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Sodium in PDB 1o04: CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+

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

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

Protein crystallography data

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+, PDB code: 1o04 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) 50.00 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.211, 152.487, 177.200, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 17.1

Other elements in 1o04:

The structure of CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ (pdb code 1o04). 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 Nad+ and MG2+, PDB code: 1o04:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1o04

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Sodium binding site 1 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na6601

b:15.0
occ:1.00
 O A:HOH7169 2.4 21.2 1.0
O A:VAL40 2.4 14.0 1.0
O A:ASP109 2.4 10.8 1.0
OD1 A:ASP109 2.4 14.3 1.0
O A:GLN196 2.5 14.9 1.0
OG1 A:THR39 2.9 15.3 1.0
C A:ASP109 3.4 10.0 1.0
O A:HOH7167 3.4 18.4 1.0
CG A:ASP109 3.5 15.5 1.0
C A:VAL40 3.5 15.3 1.0
C A:GLN196 3.7 13.8 1.0
N A:VAL40 3.7 13.6 1.0
CA A:ASP109 3.8 9.7 1.0
CB A:ASP109 4.2 11.1 1.0
CA A:VAL40 4.2 14.7 1.0
OD2 A:ASP109 4.3 15.2 1.0
CB A:THR39 4.3 13.9 1.0
CD A:PRO42 4.3 10.8 1.0
C A:THR39 4.4 14.6 1.0
N A:ASN41 4.6 13.3 1.0
CA A:GLN196 4.6 12.6 1.0
N A:THR197 4.6 10.5 1.0
N A:ASN110 4.6 10.3 1.0
CG2 A:THR197 4.6 13.5 1.0
CA A:THR197 4.6 12.4 1.0
CD1 A:ILE48 4.7 14.1 1.0
CA A:THR39 4.7 13.6 1.0
CG2 A:THR39 4.9 15.9 1.0
CB A:VAL40 4.9 16.6 1.0
O A:VAL345 4.9 13.7 1.0
CA A:ASN41 4.9 11.3 1.0

Sodium binding site 2 out of 8 in 1o04

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Sodium binding site 2 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6602

b:10.8
occ:1.00
 O B:HOH7433 2.3 17.4 1.0
O B:ASP109 2.4 9.2 1.0
O B:VAL40 2.4 11.9 1.0
OD1 B:ASP109 2.4 13.3 1.0
O B:GLN196 2.5 15.4 1.0
OG1 B:THR39 2.9 14.3 1.0
O B:HOH7432 3.3 18.3 1.0
C B:ASP109 3.4 7.7 1.0
CG B:ASP109 3.4 13.7 1.0
C B:VAL40 3.5 10.7 1.0
N B:VAL40 3.6 11.5 1.0
C B:GLN196 3.7 12.8 1.0
CA B:ASP109 3.7 8.7 1.0
CB B:ASP109 4.1 8.8 1.0
CA B:VAL40 4.1 11.3 1.0
OD2 B:ASP109 4.3 13.9 1.0
CB B:THR39 4.3 12.4 1.0
C B:THR39 4.4 11.1 1.0
CD B:PRO42 4.4 8.4 1.0
O B:HOH7434 4.4 26.8 1.0
N B:ASN110 4.6 7.3 1.0
CD1 B:ILE48 4.6 11.0 1.0
N B:ASN41 4.6 10.1 1.0
N B:THR197 4.6 9.3 1.0
CG2 B:THR197 4.6 11.4 1.0
CA B:GLN196 4.7 12.3 1.0
CA B:THR197 4.7 9.8 1.0
CA B:THR39 4.7 11.5 1.0
O B:VAL345 4.9 11.1 1.0
CB B:VAL40 4.9 15.2 1.0
CG2 B:THR39 4.9 13.6 1.0
CA B:ASN41 5.0 9.4 1.0

Sodium binding site 3 out of 8 in 1o04

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Sodium binding site 3 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na6603

b:10.9
occ:1.00
 O C:VAL40 2.4 10.6 1.0
O C:HOH7317 2.4 20.9 1.0
O C:ASP109 2.4 8.0 1.0
O C:GLN196 2.4 12.7 1.0
OD1 C:ASP109 2.5 11.8 1.0
OG1 C:THR39 3.1 12.9 1.0
O C:HOH7316 3.2 16.3 1.0
C C:ASP109 3.4 7.1 1.0
CG C:ASP109 3.4 9.3 1.0
C C:VAL40 3.5 9.7 1.0
C C:GLN196 3.7 10.7 1.0
N C:VAL40 3.7 8.4 1.0
CA C:ASP109 3.8 6.9 1.0
CB C:ASP109 4.1 8.6 1.0
CA C:VAL40 4.2 8.5 1.0
OD2 C:ASP109 4.3 9.9 1.0
O C:HOH7318 4.4 20.7 1.0
CD C:PRO42 4.4 7.6 1.0
CB C:THR39 4.4 11.0 1.0
C C:THR39 4.5 8.7 1.0
CA C:THR197 4.6 9.9 1.0
N C:THR197 4.6 8.5 1.0
N C:ASN41 4.6 7.7 1.0
CG2 C:THR197 4.6 9.5 1.0
CA C:GLN196 4.6 9.4 1.0
N C:ASN110 4.6 7.8 1.0
CD1 C:ILE48 4.7 8.5 1.0
CA C:THR39 4.8 8.5 1.0
O C:VAL345 4.9 8.2 1.0
CA C:ASN41 4.9 7.2 1.0
CB C:VAL40 4.9 8.8 1.0

Sodium binding site 4 out of 8 in 1o04

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Sodium binding site 4 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na6604

b:11.4
occ:1.00
 O D:HOH7466 2.4 17.1 1.0
O D:VAL40 2.4 10.5 1.0
O D:ASP109 2.4 9.9 1.0
OD1 D:ASP109 2.4 13.7 1.0
O D:GLN196 2.5 14.0 1.0
OG1 D:THR39 3.0 12.6 1.0
C D:ASP109 3.4 9.1 1.0
CG D:ASP109 3.4 14.5 1.0
C D:VAL40 3.5 11.1 1.0
O D:HOH7465 3.6 15.8 1.0
N D:VAL40 3.7 11.0 1.0
CA D:ASP109 3.7 8.0 1.0
C D:GLN196 3.7 11.9 1.0
CA D:VAL40 4.1 11.5 1.0
CB D:ASP109 4.1 8.4 1.0
OD2 D:ASP109 4.3 13.0 1.0
CD D:PRO42 4.3 8.5 1.0
CB D:THR39 4.3 10.3 1.0
C D:THR39 4.4 10.2 1.0
N D:ASN41 4.6 8.6 1.0
CG2 D:THR197 4.6 10.0 1.0
N D:ASN110 4.6 8.5 1.0
CA D:GLN196 4.6 11.0 1.0
N D:THR197 4.6 9.5 1.0
CD1 D:ILE48 4.6 10.0 1.0
CA D:THR197 4.7 11.1 1.0
CA D:THR39 4.7 9.6 1.0
O D:VAL345 4.9 9.1 1.0
CB D:VAL40 4.9 13.4 1.0
CA D:ASN41 4.9 7.4 1.0
CG2 D:THR39 5.0 13.6 1.0

Sodium binding site 5 out of 8 in 1o04

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Sodium binding site 5 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na6605

b:10.9
occ:1.00
 O E:VAL40 2.3 10.4 1.0
O E:HOH3885 2.3 17.3 1.0
O E:ASP109 2.4 8.4 1.0
OD1 E:ASP109 2.4 11.0 1.0
O E:GLN196 2.5 12.7 1.0
OG1 E:THR39 2.9 13.2 1.0
C E:ASP109 3.3 7.7 1.0
CG E:ASP109 3.4 11.1 1.0
C E:VAL40 3.5 9.9 1.0
O E:HOH3884 3.5 14.4 1.0
N E:VAL40 3.7 10.5 1.0
CA E:ASP109 3.7 7.9 1.0
C E:GLN196 3.7 11.4 1.0
CB E:ASP109 4.1 7.4 1.0
CA E:VAL40 4.2 11.0 1.0
OD2 E:ASP109 4.3 11.1 1.0
CB E:THR39 4.3 12.1 1.0
CD E:PRO42 4.4 8.1 1.0
C E:THR39 4.4 9.8 1.0
N E:ASN110 4.6 8.0 1.0
N E:ASN41 4.6 8.8 1.0
CD1 E:ILE48 4.6 12.4 1.0
N E:THR197 4.6 9.3 1.0
CG2 E:THR197 4.6 10.2 1.0
CA E:THR197 4.7 9.4 1.0
CA E:GLN196 4.7 9.6 1.0
CA E:THR39 4.7 9.3 1.0
O E:VAL345 4.8 9.2 1.0
CG2 E:THR39 4.9 10.2 1.0
CB E:VAL40 4.9 12.8 1.0
CA E:ASN41 4.9 7.8 1.0

Sodium binding site 6 out of 8 in 1o04

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Sodium binding site 6 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na6606

b:11.3
occ:1.00
 O F:HOH2809 2.3 20.4 1.0
O F:VAL40 2.4 9.7 1.0
O F:ASP109 2.4 7.6 1.0
OD1 F:ASP109 2.4 10.9 1.0
O F:GLN196 2.4 11.5 1.0
OG1 F:THR39 3.0 12.9 1.0
O F:HOH2810 3.3 16.6 1.0
C F:ASP109 3.4 7.9 1.0
CG F:ASP109 3.4 10.6 1.0
C F:VAL40 3.5 9.0 1.0
C F:GLN196 3.7 8.9 1.0
CA F:ASP109 3.7 7.1 1.0
N F:VAL40 3.8 9.3 1.0
CB F:ASP109 4.1 8.6 1.0
CA F:VAL40 4.2 8.9 1.0
OD2 F:ASP109 4.3 10.5 1.0
CD F:PRO42 4.3 7.4 1.0
CB F:THR39 4.4 10.3 1.0
O F:HOH2808 4.4 20.4 1.0
C F:THR39 4.5 7.6 1.0
N F:THR197 4.6 7.8 1.0
CG2 F:THR197 4.6 8.6 1.0
N F:ASN41 4.6 7.4 1.0
CA F:THR197 4.6 8.1 1.0
CA F:GLN196 4.6 9.1 1.0
N F:ASN110 4.6 7.7 1.0
CD1 F:ILE48 4.7 8.5 1.0
CA F:THR39 4.8 7.8 1.0
CA F:ASN41 4.9 6.0 1.0
CB F:VAL40 4.9 8.4 1.0
O F:VAL345 4.9 9.0 1.0

Sodium binding site 7 out of 8 in 1o04

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Sodium binding site 7 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na6607

b:12.9
occ:1.00
 O G:HOH3200 2.3 19.5 1.0
O G:ASP109 2.4 9.5 1.0
O G:VAL40 2.4 12.6 1.0
OD1 G:ASP109 2.4 12.5 1.0
O G:GLN196 2.5 15.4 1.0
OG1 G:THR39 2.9 13.9 1.0
C G:ASP109 3.4 9.0 1.0
O G:HOH3199 3.4 16.0 1.0
CG G:ASP109 3.4 14.4 1.0
C G:VAL40 3.5 13.6 1.0
N G:VAL40 3.7 11.5 1.0
CA G:ASP109 3.7 8.7 1.0
C G:GLN196 3.7 12.2 1.0
CB G:ASP109 4.1 11.1 1.0
CA G:VAL40 4.2 14.1 1.0
OD2 G:ASP109 4.3 13.3 1.0
CB G:THR39 4.3 15.4 1.0
C G:THR39 4.4 12.1 1.0
CD G:PRO42 4.4 10.6 1.0
CD1 G:ILE48 4.6 13.7 1.0
N G:ASN110 4.6 10.1 1.0
N G:ASN41 4.6 9.8 1.0
CG2 G:THR197 4.6 10.0 1.0
CA G:THR197 4.6 11.0 1.0
N G:THR197 4.6 9.2 1.0
CA G:GLN196 4.7 10.6 1.0
CA G:THR39 4.7 10.3 1.0
O G:VAL345 4.8 9.0 1.0
CG2 G:THR39 4.9 14.9 1.0
CB G:VAL40 4.9 17.6 1.0
CA G:ASN41 5.0 9.8 1.0

Sodium binding site 8 out of 8 in 1o04

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Sodium binding site 8 out of 8 in the CYS302SER Mutant of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ 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 Nad+ and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na6608

b:11.5
occ:1.00
 O H:HOH4701 2.4 20.7 1.0
O H:ASP109 2.4 9.9 1.0
O H:VAL40 2.4 11.9 1.0
O H:GLN196 2.4 13.2 1.0
OD1 H:ASP109 2.5 12.5 1.0
OG1 H:THR39 3.0 13.3 1.0
O H:HOH4700 3.2 16.9 1.0
C H:ASP109 3.4 7.7 1.0
CG H:ASP109 3.5 13.2 1.0
C H:VAL40 3.6 11.2 1.0
C H:GLN196 3.7 10.7 1.0
N H:VAL40 3.7 10.9 1.0
CA H:ASP109 3.8 8.2 1.0
CB H:ASP109 4.2 9.1 1.0
CA H:VAL40 4.2 12.0 1.0
CD H:PRO42 4.3 8.2 1.0
OD2 H:ASP109 4.3 12.9 1.0
CB H:THR39 4.4 12.5 1.0
O H:HOH4702 4.4 27.8 1.0
C H:THR39 4.5 12.1 1.0
CA H:GLN196 4.5 11.5 1.0
N H:THR197 4.6 8.5 1.0
N H:ASN110 4.6 7.9 1.0
N H:ASN41 4.6 9.6 1.0
CG2 H:THR197 4.6 10.0 1.0
CA H:THR197 4.7 8.9 1.0
CD1 H:ILE48 4.7 9.2 1.0
CA H:THR39 4.8 12.5 1.0
O H:VAL345 4.9 12.1 1.0
CA H:ASN41 5.0 7.1 1.0
CB H:VAL40 5.0 12.0 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 21:03:41 2024

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