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Magnesium in PDB 1o01: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+

Enzymatic activity of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+

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

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+, PDB code: 1o01 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) 34.84 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.133, 150.571, 176.782, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Other elements in 1o01:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Crotonaldehyde, Nad(H) and MG2+ 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 Crotonaldehyde, Nad(H) and MG2+ (pdb code 1o01). 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 Crotonaldehyde, Nad(H) and MG2+, PDB code: 1o01:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4601

b:47.5
occ:1.00
 O1N A:NAD5501 2.2 32.7 1.0
O2A A:NAD5501 2.2 24.7 1.0
O A:HOH5830 2.7 34.7 1.0
O A:HOH5513 3.0 52.0 1.0
O A:HOH5524 3.0 30.1 1.0
PN A:NAD5501 3.5 34.0 1.0
O A:HOH5514 3.5 38.3 1.0
PA A:NAD5501 3.5 23.1 1.0
O3 A:NAD5501 3.8 29.3 1.0
O2N A:NAD5501 4.3 33.0 1.0
O5B A:NAD5501 4.4 21.4 1.0
O1A A:NAD5501 4.5 22.2 1.0
C8A A:NAD5501 4.5 17.5 1.0
O5D A:NAD5501 4.5 33.6 1.0
C5D A:NAD5501 4.5 35.0 1.0
CG1 A:ILE249 4.5 18.6 1.0
O A:HOH5829 4.6 41.3 1.0
O A:HOH5515 4.8 45.9 1.0
N7A A:NAD5501 4.8 20.2 1.0

Magnesium binding site 2 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg4602

b:37.2
occ:1.00
 O2A B:NAD5502 2.2 26.1 1.0
O1N B:NAD5502 2.2 31.8 1.0
O B:HOH5543 2.7 29.1 1.0
O B:HOH5977 3.5 43.8 1.0
PA B:NAD5502 3.6 24.2 1.0
PN B:NAD5502 3.6 34.3 1.0
O3 B:NAD5502 3.9 29.7 1.0
O B:HOH5541 4.2 48.6 1.0
O2N B:NAD5502 4.4 34.1 1.0
C8A B:NAD5502 4.5 15.6 1.0
O5B B:NAD5502 4.5 24.4 1.0
O1A B:NAD5502 4.5 26.2 1.0
CG1 B:ILE249 4.5 22.1 1.0
O5D B:NAD5502 4.6 31.8 1.0
C5D B:NAD5502 4.7 33.0 1.0
N7A B:NAD5502 4.7 16.1 1.0
CD1 B:ILE249 4.8 22.0 1.0

Magnesium binding site 3 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg4603

b:39.3
occ:1.00
 O2A C:NAD5503 2.2 24.0 1.0
O1N C:NAD5503 2.2 27.7 1.0
O C:HOH5927 3.0 38.1 1.0
O C:HOH5614 3.1 32.4 1.0
O C:HOH5926 3.5 26.7 1.0
PA C:NAD5503 3.5 22.4 1.0
PN C:NAD5503 3.6 27.1 1.0
O3 C:NAD5503 4.0 26.0 1.0
CG1 C:ILE249 4.4 14.6 1.0
O1A C:NAD5503 4.5 22.8 1.0
O5B C:NAD5503 4.5 20.8 1.0
C5D C:NAD5503 4.5 30.5 1.0
O5D C:NAD5503 4.5 28.4 1.0
O2N C:NAD5503 4.5 27.9 1.0
C8A C:NAD5503 4.6 10.4 1.0
O C:HOH5612 4.7 49.5 1.0
CD1 C:ILE249 4.8 17.9 1.0
N7A C:NAD5503 4.8 15.9 1.0
OG C:SER246 4.9 18.5 1.0

Magnesium binding site 4 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4604

b:43.9
occ:1.00
 O2A D:NAD5504 2.3 21.6 1.0
O1N D:NAD5504 2.3 31.9 1.0
O D:HOH5676 2.6 47.5 1.0
O D:HOH5679 2.6 40.7 1.0
O D:HOH5684 3.5 23.9 1.0
O D:HOH5680 3.5 29.7 1.0
PA D:NAD5504 3.6 22.5 1.0
PN D:NAD5504 3.6 32.4 1.0
O D:HOH5677 3.9 49.9 1.0
O3 D:NAD5504 4.0 27.2 1.0
O D:HOH5687 4.2 47.0 1.0
CG1 D:ILE249 4.3 16.5 1.0
O1A D:NAD5504 4.4 21.4 1.0
C5D D:NAD5504 4.5 34.5 1.0
O5D D:NAD5504 4.5 33.6 1.0
O5B D:NAD5504 4.6 19.2 1.0
C8A D:NAD5504 4.6 11.5 1.0
O2N D:NAD5504 4.6 32.8 1.0
CD1 D:ILE249 4.7 13.1 1.0
OG D:SER246 4.8 17.7 1.0
N7A D:NAD5504 4.8 13.1 1.0

Magnesium binding site 5 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg4605

b:48.9
occ:1.00
 O1N E:NAD5505 2.2 31.4 1.0
O2A E:NAD5505 2.2 23.5 1.0
O E:HOH5922 2.4 43.7 1.0
O E:HOH5921 2.5 47.8 1.0
O E:HOH5674 3.1 29.5 1.0
O E:HOH5673 3.5 26.9 1.0
PN E:NAD5505 3.5 33.4 1.0
PA E:NAD5505 3.5 21.2 1.0
O3 E:NAD5505 3.9 29.2 1.0
O2N E:NAD5505 4.4 32.9 1.0
O5B E:NAD5505 4.4 21.0 1.0
CG1 E:ILE249 4.5 15.4 1.0
O1A E:NAD5505 4.5 21.5 1.0
C8A E:NAD5505 4.5 13.3 1.0
O5D E:NAD5505 4.6 32.4 1.0
C5D E:NAD5505 4.6 31.8 1.0
N7A E:NAD5505 4.8 15.5 1.0
CD1 E:ILE249 4.9 11.7 1.0
O E:HOH5920 5.0 48.8 1.0

Magnesium binding site 6 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg4606

b:40.7
occ:1.00
 O2A F:NAD5506 2.2 19.5 1.0
O1N F:NAD5506 2.3 25.8 1.0
O F:HOH2365 2.4 37.4 1.0
O F:HOH2363 2.6 30.9 1.0
PA F:NAD5506 3.5 17.2 1.0
PN F:NAD5506 3.5 24.5 1.0
O F:HOH2375 3.7 31.6 1.0
O3 F:NAD5506 3.7 23.6 1.0
O F:HOH2366 4.0 24.3 1.0
C5D F:NAD5506 4.1 27.2 1.0
O5D F:NAD5506 4.3 25.7 1.0
O1A F:NAD5506 4.4 19.4 1.0
CG1 F:ILE249 4.4 13.3 1.0
O5B F:NAD5506 4.5 18.3 1.0
O2N F:NAD5506 4.5 24.8 1.0
OG F:SER246 4.6 15.7 1.0
O F:HOH2364 4.7 49.6 1.0
CD1 F:ILE249 4.9 14.8 1.0
C8A F:NAD5506 4.9 8.9 1.0

Magnesium binding site 7 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg4607

b:45.9
occ:1.00
 O2A G:NAD5507 2.1 30.1 1.0
O1N G:NAD5507 2.3 36.5 1.0
O G:HOH1800 2.7 37.6 1.0
O G:HOH1804 3.3 46.9 1.0
PA G:NAD5507 3.5 27.7 1.0
PN G:NAD5507 3.6 35.6 1.0
O3 G:NAD5507 3.9 33.8 1.0
O5B G:NAD5507 4.3 27.0 1.0
O2N G:NAD5507 4.4 36.1 1.0
C8A G:NAD5507 4.4 19.5 1.0
O1A G:NAD5507 4.5 29.8 1.0
CG1 G:ILE249 4.5 20.0 1.0
O G:HOH1799 4.5 43.0 1.0
N7A G:NAD5507 4.7 19.8 1.0
C5D G:NAD5507 4.7 37.9 1.0
O5D G:NAD5507 4.7 35.1 1.0
CD1 G:ILE249 4.7 18.8 1.0

Magnesium binding site 8 out of 8 in 1o01

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


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 Crotonaldehyde, Nad(H) and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg4608

b:32.6
occ:1.00
 O1N H:NAD5508 2.2 38.0 1.0
O2A H:NAD5508 2.2 34.1 1.0
O H:HOH3284 2.7 44.3 1.0
O H:HOH1827 3.3 44.0 1.0
O H:HOH1825 3.3 31.8 1.0
O H:HOH1824 3.4 36.4 1.0
PN H:NAD5508 3.5 39.0 1.0
PA H:NAD5508 3.5 29.9 1.0
O3 H:NAD5508 3.9 37.2 1.0
O5B H:NAD5508 4.3 28.7 1.0
O2N H:NAD5508 4.4 38.1 1.0
CG1 H:ILE249 4.5 23.9 1.0
C8A H:NAD5508 4.5 25.2 1.0
O5D H:NAD5508 4.6 39.8 1.0
O1A H:NAD5508 4.6 32.5 1.0
C5D H:NAD5508 4.6 42.3 1.0
N7A H:NAD5508 4.8 25.4 1.0
CD1 H:ILE249 4.8 24.9 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: Tue Aug 13 10:29:58 2024

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