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Sodium in PDB 1nzw: CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+

Enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+

All present enzymatic activity of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+:
1.2.1.3;

Protein crystallography data

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+, PDB code: 1nzw 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) 24.65 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.361, 150.494, 176.923, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 25.2

Other elements in 1nzw:

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ (pdb code 1nzw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+, PDB code: 1nzw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1nzw

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Sodium binding site 1 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1601

b:31.2
occ:1.00
 O A:GLN196 2.3 34.1 1.0
OD1 A:ASP109 2.4 31.8 1.0
O A:VAL40 2.4 39.0 1.0
O A:ASP109 2.7 30.2 1.0
OG1 A:THR39 3.4 36.5 1.0
CG A:ASP109 3.4 33.3 1.0
C A:GLN196 3.5 32.6 1.0
C A:VAL40 3.6 38.8 1.0
N A:VAL40 3.7 39.2 1.0
C A:ASP109 3.7 30.1 1.0
CA A:ASP109 4.1 30.2 1.0
CA A:VAL40 4.1 38.9 1.0
OD2 A:ASP109 4.2 34.7 1.0
CA A:GLN196 4.2 32.9 1.0
CB A:ASP109 4.4 31.8 1.0
CD A:PRO42 4.4 36.3 1.0
C A:THR39 4.4 39.2 1.0
N A:THR197 4.5 31.4 1.0
CG2 A:THR197 4.6 26.2 1.0
CB A:THR39 4.6 38.2 1.0
CB A:GLN196 4.7 31.7 1.0
CA A:THR197 4.7 29.9 1.0
N A:ASN41 4.7 38.4 1.0
CA A:THR39 4.7 38.1 1.0
O A:VAL345 4.8 35.1 1.0
CB A:VAL40 4.8 38.3 1.0
N A:ASN110 4.9 29.5 1.0

Sodium binding site 2 out of 8 in 1nzw

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Sodium binding site 2 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1602

b:41.9
occ:1.00
 OD1 B:ASP109 2.2 30.5 1.0
O B:GLN196 2.2 24.8 1.0
O B:VAL40 2.5 34.8 1.0
O B:HOH2582 2.5 35.6 1.0
OG1 B:THR39 2.8 33.0 1.0
O B:ASP109 3.0 27.7 1.0
O B:HOH2571 3.1 26.7 1.0
C B:GLN196 3.4 27.7 1.0
CG B:ASP109 3.4 30.8 1.0
N B:VAL40 3.5 34.7 1.0
C B:VAL40 3.6 33.5 1.0
C B:ASP109 4.0 28.6 1.0
CA B:VAL40 4.0 33.8 1.0
C B:THR39 4.1 34.9 1.0
CB B:THR39 4.1 34.9 1.0
CA B:GLN196 4.2 28.5 1.0
CA B:ASP109 4.2 27.8 1.0
OD2 B:ASP109 4.2 30.8 1.0
CA B:THR39 4.3 34.6 1.0
CB B:ASP109 4.4 28.6 1.0
N B:THR197 4.4 28.4 1.0
CG2 B:THR197 4.6 32.1 1.0
CA B:THR197 4.6 30.0 1.0
N B:ASN41 4.7 31.8 1.0
CD B:PRO42 4.8 31.4 1.0
CB B:GLN196 4.8 25.6 1.0
CB B:VAL40 4.8 33.0 1.0
O B:THR39 4.9 32.5 1.0
CD1 B:ILE48 5.0 30.9 1.0
CG2 B:THR39 5.0 34.7 1.0

Sodium binding site 3 out of 8 in 1nzw

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Sodium binding site 3 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1603

b:27.4
occ:1.00
 O C:HOH3549 2.1 26.0 1.0
O C:VAL40 2.3 24.8 1.0
O C:GLN196 2.4 22.5 1.0
OD1 C:ASP109 2.4 16.2 1.0
O C:ASP109 2.8 17.9 1.0
OG1 C:THR39 3.4 26.4 1.0
C C:VAL40 3.4 24.6 1.0
O C:HOH3561 3.5 40.8 1.0
N C:VAL40 3.5 23.9 1.0
C C:GLN196 3.5 22.3 1.0
CG C:ASP109 3.6 15.9 1.0
C C:ASP109 3.9 16.7 1.0
CA C:VAL40 3.9 24.7 1.0
CA C:ASP109 4.2 17.3 1.0
CA C:GLN196 4.3 21.7 1.0
CD C:PRO42 4.3 21.6 1.0
C C:THR39 4.3 23.8 1.0
OD2 C:ASP109 4.5 12.4 1.0
CB C:ASP109 4.5 17.1 1.0
N C:ASN41 4.5 24.1 1.0
CB C:THR39 4.6 24.3 1.0
N C:THR197 4.6 22.7 1.0
CG2 C:THR197 4.7 22.0 1.0
CA C:THR39 4.7 23.7 1.0
CB C:VAL40 4.7 25.9 1.0
CB C:GLN196 4.7 22.1 1.0
O C:VAL345 4.7 22.8 1.0
CA C:THR197 4.8 21.3 1.0
CD1 C:ILE48 4.9 24.9 1.0
CA C:ASN41 5.0 22.0 1.0

Sodium binding site 4 out of 8 in 1nzw

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Sodium binding site 4 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1604

b:41.6
occ:1.00
 O D:VAL40 2.3 33.6 1.0
OD1 D:ASP109 2.4 34.4 1.0
O D:GLN196 2.4 33.3 1.0
O D:ASP109 2.5 29.8 1.0
OG1 D:THR39 3.3 32.7 1.0
C D:VAL40 3.5 34.1 1.0
C D:ASP109 3.6 30.9 1.0
CG D:ASP109 3.6 35.0 1.0
C D:GLN196 3.6 31.4 1.0
N D:VAL40 3.7 34.1 1.0
CA D:ASP109 4.0 30.6 1.0
CA D:VAL40 4.1 34.7 1.0
CD D:PRO42 4.3 35.6 1.0
CG2 D:THR197 4.3 30.8 1.0
CB D:ASP109 4.4 32.0 1.0
CA D:GLN196 4.4 30.8 1.0
C D:THR39 4.5 33.3 1.0
OD2 D:ASP109 4.5 35.3 1.0
CD1 D:ILE48 4.6 34.8 1.0
N D:ASN41 4.6 33.6 1.0
N D:THR197 4.6 30.4 1.0
CB D:THR39 4.6 32.6 1.0
O D:VAL345 4.7 35.7 1.0
CA D:THR197 4.7 30.4 1.0
N D:ASN110 4.8 30.8 1.0
CB D:GLN196 4.8 31.6 1.0
CA D:THR39 4.8 33.5 1.0
CB D:VAL40 4.9 34.7 1.0
CA D:ASN41 4.9 34.8 1.0

Sodium binding site 5 out of 8 in 1nzw

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Sodium binding site 5 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1605

b:40.3
occ:1.00
 O E:GLN196 2.3 32.2 1.0
O E:ASP109 2.4 30.0 1.0
OD1 E:ASP109 2.4 30.1 1.0
O E:VAL40 2.7 34.7 1.0
C E:GLN196 3.4 32.4 1.0
OG1 E:THR39 3.5 29.9 1.0
C E:ASP109 3.5 32.0 1.0
CG E:ASP109 3.5 30.1 1.0
C E:VAL40 3.8 33.8 1.0
CA E:ASP109 4.0 32.2 1.0
N E:VAL40 4.1 33.2 1.0
CG2 E:THR197 4.2 34.9 1.0
CA E:GLN196 4.2 32.2 1.0
CD E:PRO42 4.3 36.2 1.0
CB E:ASP109 4.3 31.7 1.0
OD2 E:ASP109 4.4 32.1 1.0
N E:THR197 4.4 32.5 1.0
O E:VAL345 4.5 32.7 1.0
CA E:VAL40 4.5 33.6 1.0
CA E:THR197 4.6 32.3 1.0
CB E:GLN196 4.6 31.2 1.0
N E:ASN110 4.6 32.1 1.0
CB E:THR39 4.8 33.9 1.0
C E:THR39 4.8 33.9 1.0
CG2 E:VAL345 4.9 28.4 1.0
N E:ASN41 4.9 33.8 1.0

Sodium binding site 6 out of 8 in 1nzw

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Sodium binding site 6 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1606

b:27.6
occ:1.00
 O F:GLN196 2.3 22.8 1.0
O F:VAL40 2.4 25.6 1.0
OD1 F:ASP109 2.5 23.9 1.0
O F:ASP109 2.7 21.9 1.0
OG1 F:THR39 3.4 24.1 1.0
C F:GLN196 3.5 21.1 1.0
C F:VAL40 3.5 25.9 1.0
CG F:ASP109 3.7 22.7 1.0
C F:ASP109 3.7 21.3 1.0
N F:VAL40 3.8 25.5 1.0
CA F:VAL40 4.1 25.3 1.0
CA F:ASP109 4.2 20.3 1.0
CA F:GLN196 4.2 19.7 1.0
CD F:PRO42 4.3 22.8 1.0
CG2 F:THR197 4.5 16.6 1.0
O F:VAL345 4.5 28.1 1.0
CB F:ASP109 4.5 21.5 1.0
C F:THR39 4.5 24.0 1.0
N F:THR197 4.5 20.9 1.0
CB F:GLN196 4.5 21.8 1.0
OD2 F:ASP109 4.5 20.8 1.0
O F:HOH6593 4.6 31.6 1.0
N F:ASN41 4.7 26.2 1.0
CB F:THR39 4.7 22.6 1.0
CA F:THR197 4.8 18.4 1.0
CA F:THR39 4.8 22.6 1.0
CB F:VAL40 4.9 23.9 1.0
N F:ASN110 4.9 19.8 1.0

Sodium binding site 7 out of 8 in 1nzw

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Sodium binding site 7 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1607

b:34.9
occ:1.00
 O G:VAL40 2.3 30.9 1.0
OD1 G:ASP109 2.4 23.2 1.0
O G:GLN196 2.4 29.5 1.0
O G:ASP109 2.5 25.5 1.0
OG1 G:THR39 3.3 35.0 1.0
C G:VAL40 3.4 31.9 1.0
CG G:ASP109 3.5 22.9 1.0
C G:ASP109 3.6 26.5 1.0
C G:GLN196 3.6 30.5 1.0
N G:VAL40 3.7 33.7 1.0
CA G:ASP109 3.9 25.6 1.0
CA G:VAL40 4.1 32.4 1.0
CD G:PRO42 4.2 28.5 1.0
CB G:ASP109 4.3 24.1 1.0
OD2 G:ASP109 4.4 22.2 1.0
C G:THR39 4.4 33.9 1.0
CG2 G:THR197 4.4 29.5 1.0
CA G:GLN196 4.5 29.8 1.0
N G:ASN41 4.5 29.9 1.0
CB G:THR39 4.6 34.2 1.0
CD1 G:ILE48 4.6 34.3 1.0
N G:THR197 4.6 30.9 1.0
CA G:THR197 4.7 30.1 1.0
CA G:THR39 4.8 33.7 1.0
N G:ASN110 4.8 28.5 1.0
CB G:VAL40 4.8 32.0 1.0
O G:VAL345 4.8 30.3 1.0
CA G:ASN41 4.9 30.2 1.0
CB G:GLN196 4.9 29.0 1.0

Sodium binding site 8 out of 8 in 1nzw

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Sodium binding site 8 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1608

b:34.5
occ:1.00
 O H:GLN196 2.3 36.4 1.0
OD1 H:ASP109 2.4 35.1 1.0
O H:VAL40 2.5 41.4 1.0
O H:ASP109 2.6 29.3 1.0
O H:HOH8543 3.1 28.2 1.0
C H:GLN196 3.5 34.1 1.0
OG1 H:THR39 3.5 38.4 1.0
CG H:ASP109 3.6 34.6 1.0
C H:VAL40 3.6 39.4 1.0
C H:ASP109 3.7 30.8 1.0
N H:VAL40 3.9 38.4 1.0
CA H:ASP109 4.1 31.6 1.0
CA H:GLN196 4.2 32.8 1.0
CA H:VAL40 4.3 38.8 1.0
CD H:PRO42 4.3 38.8 1.0
CB H:ASP109 4.5 32.8 1.0
O H:VAL345 4.5 37.2 1.0
CG2 H:THR197 4.5 31.8 1.0
OD2 H:ASP109 4.5 35.1 1.0
N H:THR197 4.5 34.3 1.0
CB H:GLN196 4.6 29.8 1.0
C H:THR39 4.6 38.1 1.0
CA H:THR197 4.7 33.3 1.0
N H:ASN41 4.8 38.4 1.0
CB H:THR39 4.8 37.9 1.0
N H:ASN110 4.8 30.6 1.0
CA H:THR39 4.9 37.8 1.0
CG2 H:VAL345 4.9 34.4 1.0
CB H:VAL40 4.9 38.7 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 21:01:24 2024

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