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Magnesium in PDB 1o00: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations

All present enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations:
1.2.1.3;

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations, PDB code: 1o00 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) 29.81 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.911, 150.671, 177.133, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.2

Other elements in 1o00:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations (pdb code 1o00). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations, PDB code: 1o00:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o00

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Magnesium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2601

b:54.4
occ:1.00
 O1N A:NAD1502 2.1 29.4 0.5
O2A A:NAD1502 2.5 25.9 0.5
O2A A:NAD1502 2.6 30.7 0.5
PN A:NAD1502 3.5 29.3 0.5
O1A A:NAD1502 3.6 29.0 0.5
PA A:NAD1502 3.6 27.6 0.5
PA A:NAD1502 3.7 24.2 0.5
CG1 A:ILE249 3.9 19.8 1.0
O3 A:NAD1502 4.0 28.2 0.5
O2N A:NAD1502 4.1 29.1 0.5
C8A A:NAD1502 4.2 20.8 0.5
C8A A:NAD1502 4.2 19.0 0.5
CD1 A:ILE249 4.3 20.1 1.0
O5B A:NAD1502 4.4 28.6 0.5
N7A A:NAD1502 4.5 20.5 0.5
N7A A:NAD1502 4.5 18.4 0.5
O5B A:NAD1502 4.5 25.9 0.5
O5D A:NAD1502 4.6 29.9 0.5
C5D A:NAD1502 4.7 33.0 0.5
OG A:SER246 4.8 14.4 1.0
O1A A:NAD1502 4.8 26.3 0.5
O3 A:NAD1502 4.9 30.8 0.5

Magnesium binding site 2 out of 8 in 1o00

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Magnesium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2602

b:41.0
occ:1.00
 O1N B:NAD2502 2.1 28.8 0.5
O2A B:NAD2502 2.3 28.8 0.5
O2A B:NAD2502 2.7 29.3 0.5
PN B:NAD2502 3.4 30.2 0.5
PA B:NAD2502 3.6 26.9 0.5
O3 B:NAD2502 3.9 29.1 0.5
PA B:NAD2502 3.9 27.4 0.5
C8A B:NAD2502 4.1 17.8 0.5
C8A B:NAD2502 4.1 17.2 0.5
O2N B:NAD2502 4.1 30.2 0.5
O1A B:NAD2502 4.3 30.1 0.5
O5B B:NAD2502 4.3 26.9 0.5
N7A B:NAD2502 4.4 17.5 0.5
N7A B:NAD2502 4.4 17.9 0.5
O5B B:NAD2502 4.5 28.0 0.5
CG1 B:ILE249 4.5 22.1 1.0
O5D B:NAD2502 4.6 30.4 0.5
O1A B:NAD2502 4.7 29.6 0.5
C5D B:NAD2502 4.7 31.1 0.5
CD1 B:ILE249 4.8 20.6 1.0

Magnesium binding site 3 out of 8 in 1o00

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Magnesium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2603

b:23.8
occ:1.00
 O2A C:NAD3502 2.2 26.2 0.5
O2A C:NAD3502 2.3 33.8 0.5
O1N C:NAD3502 2.7 27.6 0.5
PA C:NAD3502 3.5 25.7 0.5
PA C:NAD3502 3.6 31.8 0.5
PN C:NAD3502 3.8 28.0 0.5
O3 C:NAD3502 3.9 28.2 0.5
O1A C:NAD3502 4.0 32.4 0.5
O1A C:NAD3502 4.4 26.1 0.5
O5B C:NAD3502 4.4 30.6 0.5
CG1 C:ILE249 4.5 20.8 1.0
O5B C:NAD3502 4.5 25.4 0.5
C8A C:NAD3502 4.5 18.4 0.5
C8A C:NAD3502 4.5 18.9 0.5
C5D C:NAD3502 4.6 28.8 0.5
O1N C:NAD3502 4.7 37.9 0.5
O5D C:NAD3502 4.7 29.6 0.5
O3 C:NAD3502 4.8 35.5 0.5
CD1 C:ILE249 4.8 18.9 1.0
O2N C:NAD3502 4.9 30.2 0.5
N7A C:NAD3502 4.9 18.1 0.5
O C:HOH3564 5.0 19.9 1.0
N7A C:NAD3502 5.0 18.4 0.5

Magnesium binding site 4 out of 8 in 1o00

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Magnesium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2604

b:37.4
occ:1.00
 O2A D:NAD4502 2.2 23.6 0.5
O1N D:NAD4502 2.3 28.6 0.5
O2A D:NAD4502 2.5 27.3 0.5
PA D:NAD4502 3.5 22.6 0.5
PA D:NAD4502 3.6 25.4 0.5
PN D:NAD4502 3.6 30.3 0.5
O1A D:NAD4502 3.6 26.4 0.5
O3 D:NAD4502 3.9 27.4 0.5
CG1 D:ILE249 4.0 22.6 1.0
O D:HOH4674 4.3 24.6 1.0
O1A D:NAD4502 4.3 22.4 0.5
C5D D:NAD4502 4.4 35.8 0.5
C8A D:NAD4502 4.4 14.9 0.5
CD1 D:ILE249 4.4 24.3 1.0
O5D D:NAD4502 4.5 33.7 0.5
C8A D:NAD4502 4.5 18.2 0.5
O5B D:NAD4502 4.5 25.8 0.5
OG D:SER246 4.5 19.0 1.0
N7A D:NAD4502 4.6 14.5 0.5
O5B D:NAD4502 4.6 22.0 0.5
O2N D:NAD4502 4.7 29.6 0.5
N7A D:NAD4502 4.8 17.6 0.5
O3 D:NAD4502 4.8 29.5 0.5
O1N D:NAD4502 4.9 32.9 0.5

Magnesium binding site 5 out of 8 in 1o00

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Magnesium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg2605

b:46.1
occ:1.00
 O1N E:NAD5502 2.2 31.4 0.5
O2A E:NAD5502 2.3 26.6 0.5
O2A E:NAD5502 2.5 27.6 0.5
PN E:NAD5502 3.5 31.8 0.5
PA E:NAD5502 3.6 24.9 0.5
PA E:NAD5502 3.8 26.2 0.5
O3 E:NAD5502 4.0 29.7 0.5
O1A E:NAD5502 4.2 28.6 0.5
O2N E:NAD5502 4.2 32.4 0.5
O5B E:NAD5502 4.3 25.3 0.5
C8A E:NAD5502 4.3 16.4 0.5
C8A E:NAD5502 4.3 18.9 0.5
O5B E:NAD5502 4.4 27.1 0.5
O1A E:NAD5502 4.7 27.6 0.5
O5D E:NAD5502 4.7 32.8 0.5
N7A E:NAD5502 4.8 18.4 0.5
N7A E:NAD5502 4.8 15.8 0.5
O1N E:NAD5502 4.8 32.6 0.5
C5D E:NAD5502 4.8 33.9 0.5
O E:HOH850 4.8 19.6 1.0
CG1 E:ILE249 4.9 18.4 1.0

Magnesium binding site 6 out of 8 in 1o00

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Magnesium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2606

b:22.1
occ:1.00
 O2A F:NAD6502 2.3 16.2 0.5
O2A F:NAD6502 2.4 30.9 0.5
O1N F:NAD6502 2.4 21.8 0.5
O F:HOH800 2.5 15.1 1.0
PA F:NAD6502 3.5 15.6 0.5
PN F:NAD6502 3.5 19.8 0.5
O3 F:NAD6502 3.7 19.6 0.5
PA F:NAD6502 3.7 28.9 0.5
O1A F:NAD6502 4.0 30.3 0.5
C5D F:NAD6502 4.2 26.3 0.5
O1A F:NAD6502 4.4 17.1 0.5
O5D F:NAD6502 4.4 23.1 0.5
O5B F:NAD6502 4.5 28.3 0.5
O5B F:NAD6502 4.5 15.8 0.5
CG1 F:ILE249 4.6 20.6 1.0
O1N F:NAD6502 4.6 34.6 0.5
O2N F:NAD6502 4.6 21.8 0.5
C8A F:NAD6502 4.7 14.4 0.5
C8A F:NAD6502 4.7 18.8 0.5
O3 F:NAD6502 4.8 32.4 0.5

Magnesium binding site 7 out of 8 in 1o00

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Magnesium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg2607

b:42.1
occ:1.00
 O1N G:NAD7502 2.0 36.5 0.5
O2A G:NAD7502 2.0 36.1 0.5
O G:HOH1247 2.3 28.5 1.0
O2A G:NAD7502 2.4 29.0 0.5
PA G:NAD7502 3.3 34.7 0.5
PN G:NAD7502 3.3 37.7 0.5
O3 G:NAD7502 3.7 37.3 0.5
PA G:NAD7502 3.7 28.3 0.5
O1A G:NAD7502 4.1 28.9 0.5
O5B G:NAD7502 4.1 34.6 0.5
O2N G:NAD7502 4.2 38.2 0.5
C8A G:NAD7502 4.2 20.2 0.5
C8A G:NAD7502 4.2 25.6 0.5
O5B G:NAD7502 4.3 28.3 0.5
O5D G:NAD7502 4.4 38.1 0.5
O1A G:NAD7502 4.4 36.0 0.5
O G:HOH1391 4.4 30.8 1.0
C5D G:NAD7502 4.4 37.9 0.5
N7A G:NAD7502 4.7 19.1 0.5
N7A G:NAD7502 4.7 24.6 0.5
CG1 G:ILE249 4.9 16.9 1.0
O1N G:NAD7502 4.9 31.1 0.5
O G:HOH1246 4.9 25.6 1.0
O3 G:NAD7502 5.0 30.2 0.5

Magnesium binding site 8 out of 8 in 1o00

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Magnesium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nad+ and MG2+ Showing Dual Nad(H) Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg2608

b:38.0
occ:1.00
 O2A H:NAD8502 2.2 30.5 0.5
O1N H:NAD8502 2.5 33.5 0.5
O H:HOH8589 2.6 35.2 1.0
O2A H:NAD8502 2.9 32.4 0.5
PA H:NAD8502 3.5 29.6 0.5
PN H:NAD8502 3.7 33.6 0.5
O H:HOH8590 3.8 42.1 1.0
O3 H:NAD8502 3.9 32.4 0.5
O1A H:NAD8502 4.0 32.3 0.5
PA H:NAD8502 4.0 30.7 0.5
CG1 H:ILE249 4.2 23.1 1.0
O1A H:NAD8502 4.4 31.5 0.5
C8A H:NAD8502 4.5 17.2 0.5
C8A H:NAD8502 4.6 18.5 0.5
O5B H:NAD8502 4.6 28.6 0.5
CD1 H:ILE249 4.6 23.3 1.0
C5D H:NAD8502 4.6 36.4 0.5
OG H:SER246 4.7 23.9 1.0
O5D H:NAD8502 4.7 34.2 0.5
N7A H:NAD8502 4.7 17.8 0.5
N7A H:NAD8502 4.7 16.8 0.5
O2N H:NAD8502 4.7 34.2 0.5
O5B H:NAD8502 4.9 30.0 0.5

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: Tue Aug 13 10:29:59 2024

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