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Magnesium in PDB 1o02: Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of MG2+

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

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

Protein crystallography data

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of MG2+, PDB code: 1o02 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) 24.97 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.492, 150.873, 177.195, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.3

Other elements in 1o02:

The structure of Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ (pdb code 1o02). 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 Nadh in the Presence of MG2+, PDB code: 1o02:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1o02

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Magnesium binding site 1 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4601

b:32.1
occ:1.00
 O2A A:NAI4606 2.1 23.4 1.0
O A:HOH4866 2.1 26.6 1.0
O A:HOH4731 2.2 33.9 1.0
O A:HOH4733 2.2 32.9 1.0
O A:HOH4867 2.2 28.2 1.0
O1N A:NAI4606 2.2 21.9 1.0
PA A:NAI4606 3.3 23.6 1.0
PN A:NAI4606 3.4 24.3 1.0
O3 A:NAI4606 3.5 23.8 1.0
O A:HOH4865 4.2 33.1 1.0
O A:HOH4734 4.2 38.7 1.0
O1A A:NAI4606 4.2 21.6 1.0
O5B A:NAI4606 4.3 22.5 1.0
O A:HOH4732 4.3 47.5 1.0
C5D A:NAI4606 4.3 24.9 1.0
O2N A:NAI4606 4.4 23.9 1.0
CG1 A:ILE249 4.4 26.7 1.0
O5D A:NAI4606 4.4 23.9 1.0
C8A A:NAI4606 4.7 23.9 1.0
OG A:SER246 4.7 20.7 1.0
OE2 A:GLU248 4.8 47.4 1.0
CD1 A:ILE249 4.9 26.2 1.0
N7A A:NAI4606 5.0 24.6 1.0

Magnesium binding site 2 out of 8 in 1o02

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Magnesium binding site 2 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:29.2
occ:1.00
 O B:HOH788 2.0 32.2 1.0
O1N B:NAI606 2.0 23.6 1.0
O B:HOH787 2.1 32.5 1.0
O B:HOH786 2.2 41.5 1.0
O B:HOH785 2.2 28.8 1.0
O2A B:NAI606 2.2 22.9 1.0
PN B:NAI606 3.3 24.7 1.0
PA B:NAI606 3.3 22.9 1.0
O3 B:NAI606 3.5 22.9 1.0
O B:HOH789 4.0 30.6 1.0
O B:HOH775 4.2 31.8 1.0
C5D B:NAI606 4.2 23.0 1.0
O2N B:NAI606 4.3 23.6 1.0
O5D B:NAI606 4.3 23.1 1.0
O5B B:NAI606 4.3 22.5 1.0
O1A B:NAI606 4.3 21.6 1.0
O B:HOH784 4.5 41.2 1.0
CG1 B:ILE249 4.5 23.1 1.0
O B:HOH782 4.7 48.0 1.0
C8A B:NAI606 4.8 21.1 1.0
OG B:SER246 4.8 20.5 1.0
O B:HOH783 4.8 44.1 1.0
OE2 B:GLU248 4.9 44.3 1.0

Magnesium binding site 3 out of 8 in 1o02

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Magnesium binding site 3 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:27.2
occ:1.00
 O C:HOH1039 2.0 30.1 1.0
O C:HOH1066 2.1 32.0 1.0
O2A C:NAI606 2.1 20.4 1.0
O1N C:NAI606 2.2 21.0 1.0
O C:HOH1040 2.3 36.3 1.0
O C:HOH1067 2.4 31.8 1.0
PA C:NAI606 3.3 19.6 1.0
PN C:NAI606 3.4 21.4 1.0
O3 C:NAI606 3.6 21.4 1.0
O C:HOH1037 4.0 29.2 1.0
O C:HOH1068 4.2 31.4 1.0
O1A C:NAI606 4.2 20.9 1.0
C5D C:NAI606 4.3 20.9 1.0
O5D C:NAI606 4.3 22.2 1.0
O5B C:NAI606 4.3 20.1 1.0
CG1 C:ILE249 4.4 21.9 1.0
O2N C:NAI606 4.4 23.6 1.0
O C:HOH1041 4.4 32.3 1.0
OG C:SER246 4.6 19.4 1.0
C8A C:NAI606 4.8 17.7 1.0
CD1 C:ILE249 4.9 23.1 1.0

Magnesium binding site 4 out of 8 in 1o02

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Magnesium binding site 4 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:27.7
occ:1.00
 O D:HOH720 2.0 30.8 1.0
O2A D:NAI606 2.1 20.2 1.0
O D:HOH717 2.2 28.6 1.0
O1N D:NAI606 2.3 24.7 1.0
O D:HOH719 2.3 31.6 1.0
O D:HOH718 2.5 47.8 1.0
PA D:NAI606 3.3 21.9 1.0
PN D:NAI606 3.5 24.3 1.0
O3 D:NAI606 3.7 23.1 1.0
O D:HOH716 3.9 32.8 1.0
O D:HOH721 4.1 28.1 1.0
O1A D:NAI606 4.3 22.2 1.0
CG1 D:ILE249 4.3 20.5 1.0
C5D D:NAI606 4.4 24.7 1.0
O5B D:NAI606 4.4 21.7 1.0
O5D D:NAI606 4.4 25.4 1.0
OG D:SER246 4.5 21.9 1.0
O2N D:NAI606 4.5 26.1 1.0
C8A D:NAI606 4.7 19.8 1.0
OE2 D:GLU248 4.7 42.2 1.0
CD1 D:ILE249 4.9 22.2 1.0
N7A D:NAI606 5.0 19.0 1.0

Magnesium binding site 5 out of 8 in 1o02

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Magnesium binding site 5 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:31.0
occ:1.00
 O E:HOH921 1.9 29.7 1.0
O2A E:NAI606 2.1 18.2 1.0
O1N E:NAI606 2.1 22.4 1.0
O E:HOH920 2.2 30.1 1.0
O E:HOH788 2.3 33.6 1.0
O E:HOH787 2.4 31.3 1.0
PA E:NAI606 3.3 20.3 1.0
PN E:NAI606 3.3 23.7 1.0
O3 E:NAI606 3.6 20.8 1.0
O E:HOH922 3.8 28.9 1.0
O E:HOH789 4.0 40.1 1.0
O1A E:NAI606 4.2 18.2 1.0
O5B E:NAI606 4.3 19.3 1.0
O2N E:NAI606 4.3 21.8 1.0
O5D E:NAI606 4.3 24.1 1.0
C5D E:NAI606 4.4 22.1 1.0
O E:HOH926 4.4 47.7 1.0
CG1 E:ILE249 4.5 20.7 1.0
OG E:SER246 4.7 17.5 1.0
C8A E:NAI606 4.7 17.6 1.0
OE1 E:GLU248 4.9 39.6 1.0

Magnesium binding site 6 out of 8 in 1o02

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Magnesium binding site 6 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:25.7
occ:1.00
 O F:HOH784 1.9 26.9 1.0
O2A F:NAI607 2.0 16.9 1.0
O F:HOH783 2.1 28.0 1.0
O1N F:NAI607 2.2 17.8 1.0
O F:HOH817 2.3 31.5 1.0
O F:HOH816 2.3 24.9 1.0
PA F:NAI607 3.2 17.9 1.0
PN F:NAI607 3.4 19.5 1.0
O3 F:NAI607 3.5 17.4 1.0
O F:HOH785 3.9 25.9 1.0
O1A F:NAI607 4.1 15.4 1.0
O F:HOH782 4.2 30.9 1.0
O5B F:NAI607 4.3 16.2 1.0
C5D F:NAI607 4.3 17.1 1.0
O5D F:NAI607 4.3 18.5 1.0
CG1 F:ILE249 4.4 20.1 1.0
O2N F:NAI607 4.4 18.1 1.0
OG F:SER246 4.6 22.5 1.0
C8A F:NAI607 4.8 15.8 1.0
CD1 F:ILE249 4.9 23.1 1.0

Magnesium binding site 7 out of 8 in 1o02

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Magnesium binding site 7 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:28.8
occ:1.00
 O2A G:NAI606 1.9 24.6 1.0
O1N G:NAI606 2.1 26.7 1.0
O G:HOH706 2.1 33.0 1.0
O G:HOH707 2.2 36.1 1.0
O G:HOH709 2.2 34.5 1.0
O G:HOH708 2.4 38.4 1.0
PA G:NAI606 3.1 25.0 1.0
PN G:NAI606 3.2 27.9 1.0
O3 G:NAI606 3.4 25.2 1.0
O G:HOH710 4.0 42.2 1.0
O5B G:NAI606 4.1 23.8 1.0
O1A G:NAI606 4.2 24.0 1.0
O2N G:NAI606 4.3 25.4 1.0
O5D G:NAI606 4.3 25.8 1.0
O G:HOH705 4.3 46.9 1.0
C5D G:NAI606 4.4 25.0 1.0
CG1 G:ILE249 4.4 24.8 1.0
C8A G:NAI606 4.6 23.7 1.0
OG G:SER246 4.6 22.2 1.0
CD1 G:ILE249 4.8 23.1 1.0
O G:HOH742 4.9 44.6 1.0
N7A G:NAI606 4.9 24.5 1.0

Magnesium binding site 8 out of 8 in 1o02

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Magnesium binding site 8 out of 8 in the Human Mitochondrial Aldehyde Dehydrogenase Complexed with Nadh in the Presence of 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 Nadh in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:31.8
occ:1.00
 O H:HOH763 2.0 48.6 1.0
O2A H:NAI605 2.0 27.7 1.0
O1N H:NAI605 2.2 28.4 1.0
O H:HOH768 2.2 42.7 1.0
O H:HOH770 2.4 33.6 1.0
O H:HOH769 2.4 37.5 1.0
PA H:NAI605 3.2 26.7 1.0
PN H:NAI605 3.3 28.5 1.0
O3 H:NAI605 3.5 27.6 1.0
O H:HOH762 3.8 44.7 1.0
O H:HOH767 4.1 35.3 1.0
O5B H:NAI605 4.2 25.1 1.0
O1A H:NAI605 4.2 26.3 1.0
O H:HOH764 4.2 46.6 1.0
C5D H:NAI605 4.3 29.8 1.0
O2N H:NAI605 4.3 26.3 1.0
O5D H:NAI605 4.3 28.6 1.0
CG1 H:ILE249 4.4 26.5 1.0
OG H:SER246 4.5 25.1 1.0
C8A H:NAI605 4.8 27.0 1.0
OE2 H:GLU248 5.0 44.7 1.0
CD1 H:ILE249 5.0 25.5 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 10:29:59 2024

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