.8 14.9 1.0
N C:ALA290 4.9 13.5 1.0

Sodium binding site 5 out of 8 in 1o05

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Sodium binding site 5 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na5005

b:20.1
occ:1.00
 O E:VAL40 2.3 15.8 1.0
O E:ASP109 2.4 12.3 1.0
O E:GLN196 2.4 14.0 1.0
OD1 E:ASP109 2.4 13.6 1.0
O E:HOH2942 2.5 34.6 1.0
O E:HOH2575 2.9 32.3 1.0
OG1 E:THR39 3.2 17.7 1.0
C E:ASP109 3.4 13.5 1.0
CG E:ASP109 3.4 14.1 1.0
C E:VAL40 3.5 15.7 1.0
C E:GLN196 3.6 14.2 1.0
CA E:ASP109 3.7 11.7 1.0
N E:VAL40 3.8 17.0 1.0
CB E:ASP109 4.1 13.1 1.0
CA E:VAL40 4.1 16.4 1.0
CD E:PRO42 4.1 10.5 1.0
OD2 E:ASP109 4.3 15.3 1.0
C E:THR39 4.4 16.5 1.0
CA E:GLN196 4.4 14.6 1.0
CB E:THR39 4.5 16.9 1.0
CG2 E:THR197 4.5 12.2 1.0
N E:ASN41 4.6 15.0 1.0
N E:ASN110 4.6 13.1 1.0
N E:THR197 4.6 13.3 1.0
CD1 E:ILE48 4.7 15.2 1.0
CA E:THR197 4.7 13.4 1.0
CA E:THR39 4.8 17.4 1.0
CB E:GLN196 4.9 14.8 1.0
CB E:VAL40 4.9 17.7 1.0
CA E:ASN41 4.9 14.2 1.0
O E:VAL345 5.0 13.3 1.0

Sodium binding site 6 out of 8 in 1o05

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Sodium binding site 6 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na5006

b:28.4
occ:1.00
 O F:HOH2891 2.5 30.4 1.0
O F:HOH1374 2.8 18.2 1.0
NH2 F:ARG99 2.9 7.1 1.0
OE1 F:GLU96 2.9 16.0 1.0
CD F:ARG99 3.4 5.3 1.0
CG F:GLU96 3.7 11.6 1.0
CD F:GLU96 3.7 13.3 1.0
CZ F:ARG99 3.9 6.7 1.0
OH F:TYR118 4.0 13.4 1.0
O F:HOH2832 4.1 31.1 1.0
NE F:ARG99 4.1 6.2 1.0
O F:HOH1372 4.3 14.6 1.0
CG F:ARG99 4.6 6.4 1.0
O F:GLU96 4.7 10.2 1.0
CB F:ARG99 4.7 8.0 1.0
CZ F:TYR118 4.9 11.4 1.0
OE2 F:GLU96 4.9 16.5 1.0

Sodium binding site 7 out of 8 in 1o05

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Sodium binding site 7 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na5007

b:28.6
occ:1.00
 O G:VAL40 2.3 21.4 1.0
O G:GLN196 2.4 17.6 1.0
OD1 G:ASP109 2.4 14.4 1.0
O G:ASP109 2.5 16.0 1.0
O G:HOH1582 3.3 27.0 1.0
OG1 G:THR39 3.3 21.2 1.0
CG G:ASP109 3.3 15.1 1.0
C G:VAL40 3.4 19.5 1.0
C G:ASP109 3.5 15.4 1.0
C G:GLN196 3.6 16.6 1.0
N G:VAL40 3.6 19.4 1.0
CA G:ASP109 3.8 14.9 1.0
CA G:VAL40 4.0 18.9 1.0
OD2 G:ASP109 4.1 16.4 1.0
CB G:ASP109 4.1 14.7 1.0
CD G:PRO42 4.3 16.4 1.0
CA G:GLN196 4.4 16.0 1.0
C G:THR39 4.4 18.7 1.0
CB G:THR39 4.5 19.6 1.0
N G:ASN41 4.6 18.6 1.0
N G:THR197 4.6 14.8 1.0
CD1 G:ILE48 4.6 19.3 1.0
CG2 G:THR197 4.6 14.2 1.0
CA G:THR39 4.7 18.5 1.0
N G:ASN110 4.7 15.1 1.0
CA G:THR197 4.7 14.8 1.0
CB G:VAL40 4.8 19.6 1.0
CB G:GLN196 4.9 17.0 1.0
O G:VAL345 4.9 14.4 1.0
CA G:ASN41 5.0 17.0 1.0

Sodium binding site 8 out of 8 in 1o05

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Sodium binding site 8 out of 8 in the Apo Form of Human Mitochondrial Aldehyde Dehydrogenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Apo Form of Human Mitochondrial Aldehyde Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na5008

b:21.4
occ:1.00
 O H:GLN196 2.3 14.5 1.0
O H:VAL40 2.4 20.2 1.0
OD1 H:ASP109 2.5 13.7 1.0
O H:ASP109 2.5 15.4 1.0
O H:HOH2601 2.6 32.5 1.0
O H:HOH2621 2.7 37.8 1.0
OG1 H:THR39 3.3 15.7 1.0
CG H:ASP109 3.4 14.7 1.0
C H:ASP109 3.5 14.4 1.0
C H:GLN196 3.5 15.0 1.0
C H:VAL40 3.6 19.0 1.0
N H:VAL40 3.8 17.9 1.0
CA H:ASP109 3.8 13.7 1.0
CB H:ASP109 4.1 13.7 1.0
OD2 H:ASP109 4.2 11.8 1.0
CA H:VAL40 4.2 18.8 1.0
CD H:PRO42 4.3 17.2 1.0
CA H:GLN196 4.3 14.9 1.0
C H:THR39 4.5 16.8 1.0
N H:THR197 4.5 13.8 1.0
CB H:THR39 4.6 17.2 1.0
CG2 H:THR197 4.6 11.4 1.0
N H:ASN41 4.7 18.2 1.0
N H:ASN110 4.7 15.1 1.0
CD1 H:ILE48 4.7 8.7 1.0
CA H:THR197 4.7 15.2 1.0
CB H:GLN196 4.8 15.1 1.0
CA H:THR39 4.8 17.1 1.0
O H:VAL345 5.0 16.8 1.0
CA H:ASN41 5.0 17.4 1.0
CB H:VAL40 5.0 20.2 1.0

Reference:

T.D.Hurley, S.Perez-Miller, H.Breen. Order and Disorder in Mitochondrial Aldehyde Dehydrogenase Chem.Biol.Interact. V.-132 3 2001.
ISSN: ISSN 0009-2797
PubMed: 11306026
DOI: 10.1016/S0009-2797(00)00217-9
Page generated: Tue Dec 15 05:32:00 2020

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