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Sodium in PDB 1nzx: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low MG2+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low MG2+

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low MG2+:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low MG2+, PDB code: 1nzx 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) 19.99 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.310, 151.099, 176.952, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.5

Sodium Binding Sites:

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

Sodium binding site 1 out of 8 in 1nzx

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Sodium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1701

b:50.1
occ:1.00
 O A:VAL40 2.4 40.8 1.0
OD1 A:ASP109 2.4 37.8 1.0
O A:GLN196 2.4 42.5 1.0
O A:ASP109 2.5 32.8 1.0
O A:HOH1835 2.5 35.5 1.0
CG A:ASP109 3.4 36.2 1.0
C A:ASP109 3.4 33.3 1.0
OG1 A:THR39 3.4 40.8 1.0
C A:VAL40 3.5 41.5 1.0
C A:GLN196 3.6 41.0 1.0
CA A:ASP109 3.7 33.8 1.0
N A:VAL40 3.8 41.8 1.0
CD A:PRO42 4.1 41.6 1.0
CB A:ASP109 4.1 34.4 1.0
CA A:VAL40 4.2 41.5 1.0
OD2 A:ASP109 4.2 37.0 1.0
CA A:GLN196 4.4 41.0 1.0
C A:THR39 4.4 42.0 1.0
N A:ASN41 4.5 41.4 1.0
CG2 A:THR197 4.6 35.7 1.0
N A:ASN110 4.6 33.3 1.0
N A:THR197 4.6 38.8 1.0
CB A:THR39 4.7 41.8 1.0
CA A:THR197 4.8 36.8 1.0
CA A:THR39 4.8 42.0 1.0
CA A:ASN41 4.9 40.9 1.0
CB A:GLN196 4.9 42.0 1.0
O A:VAL345 4.9 43.1 1.0
N A:PRO42 5.0 42.0 1.0

Sodium binding site 2 out of 8 in 1nzx

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Sodium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1702

b:44.4
occ:1.00
 O B:GLN196 2.3 33.5 1.0
OD1 B:ASP109 2.4 34.0 1.0
O B:VAL40 2.5 34.6 1.0
O B:ASP109 2.5 29.1 1.0
C B:GLN196 3.5 35.1 1.0
CG B:ASP109 3.5 33.1 1.0
OG1 B:THR39 3.5 35.7 1.0
C B:ASP109 3.6 31.1 1.0
C B:VAL40 3.6 34.2 1.0
N B:VAL40 4.0 35.0 1.0
CA B:ASP109 4.0 31.5 1.0
CD B:PRO42 4.1 34.6 1.0
CA B:GLN196 4.1 35.8 1.0
CA B:VAL40 4.3 34.4 1.0
CB B:ASP109 4.3 32.1 1.0
OD2 B:ASP109 4.4 33.9 1.0
CB B:GLN196 4.5 35.3 1.0
O B:VAL345 4.5 32.7 1.0
N B:THR197 4.6 35.1 1.0
CG2 B:THR197 4.6 35.8 1.0
C B:THR39 4.6 33.8 1.0
N B:ASN110 4.7 31.6 1.0
N B:ASN41 4.7 34.2 1.0
CA B:THR197 4.8 35.1 1.0
CB B:THR39 4.8 36.0 1.0
O B:HOH2510 4.9 34.5 1.0
CD1 B:ILE48 5.0 37.0 1.0
CB B:VAL40 5.0 33.8 1.0
CA B:THR39 5.0 34.9 1.0
CG2 B:VAL345 5.0 29.7 1.0
N B:PRO42 5.0 35.4 1.0

Sodium binding site 3 out of 8 in 1nzx

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Sodium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1703

b:55.3
occ:1.00
 O C:VAL40 2.4 28.3 1.0
O C:GLN196 2.4 25.3 1.0
OD1 C:ASP109 2.7 29.2 1.0
O C:ASP109 2.7 27.9 1.0
O C:HOH3606 2.9 32.4 1.0
C C:GLN196 3.5 24.3 1.0
C C:VAL40 3.5 29.0 1.0
OG1 C:THR39 3.6 28.2 1.0
O C:HOH3681 3.7 32.9 1.0
C C:ASP109 3.8 26.2 1.0
N C:VAL40 3.8 28.3 1.0
CG C:ASP109 3.8 28.1 1.0
CD C:PRO42 4.1 25.7 1.0
CA C:GLN196 4.1 24.9 1.0
CA C:VAL40 4.1 29.3 1.0
CA C:ASP109 4.3 26.4 1.0
O C:VAL345 4.3 22.7 1.0
CB C:GLN196 4.4 25.4 1.0
C C:THR39 4.6 28.4 1.0
CG2 C:THR197 4.6 17.1 1.0
CB C:ASP109 4.6 26.8 1.0
N C:THR197 4.6 22.8 1.0
N C:ASN41 4.7 28.7 1.0
OD2 C:ASP109 4.7 25.6 1.0
CB C:VAL40 4.8 29.5 1.0
CB C:THR39 4.8 28.3 1.0
CA C:THR39 4.9 28.0 1.0
CA C:THR197 4.9 20.7 1.0
N C:PRO42 4.9 26.6 1.0
N C:ASN110 5.0 26.4 1.0
CG C:PRO42 5.0 27.1 1.0

Sodium binding site 4 out of 8 in 1nzx

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Sodium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1704

b:95.0
occ:1.00
 O D:GLN196 2.4 49.6 1.0
OD1 D:ASP109 2.4 51.9 1.0
O D:VAL40 2.4 47.5 1.0
OG1 D:THR39 2.9 46.2 1.0
O D:ASP109 3.2 44.9 1.0
N D:VAL40 3.3 46.1 1.0
C D:VAL40 3.4 45.7 1.0
C D:GLN196 3.5 47.0 1.0
CG D:ASP109 3.6 48.8 1.0
CA D:VAL40 3.8 45.6 1.0
C D:THR39 3.9 46.1 1.0
CA D:GLN196 4.1 46.3 1.0
CB D:THR39 4.1 46.6 1.0
C D:ASP109 4.1 45.2 1.0
CA D:THR39 4.2 45.2 1.0
OD2 D:ASP109 4.4 49.4 1.0
CA D:ASP109 4.4 44.9 1.0
CB D:GLN196 4.6 46.5 1.0
N D:THR197 4.6 46.7 1.0
CB D:VAL40 4.6 46.6 1.0
N D:ASN41 4.6 46.0 1.0
CB D:ASP109 4.6 45.1 1.0
CD D:PRO42 4.7 48.9 1.0
O D:THR39 4.7 46.7 1.0
CG D:PRO42 4.8 48.7 1.0
CG2 D:THR197 4.9 46.2 1.0
CA D:THR197 4.9 46.1 1.0
O D:VAL345 5.0 47.6 1.0

Sodium binding site 5 out of 8 in 1nzx

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Sodium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1705

b:52.9
occ:1.00
 O E:GLN196 2.3 37.4 1.0
OD1 E:ASP109 2.4 36.4 1.0
O E:ASP109 2.4 33.9 1.0
O E:VAL40 2.6 37.4 1.0
OG1 E:THR39 3.3 29.4 1.0
CG E:ASP109 3.4 35.9 1.0
C E:ASP109 3.4 33.2 1.0
C E:GLN196 3.5 36.1 1.0
C E:VAL40 3.7 36.0 1.0
O E:HOH5593 3.7 34.0 1.0
CA E:ASP109 3.8 34.0 1.0
N E:VAL40 4.0 35.5 1.0
CB E:ASP109 4.1 34.2 1.0
OD2 E:ASP109 4.2 36.0 1.0
CA E:GLN196 4.3 35.8 1.0
CD E:PRO42 4.3 37.5 1.0
CG2 E:THR197 4.4 35.5 1.0
CA E:VAL40 4.4 36.1 1.0
N E:THR197 4.5 35.9 1.0
C E:THR39 4.6 34.6 1.0
CB E:THR39 4.6 33.4 1.0
CA E:THR197 4.6 35.9 1.0
N E:ASN110 4.6 32.7 1.0
CB E:GLN196 4.6 35.1 1.0
O E:VAL345 4.7 30.1 1.0
N E:ASN41 4.8 35.9 1.0
CA E:THR39 4.9 33.8 1.0

Sodium binding site 6 out of 8 in 1nzx

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Sodium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1706

b:39.8
occ:1.00
 O F:VAL40 2.3 30.9 1.0
O F:GLN196 2.5 24.5 1.0
OD1 F:ASP109 2.6 31.4 1.0
O F:ASP109 2.6 23.9 1.0
C F:VAL40 3.4 29.8 1.0
OG1 F:THR39 3.4 26.3 1.0
C F:GLN196 3.7 23.6 1.0
C F:ASP109 3.7 25.6 1.0
CG F:ASP109 3.7 26.8 1.0
N F:VAL40 3.7 29.5 1.0
CA F:VAL40 4.0 30.1 1.0
CA F:ASP109 4.1 24.6 1.0
CD F:PRO42 4.1 24.6 1.0
CA F:GLN196 4.3 23.7 1.0
O F:HOH6705 4.4 31.9 1.0
CB F:ASP109 4.4 24.8 1.0
C F:THR39 4.5 27.5 1.0
OD2 F:ASP109 4.5 23.4 1.0
N F:ASN41 4.5 29.0 1.0
O F:VAL345 4.5 23.6 1.0
CB F:GLN196 4.6 24.8 1.0
CG2 F:THR197 4.6 19.3 1.0
CB F:THR39 4.7 26.4 1.0
N F:THR197 4.7 21.7 1.0
CB F:VAL40 4.8 30.3 1.0
CA F:THR39 4.8 26.5 1.0
O F:HOH6616 4.9 32.1 1.0
N F:ASN110 4.9 24.9 1.0
N F:PRO42 4.9 26.5 1.0
CA F:ASN41 4.9 26.8 1.0
CA F:THR197 5.0 18.9 1.0

Sodium binding site 7 out of 8 in 1nzx

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Sodium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1707

b:33.8
occ:1.00
 O G:VAL40 2.2 35.5 1.0
OD1 G:ASP109 2.3 32.0 1.0
O G:GLN196 2.5 31.6 1.0
O G:ASP109 2.8 31.0 1.0
OG1 G:THR39 3.2 39.0 1.0
C G:VAL40 3.3 35.5 1.0
CG G:ASP109 3.5 32.3 1.0
N G:VAL40 3.5 36.0 1.0
C G:GLN196 3.7 32.0 1.0
C G:ASP109 3.7 30.4 1.0
CA G:VAL40 3.9 36.5 1.0
CA G:ASP109 4.0 29.8 1.0
C G:THR39 4.1 36.0 1.0
CD G:PRO42 4.2 32.6 1.0
OD2 G:ASP109 4.3 30.9 1.0
CB G:ASP109 4.3 29.9 1.0
CA G:GLN196 4.4 32.7 1.0
CB G:THR39 4.4 38.1 1.0
N G:ASN41 4.4 34.6 1.0
CA G:THR39 4.5 36.8 1.0
CB G:VAL40 4.7 36.6 1.0
N G:THR197 4.7 31.7 1.0
CD1 G:ILE48 4.8 37.3 1.0
CG2 G:THR197 4.9 30.2 1.0
CA G:ASN41 4.9 34.8 1.0
O G:THR39 4.9 36.7 1.0
CB G:GLN196 4.9 32.4 1.0
CA G:THR197 4.9 30.1 1.0
O G:VAL345 4.9 28.5 1.0
N G:ASN110 5.0 30.2 1.0

Sodium binding site 8 out of 8 in 1nzx

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Sodium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ in the Presence of Low 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 Nad+ in the Presence of Low MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1708

b:55.2
occ:1.00
 O H:GLN196 2.3 41.9 1.0
O H:VAL40 2.4 48.1 1.0
OD1 H:ASP109 2.6 44.0 1.0
O H:ASP109 2.8 38.0 1.0
C H:GLN196 3.4 41.0 1.0
OG1 H:THR39 3.5 48.2 1.0
C H:VAL40 3.5 46.2 1.0
N H:VAL40 3.6 45.9 1.0
CG H:ASP109 3.8 42.6 1.0
C H:ASP109 3.9 37.5 1.0
CA H:VAL40 4.0 46.2 1.0
CA H:GLN196 4.0 41.4 1.0
CA H:ASP109 4.3 38.9 1.0
C H:THR39 4.3 46.2 1.0
CD H:PRO42 4.3 44.4 1.0
CB H:GLN196 4.4 40.8 1.0
N H:THR197 4.6 39.8 1.0
CB H:ASP109 4.6 40.1 1.0
O H:VAL345 4.6 38.3 1.0
OD2 H:ASP109 4.6 41.6 1.0
CA H:THR39 4.6 46.7 1.0
CB H:THR39 4.7 46.4 1.0
N H:ASN41 4.7 45.5 1.0
CB H:VAL40 4.7 46.9 1.0
CG2 H:THR197 4.7 37.8 1.0
CA H:THR197 4.9 38.0 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 21:01:30 2024

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