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Sodium in PDB 2onp: ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+

Enzymatic activity of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+

All present enzymatic activity of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+:
1.2.1.3;

Protein crystallography data

The structure of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+, PDB code: 2onp 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) 29.97 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.854, 150.837, 177.482, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24

Other elements in 2onp:

The structure of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ (pdb code 2onp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+, PDB code: 2onp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 2onp

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Sodium binding site 1 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:40.1
occ:1.00
 O A:GLN196 2.3 33.8 1.0
O A:VAL40 2.5 37.2 1.0
OD1 A:ASP109 2.5 36.9 1.0
O A:ASP109 2.5 32.1 1.0
OG1 A:THR39 3.3 42.4 1.0
CG A:ASP109 3.5 36.2 1.0
C A:GLN196 3.5 33.9 1.0
C A:ASP109 3.6 31.2 1.0
C A:VAL40 3.6 37.5 1.0
N A:VAL40 3.8 37.8 1.0
CA A:ASP109 4.0 31.2 1.0
CA A:VAL40 4.2 37.7 1.0
CD A:PRO42 4.2 39.4 1.0
OD2 A:ASP109 4.3 37.8 1.0
CB A:ASP109 4.3 32.9 1.0
CA A:GLN196 4.3 32.7 1.0
C A:THR39 4.5 39.0 1.0
CG2 A:THR197 4.5 31.1 1.0
N A:THR197 4.5 33.0 1.0
CB A:THR39 4.6 40.5 1.0
CA A:THR197 4.7 33.8 1.0
CB A:GLN196 4.7 34.6 1.0
N A:ASN41 4.7 36.6 1.0
N A:ASN110 4.8 30.9 1.0
CA A:THR39 4.8 39.9 1.0
O A:VAL345 4.8 36.7 1.0
CB A:VAL40 4.9 36.6 1.0

Sodium binding site 2 out of 8 in 2onp

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Sodium binding site 2 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:34.4
occ:1.00
 OD1 B:ASP109 2.2 33.6 1.0
O B:GLN196 2.3 26.0 1.0
O B:HOH2405 2.5 29.8 1.0
O B:ASP109 2.5 25.9 1.0
O B:VAL40 2.6 33.5 1.0
OG1 B:THR39 3.0 34.0 1.0
CG B:ASP109 3.3 33.1 1.0
C B:ASP109 3.4 28.6 1.0
C B:GLN196 3.5 27.4 1.0
O B:HOH2317 3.6 42.7 1.0
C B:VAL40 3.7 34.0 1.0
CA B:ASP109 3.7 28.5 1.0
N B:VAL40 3.8 34.0 1.0
CB B:ASP109 4.1 30.1 1.0
OD2 B:ASP109 4.2 33.2 1.0
CA B:VAL40 4.3 33.8 1.0
CB B:THR39 4.3 33.9 1.0
CA B:GLN196 4.4 27.1 1.0
C B:THR39 4.4 34.3 1.0
CD B:PRO42 4.4 29.5 1.0
N B:THR197 4.5 25.9 1.0
CG2 B:THR197 4.5 23.1 1.0
CA B:THR197 4.5 25.8 1.0
N B:ASN110 4.6 28.6 1.0
CA B:THR39 4.7 34.4 1.0
CD1 B:ILE48 4.7 33.7 1.0
N B:ASN41 4.8 33.4 1.0
CB B:GLN196 4.8 29.6 1.0
CG2 B:THR39 5.0 33.4 1.0

Sodium binding site 3 out of 8 in 2onp

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Sodium binding site 3 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na703

b:25.0
occ:1.00
 O C:HOH2442 2.4 30.9 1.0
O C:GLN196 2.4 21.9 1.0
O C:VAL40 2.4 19.9 1.0
OD1 C:ASP109 2.5 21.3 1.0
O C:ASP109 2.5 23.3 1.0
O C:HOH1740 3.1 31.1 1.0
OG1 C:THR39 3.1 23.2 1.0
CG C:ASP109 3.4 21.4 1.0
C C:ASP109 3.4 20.0 1.0
C C:VAL40 3.6 22.0 1.0
C C:GLN196 3.6 21.3 1.0
CA C:ASP109 3.7 19.2 1.0
N C:VAL40 3.8 22.0 1.0
CB C:ASP109 4.1 20.1 1.0
CA C:VAL40 4.2 21.5 1.0
OD2 C:ASP109 4.2 23.4 1.0
CD C:PRO42 4.3 17.0 1.0
CB C:THR39 4.4 20.4 1.0
C C:THR39 4.4 21.8 1.0
CA C:GLN196 4.5 21.2 1.0
N C:THR197 4.6 20.3 1.0
N C:ASN110 4.6 20.2 1.0
N C:ASN41 4.7 21.3 1.0
CG2 C:THR197 4.7 17.2 1.0
O C:HOH1625 4.7 33.8 1.0
CA C:THR197 4.7 19.1 1.0
CD1 C:ILE48 4.7 19.4 1.0
CA C:THR39 4.8 21.6 1.0
CB C:GLN196 4.9 20.6 1.0
CB C:VAL40 4.9 21.1 1.0
CA C:ASN41 5.0 19.4 1.0

Sodium binding site 4 out of 8 in 2onp

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Sodium binding site 4 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na704

b:41.4
occ:1.00
 O D:HOH2188 2.3 37.3 1.0
O D:GLN196 2.4 34.8 1.0
O D:VAL40 2.4 32.8 1.0
OD1 D:ASP109 2.5 30.6 1.0
O D:ASP109 2.6 25.6 1.0
O D:HOH3319 2.8 42.3 1.0
OG1 D:THR39 3.0 32.1 1.0
C D:VAL40 3.5 32.1 1.0
CG D:ASP109 3.5 31.8 1.0
C D:GLN196 3.6 32.4 1.0
C D:ASP109 3.6 26.6 1.0
N D:VAL40 3.6 31.2 1.0
CA D:ASP109 3.9 27.3 1.0
CA D:VAL40 4.1 31.9 1.0
C D:THR39 4.3 31.2 1.0
CB D:ASP109 4.3 28.8 1.0
CA D:GLN196 4.3 33.3 1.0
CB D:THR39 4.3 31.3 1.0
OD2 D:ASP109 4.4 30.8 1.0
CD D:PRO42 4.4 31.3 1.0
CG2 D:THR197 4.6 28.9 1.0
N D:THR197 4.6 30.6 1.0
CA D:THR39 4.6 30.9 1.0
N D:ASN41 4.6 31.8 1.0
CA D:THR197 4.7 29.8 1.0
CB D:GLN196 4.8 34.1 1.0
CB D:VAL40 4.8 32.0 1.0
CD1 D:ILE48 4.8 31.5 1.0
N D:ASN110 4.8 26.7 1.0

Sodium binding site 5 out of 8 in 2onp

Go back to Sodium Binding Sites List in 2onp
Sodium binding site 5 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na705

b:40.6
occ:1.00
 O E:ASP109 2.4 28.3 1.0
O E:GLN196 2.4 28.5 1.0
O E:VAL40 2.5 33.2 1.0
OD1 E:ASP109 2.6 28.9 1.0
OG1 E:THR39 3.2 32.1 1.0
O E:HOH1499 3.3 29.7 1.0
C E:ASP109 3.4 26.1 1.0
CG E:ASP109 3.5 27.3 1.0
C E:VAL40 3.6 33.9 1.0
C E:GLN196 3.6 29.5 1.0
CA E:ASP109 3.8 27.6 1.0
N E:VAL40 3.9 32.9 1.0
CA E:VAL40 4.2 33.6 1.0
CB E:ASP109 4.3 27.6 1.0
CD E:PRO42 4.3 32.6 1.0
OD2 E:ASP109 4.4 29.4 1.0
CA E:GLN196 4.4 28.8 1.0
CB E:THR39 4.5 33.0 1.0
CG2 E:THR197 4.5 30.6 1.0
C E:THR39 4.5 32.4 1.0
N E:ASN110 4.6 28.8 1.0
N E:THR197 4.6 29.1 1.0
N E:ASN41 4.7 33.1 1.0
CA E:THR197 4.7 30.2 1.0
O E:VAL345 4.8 28.4 1.0
CA E:THR39 4.8 33.5 1.0
CB E:GLN196 4.9 28.1 1.0
CD1 E:ILE48 4.9 35.1 1.0
CB E:VAL40 5.0 34.6 1.0
CA E:ASN41 5.0 33.0 1.0

Sodium binding site 6 out of 8 in 2onp

Go back to Sodium Binding Sites List in 2onp
Sodium binding site 6 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na706

b:26.1
occ:1.00
 O F:VAL40 2.3 18.6 1.0
OD1 F:ASP109 2.4 20.2 1.0
O F:GLN196 2.5 22.6 1.0
O F:HOH2608 2.5 40.4 1.0
O F:ASP109 2.6 21.8 1.0
OG1 F:THR39 3.0 22.5 1.0
O F:HOH1179 3.1 27.8 1.0
CG F:ASP109 3.4 19.7 1.0
C F:VAL40 3.5 22.4 1.0
C F:ASP109 3.5 20.8 1.0
N F:VAL40 3.7 22.4 1.0
C F:GLN196 3.7 20.2 1.0
CA F:ASP109 3.7 18.8 1.0
CA F:VAL40 4.1 21.5 1.0
CB F:ASP109 4.1 17.6 1.0
OD2 F:ASP109 4.3 18.9 1.0
CB F:THR39 4.3 20.7 1.0
CD F:PRO42 4.3 16.9 1.0
C F:THR39 4.3 20.6 1.0
O F:HOH1754 4.4 27.9 1.0
CA F:GLN196 4.5 20.3 1.0
N F:ASN41 4.6 20.7 1.0
CA F:THR39 4.7 20.2 1.0
N F:THR197 4.7 17.1 1.0
CD1 F:ILE48 4.7 21.1 1.0
N F:ASN110 4.7 20.7 1.0
CG2 F:THR197 4.8 18.2 1.0
CA F:THR197 4.8 19.0 1.0
CB F:VAL40 4.8 21.1 1.0
CA F:ASN41 4.9 19.9 1.0
CG2 F:THR39 5.0 19.9 1.0
CB F:GLN196 5.0 19.5 1.0

Sodium binding site 7 out of 8 in 2onp

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Sodium binding site 7 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na707

b:35.8
occ:1.00
 O G:VAL40 2.4 35.3 1.0
O G:ASP109 2.5 31.6 1.0
O G:GLN196 2.5 31.9 1.0
OD1 G:ASP109 2.5 38.2 1.0
O G:HOH2853 2.9 36.0 1.0
OG1 G:THR39 3.4 34.9 1.0
C G:VAL40 3.5 36.2 1.0
C G:ASP109 3.5 30.6 1.0
CG G:ASP109 3.6 35.2 1.0
C G:GLN196 3.7 32.9 1.0
N G:VAL40 3.8 34.5 1.0
CA G:ASP109 3.9 31.2 1.0
CA G:VAL40 4.1 35.1 1.0
CD G:PRO42 4.2 34.6 1.0
CB G:ASP109 4.3 32.9 1.0
OD2 G:ASP109 4.4 37.2 1.0
CA G:GLN196 4.4 32.5 1.0
C G:THR39 4.5 35.2 1.0
N G:ASN41 4.6 35.6 1.0
O G:VAL345 4.6 26.4 1.0
CB G:THR39 4.7 35.8 1.0
CG2 G:THR197 4.7 32.1 1.0
N G:THR197 4.7 32.9 1.0
N G:ASN110 4.7 30.9 1.0
CB G:VAL40 4.8 34.5 1.0
CB G:GLN196 4.8 31.3 1.0
CA G:THR197 4.8 32.6 1.0
CA G:THR39 4.9 35.2 1.0
CA G:ASN41 4.9 35.8 1.0
CD1 G:ILE48 4.9 38.9 1.0
N G:PRO42 5.0 35.7 1.0

Sodium binding site 8 out of 8 in 2onp

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Sodium binding site 8 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, 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 ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na708

b:55.1
occ:1.00
 O H:ASP109 2.5 34.6 1.0
O H:GLN196 2.5 37.8 1.0
O H:VAL40 2.6 41.4 1.0
O H:HOH2121 2.9 36.1 1.0
OD1 H:ASP109 3.1 36.6 1.0
C H:GLN196 3.6 38.7 1.0
C H:ASP109 3.7 34.2 1.0
C H:VAL40 3.7 40.5 1.0
OG1 H:THR39 3.8 38.0 1.0
CG H:ASP109 4.0 37.9 1.0
CD H:PRO42 4.0 38.4 1.0
O H:VAL345 4.1 36.6 1.0
N H:VAL40 4.1 39.0 1.0
CA H:GLN196 4.2 38.3 1.0
CA H:ASP109 4.3 34.5 1.0
CA H:VAL40 4.4 40.4 1.0
CB H:GLN196 4.4 38.9 1.0
CG2 H:THR197 4.5 33.4 1.0
CG2 H:VAL345 4.7 33.0 1.0
CB H:ASP109 4.7 36.1 1.0
N H:THR197 4.7 37.3 1.0
N H:ASN110 4.7 32.6 1.0
N H:ASN41 4.8 40.4 1.0
N H:PRO42 4.8 39.2 1.0
OD2 H:ASP109 4.9 37.8 1.0
CB H:VAL40 4.9 39.5 1.0
CG H:PRO42 4.9 36.6 1.0
C H:THR39 4.9 38.8 1.0
CA H:THR197 5.0 36.6 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 03:13:43 2024

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