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

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

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

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of Low MG2+, PDB code: 1nzz 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) 19.98 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.307, 150.897, 177.031, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 24.8

Other elements in 1nzz:

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

Sodium binding site 1 out of 8 in 1nzz

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

b:46.1
occ:1.00
 O A:GLN196 2.4 45.6 1.0
O A:VAL40 2.4 50.9 1.0
OD1 A:ASP109 2.4 43.3 1.0
O A:ASP109 2.7 40.5 1.0
C A:VAL40 3.5 50.6 1.0
CG A:ASP109 3.5 43.1 1.0
OG1 A:THR39 3.5 51.2 1.0
C A:GLN196 3.6 43.3 1.0
C A:ASP109 3.7 39.9 1.0
N A:VAL40 3.8 51.4 1.0
CA A:ASP109 4.1 40.5 1.0
CA A:VAL40 4.2 51.0 1.0
CD A:PRO42 4.2 49.7 1.0
CA A:GLN196 4.2 43.6 1.0
OD2 A:ASP109 4.3 43.8 1.0
CB A:ASP109 4.4 41.3 1.0
CB A:GLN196 4.6 43.6 1.0
O A:VAL345 4.6 49.3 1.0
C A:THR39 4.6 51.5 1.0
CG2 A:THR197 4.6 38.2 1.0
N A:THR197 4.6 40.4 1.0
N A:ASN41 4.6 49.9 1.0
CB A:THR39 4.8 51.8 1.0
CA A:THR197 4.9 38.6 1.0
N A:ASN110 4.9 40.1 1.0
CA A:THR39 4.9 51.1 1.0
CA A:ASN41 4.9 48.2 1.0
CB A:VAL40 5.0 50.9 1.0

Sodium binding site 2 out of 8 in 1nzz

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

b:36.2
occ:1.00
 OD1 B:ASP109 2.3 44.7 1.0
O B:VAL40 2.4 43.6 1.0
O B:ASP109 2.4 40.3 1.0
O B:GLN196 2.5 36.9 1.0
C B:ASP109 3.5 42.1 1.0
CG B:ASP109 3.5 45.4 1.0
OG1 B:THR39 3.5 43.6 1.0
C B:VAL40 3.6 42.2 1.0
C B:GLN196 3.6 38.2 1.0
CA B:ASP109 3.9 42.1 1.0
N B:VAL40 3.9 43.4 1.0
CD B:PRO42 4.1 42.4 1.0
CA B:VAL40 4.2 42.6 1.0
CB B:ASP109 4.3 43.9 1.0
CA B:GLN196 4.3 38.8 1.0
OD2 B:ASP109 4.4 48.2 1.0
CG2 B:THR197 4.5 40.1 1.0
O B:VAL345 4.6 39.2 1.0
N B:ASN41 4.6 41.7 1.0
C B:THR39 4.7 42.9 1.0
N B:ASN110 4.7 42.3 1.0
CB B:GLN196 4.7 38.6 1.0
N B:THR197 4.7 38.2 1.0
CB B:THR39 4.8 43.4 1.0
O B:HOH2582 4.9 57.0 1.0
CA B:THR197 4.9 39.3 1.0
CA B:ASN41 4.9 41.8 1.0
CD1 B:ILE48 4.9 46.4 1.0
CB B:VAL40 5.0 43.1 1.0
N B:PRO42 5.0 42.3 1.0

Sodium binding site 3 out of 8 in 1nzz

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

b:37.9
occ:1.00
 O C:GLN196 2.3 26.0 1.0
O C:VAL40 2.4 31.8 1.0
OD1 C:ASP109 2.4 35.7 1.0
O C:ASP109 2.6 32.0 1.0
O C:HOH3662 3.2 48.4 1.0
OG1 C:THR39 3.4 31.8 1.0
CG C:ASP109 3.5 32.4 1.0
C C:VAL40 3.5 30.2 1.0
C C:GLN196 3.5 25.8 1.0
C C:ASP109 3.6 29.5 1.0
N C:VAL40 3.8 28.7 1.0
CA C:ASP109 4.0 29.8 1.0
CA C:VAL40 4.2 29.7 1.0
CD C:PRO42 4.2 26.6 1.0
CA C:GLN196 4.3 25.5 1.0
CB C:ASP109 4.3 31.3 1.0
OD2 C:ASP109 4.3 32.7 1.0
CG2 C:THR197 4.5 20.8 1.0
C C:THR39 4.5 28.9 1.0
N C:THR197 4.6 23.8 1.0
CB C:GLN196 4.6 25.1 1.0
N C:ASN41 4.6 29.9 1.0
CB C:THR39 4.7 29.7 1.0
CA C:THR197 4.8 23.3 1.0
O C:VAL345 4.8 25.1 1.0
N C:ASN110 4.8 28.6 1.0
CA C:THR39 4.8 28.5 1.0
CB C:VAL40 4.9 29.5 1.0
CA C:ASN41 5.0 27.8 1.0

Sodium binding site 4 out of 8 in 1nzz

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

b:89.0
occ:1.00
 O D:VAL40 2.3 55.7 1.0
OD1 D:ASP109 2.4 52.5 1.0
O D:GLN196 2.5 55.4 1.0
OG1 D:THR39 3.0 54.4 1.0
O D:ASP109 3.1 45.7 1.0
N D:VAL40 3.3 55.2 1.0
C D:VAL40 3.3 54.5 1.0
CG D:ASP109 3.6 51.2 1.0
C D:GLN196 3.6 52.6 1.0
CA D:VAL40 3.8 55.1 1.0
C D:THR39 4.0 54.1 1.0
C D:ASP109 4.0 48.0 1.0
CB D:THR39 4.2 54.3 1.0
CA D:GLN196 4.2 52.1 1.0
CA D:ASP109 4.3 47.6 1.0
CA D:THR39 4.3 53.7 1.0
OD2 D:ASP109 4.3 50.2 1.0
CD1 D:ILE48 4.4 56.6 1.0
N D:ASN41 4.5 53.4 1.0
CB D:ASP109 4.5 48.0 1.0
CB D:VAL40 4.6 55.8 1.0
CD D:PRO42 4.7 54.6 1.0
N D:THR197 4.7 52.5 1.0
CB D:GLN196 4.8 53.3 1.0
O D:THR39 4.8 54.7 1.0
CG2 D:THR197 4.8 50.6 1.0
CA D:THR197 5.0 52.3 1.0
CA D:ASN41 5.0 53.4 1.0

Sodium binding site 5 out of 8 in 1nzz

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

b:44.5
occ:1.00
 OD1 E:ASP109 2.2 41.9 1.0
O E:ASP109 2.4 43.5 1.0
O E:GLN196 2.4 41.2 1.0
O E:VAL40 2.5 44.3 1.0
CG E:ASP109 3.2 44.4 1.0
OG1 E:THR39 3.3 37.6 1.0
C E:ASP109 3.4 43.7 1.0
O E:HOH5580 3.5 29.3 1.0
C E:VAL40 3.6 42.9 1.0
C E:GLN196 3.6 40.0 1.0
CA E:ASP109 3.7 43.9 1.0
N E:VAL40 4.0 42.4 1.0
CB E:ASP109 4.0 44.3 1.0
OD2 E:ASP109 4.0 44.4 1.0
CD E:PRO42 4.3 44.4 1.0
CA E:VAL40 4.3 42.8 1.0
CG2 E:THR197 4.4 42.7 1.0
CA E:GLN196 4.4 40.1 1.0
C E:THR39 4.5 42.3 1.0
N E:ASN110 4.6 43.0 1.0
N E:THR197 4.6 40.2 1.0
CB E:THR39 4.6 41.0 1.0
N E:ASN41 4.7 42.6 1.0
CA E:THR197 4.7 41.6 1.0
O E:VAL345 4.8 40.5 1.0
CA E:THR39 4.9 41.4 1.0
CB E:GLN196 4.9 38.6 1.0
CA E:ASN41 5.0 42.7 1.0
CD1 E:ILE48 5.0 48.3 1.0

Sodium binding site 6 out of 8 in 1nzz

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

b:31.1
occ:1.00
 O F:VAL40 2.2 33.1 1.0
OD1 F:ASP109 2.3 33.3 1.0
O F:ASP109 2.5 29.7 1.0
O F:GLN196 2.6 26.4 1.0
OG1 F:THR39 3.2 29.5 1.0
C F:VAL40 3.4 31.8 1.0
CG F:ASP109 3.4 31.6 1.0
C F:ASP109 3.5 28.8 1.0
N F:VAL40 3.7 31.0 1.0
CA F:ASP109 3.7 27.8 1.0
C F:GLN196 3.8 25.7 1.0
CA F:VAL40 4.0 31.6 1.0
CB F:ASP109 4.1 29.8 1.0
CD F:PRO42 4.2 30.1 1.0
C F:THR39 4.4 29.4 1.0
OD2 F:ASP109 4.4 31.4 1.0
N F:ASN41 4.4 32.4 1.0
CG2 F:THR197 4.5 23.3 1.0
CB F:THR39 4.5 27.6 1.0
CA F:GLN196 4.6 25.2 1.0
CD1 F:ILE48 4.6 36.1 1.0
N F:ASN110 4.7 27.4 1.0
CA F:ASN41 4.7 31.2 1.0
CA F:THR39 4.8 28.1 1.0
N F:THR197 4.8 25.1 1.0
CA F:THR197 4.9 24.2 1.0
O F:HOH6594 4.9 37.5 1.0
CB F:VAL40 4.9 30.2 1.0
O F:VAL345 4.9 28.1 1.0
N F:PRO42 5.0 30.7 1.0
CB F:GLN196 5.0 25.4 1.0

Sodium binding site 7 out of 8 in 1nzz

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

b:51.2
occ:1.00
 O G:VAL40 2.2 41.9 1.0
OD1 G:ASP109 2.4 39.2 1.0
O G:ASP109 2.5 34.3 1.0
O G:GLN196 2.5 38.0 1.0
C G:VAL40 3.4 41.6 1.0
C G:ASP109 3.5 35.9 1.0
CG G:ASP109 3.5 38.4 1.0
OG1 G:THR39 3.5 43.0 1.0
C G:GLN196 3.7 37.9 1.0
N G:VAL40 3.8 43.0 1.0
CA G:ASP109 3.9 36.6 1.0
CA G:VAL40 4.1 42.2 1.0
CD G:PRO42 4.1 38.2 1.0
CB G:ASP109 4.2 36.7 1.0
OD2 G:ASP109 4.3 37.8 1.0
N G:ASN41 4.5 39.5 1.0
C G:THR39 4.5 43.8 1.0
CA G:GLN196 4.5 37.5 1.0
CG2 G:THR197 4.5 39.1 1.0
N G:ASN110 4.7 36.6 1.0
CB G:THR39 4.7 44.3 1.0
N G:THR197 4.7 37.8 1.0
O G:VAL345 4.7 37.3 1.0
CA G:ASN41 4.8 38.8 1.0
CD1 G:ILE48 4.8 45.8 1.0
CB G:VAL40 4.8 42.2 1.0
CA G:THR197 4.8 37.8 1.0
CA G:THR39 4.9 43.4 1.0
CB G:GLN196 5.0 37.1 1.0
N G:PRO42 5.0 38.5 1.0

Sodium binding site 8 out of 8 in 1nzz

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

b:60.7
occ:1.00
 OD1 H:ASP109 2.2 42.4 1.0
O H:GLN196 2.3 50.0 1.0
O H:VAL40 2.4 57.8 1.0
OG1 H:THR39 3.0 57.9 1.0
O H:ASP109 3.0 42.9 1.0
CG H:ASP109 3.5 44.3 1.0
C H:VAL40 3.5 56.6 1.0
C H:GLN196 3.5 48.2 1.0
N H:VAL40 3.5 55.8 1.0
CA H:VAL40 4.0 56.4 1.0
C H:ASP109 4.0 42.5 1.0
C H:THR39 4.1 55.9 1.0
CA H:GLN196 4.2 48.0 1.0
CA H:ASP109 4.2 43.4 1.0
CB H:THR39 4.2 56.7 1.0
OD2 H:ASP109 4.3 43.7 1.0
CA H:THR39 4.4 56.5 1.0
CB H:ASP109 4.4 43.3 1.0
N H:THR197 4.6 47.5 1.0
CD H:PRO42 4.6 53.9 1.0
N H:ASN41 4.6 55.7 1.0
CB H:GLN196 4.7 46.7 1.0
CB H:VAL40 4.8 56.2 1.0
CD1 H:ILE48 4.8 54.6 1.0
O H:THR39 4.8 55.2 1.0
CA H:THR197 4.8 45.7 1.0
CG2 H:THR197 5.0 43.8 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 21:01:39 2024

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