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Magnesium in PDB 2onp: ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+

Enzymatic activity of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+

All present enzymatic activity of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+:
1.2.1.3;

Protein crystallography data

The structure of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+, PDB code: 2onp was solved by H.N.Larson, T.D.Hurley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 142.854, 150.837, 177.482, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 24

Other elements in 2onp:

The structure of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ (pdb code 2onp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+, PDB code: 2onp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2onp

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Magnesium binding site 1 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:49.8
occ:1.00
 O1N A:NAD501 2.4 45.2 1.0
O2A A:NAD501 2.4 45.1 1.0
O A:HOH3300 2.7 44.9 1.0
O A:HOH3154 3.5 50.8 1.0
PA A:NAD501 3.6 42.9 1.0
PN A:NAD501 3.6 46.4 1.0
O3 A:NAD501 3.8 44.6 1.0
CG1 A:ILE249 4.3 41.0 1.0
O5B A:NAD501 4.5 41.0 1.0
O2N A:NAD501 4.6 47.1 1.0
O1A A:NAD501 4.6 41.8 1.0
C5D A:NAD501 4.6 48.0 1.0
C8A A:NAD501 4.6 35.4 1.0
O5D A:NAD501 4.6 47.7 1.0
OG A:SER246 4.7 39.0 1.0
CD1 A:ILE249 4.8 39.2 1.0
N7A A:NAD501 4.9 35.6 1.0

Magnesium binding site 2 out of 8 in 2onp

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Magnesium binding site 2 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:47.0
occ:1.00
 O B:HOH3302 2.2 38.6 1.0
O B:HOH3303 2.2 46.3 1.0
O1N B:NAD502 2.4 47.3 1.0
O2A B:NAD502 2.4 42.7 1.0
PN B:NAD502 3.7 47.1 1.0
PA B:NAD502 3.7 39.6 1.0
O3 B:NAD502 4.0 43.0 1.0
CG1 B:ILE249 4.2 39.5 1.0
O B:HOH3558 4.4 46.3 1.0
CD1 B:ILE249 4.5 37.5 1.0
O2N B:NAD502 4.5 44.5 1.0
C8A B:NAD502 4.6 38.0 1.0
O1A B:NAD502 4.6 40.0 1.0
O5B B:NAD502 4.7 40.2 1.0
C5D B:NAD502 4.7 44.2 1.0
OG B:SER246 4.7 36.6 1.0
O5D B:NAD502 4.7 44.6 1.0
N7A B:NAD502 4.9 38.4 1.0

Magnesium binding site 3 out of 8 in 2onp

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Magnesium binding site 3 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:42.0
occ:1.00
 O C:HOH3306 2.2 44.8 1.0
O2A C:NAD503 2.2 26.1 1.0
O1N C:NAD503 2.3 29.4 1.0
O C:HOH3305 2.3 46.1 1.0
O C:HOH1373 2.4 35.5 1.0
PA C:NAD503 3.4 26.8 1.0
PN C:NAD503 3.4 30.6 1.0
O3 C:NAD503 3.6 28.9 1.0
O C:HOH2213 3.9 31.7 1.0
O C:HOH1710 3.9 33.7 1.0
O1A C:NAD503 4.3 27.9 1.0
CG1 C:ILE249 4.3 24.0 1.0
O5D C:NAD503 4.4 30.2 1.0
C5D C:NAD503 4.4 29.3 1.0
O5B C:NAD503 4.5 25.4 1.0
O2N C:NAD503 4.5 30.7 1.0
O C:HOH2731 4.5 35.0 1.0
OG C:SER246 4.6 26.3 1.0
C8A C:NAD503 4.7 16.8 1.0
CD1 C:ILE249 4.8 23.9 1.0

Magnesium binding site 4 out of 8 in 2onp

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Magnesium binding site 4 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:52.6
occ:1.00
 O1N D:NAD504 2.3 36.2 1.0
O2A D:NAD504 2.4 31.0 1.0
O D:HOH2967 2.5 41.3 1.0
O D:HOH3201 3.4 46.5 1.0
PA D:NAD504 3.7 34.6 1.0
PN D:NAD504 3.7 39.0 1.0
CG1 D:ILE249 4.2 30.8 1.0
O3 D:NAD504 4.2 37.3 1.0
O D:HOH3322 4.3 43.1 1.0
CD1 D:ILE249 4.5 30.1 1.0
C8A D:NAD504 4.5 28.8 1.0
O1A D:NAD504 4.6 36.7 1.0
O2N D:NAD504 4.6 40.4 1.0
C5D D:NAD504 4.6 41.1 1.0
O5D D:NAD504 4.7 39.0 1.0
O5B D:NAD504 4.7 31.6 1.0
OG D:SER246 4.7 30.8 1.0
N7A D:NAD504 4.8 27.9 1.0

Magnesium binding site 5 out of 8 in 2onp

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Magnesium binding site 5 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg605

b:50.5
occ:1.00
 O1N E:NAD505 2.1 39.0 1.0
O2A E:NAD505 2.3 33.7 1.0
O E:HOH3291 2.5 53.0 1.0
O E:HOH3292 2.6 45.9 1.0
O E:HOH3056 3.1 48.0 1.0
PN E:NAD505 3.5 41.5 1.0
PA E:NAD505 3.6 33.3 1.0
O E:HOH2017 3.8 36.1 1.0
O3 E:NAD505 4.0 36.2 1.0
O2N E:NAD505 4.3 38.7 1.0
O5B E:NAD505 4.4 32.2 1.0
C8A E:NAD505 4.4 26.4 1.0
O5D E:NAD505 4.5 39.8 1.0
CG1 E:ILE249 4.6 29.4 1.0
O1A E:NAD505 4.7 32.0 1.0
N7A E:NAD505 4.7 26.0 1.0
C5D E:NAD505 4.8 39.6 1.0
O E:HOH3357 4.8 45.2 1.0

Magnesium binding site 6 out of 8 in 2onp

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Magnesium binding site 6 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg606

b:41.4
occ:1.00
 O F:HOH3294 2.1 45.4 1.0
O F:HOH3293 2.2 30.6 1.0
O2A F:NAD506 2.2 23.9 1.0
O1N F:NAD506 2.2 29.7 1.0
O F:HOH1820 2.3 35.4 1.0
PN F:NAD506 3.4 30.4 1.0
PA F:NAD506 3.5 25.5 1.0
O3 F:NAD506 3.7 28.4 1.0
O F:HOH2813 4.0 36.5 1.0
O F:HOH2082 4.1 26.9 1.0
O5D F:NAD506 4.3 31.2 1.0
C5D F:NAD506 4.4 29.9 1.0
O1A F:NAD506 4.4 23.5 1.0
CG1 F:ILE249 4.4 21.8 1.0
O F:HOH3396 4.4 44.4 1.0
O2N F:NAD506 4.5 28.6 1.0
O5B F:NAD506 4.5 24.7 1.0
OG F:SER246 4.7 24.3 1.0
C8A F:NAD506 4.9 18.8 1.0
CD1 F:ILE249 4.9 21.0 1.0
OE1 F:GLU248 5.0 56.1 1.0

Magnesium binding site 7 out of 8 in 2onp

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Magnesium binding site 7 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg607

b:59.9
occ:1.00
 O1N G:NAD507 2.3 45.7 1.0
O2A G:NAD507 2.4 43.9 1.0
O G:HOH3297 2.5 52.7 1.0
PN G:NAD507 3.5 45.2 1.0
PA G:NAD507 3.6 40.2 1.0
O3 G:NAD507 3.7 43.5 1.0
C5D G:NAD507 4.4 42.5 1.0
CG1 G:ILE249 4.4 33.7 1.0
O2N G:NAD507 4.5 42.8 1.0
O1A G:NAD507 4.5 42.3 1.0
O5D G:NAD507 4.6 42.9 1.0
O5B G:NAD507 4.7 39.4 1.0
CD1 G:ILE249 4.7 32.7 1.0
OG G:SER246 4.8 38.3 1.0
C8A G:NAD507 4.9 36.8 1.0

Magnesium binding site 8 out of 8 in 2onp

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Magnesium binding site 8 out of 8 in the ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of ARG475GLN Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Complexed with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg608

b:59.6
occ:1.00
 O1N H:NAD508 2.3 50.1 1.0
O2A H:NAD508 2.4 46.2 1.0
O H:HOH3625 2.8 46.5 1.0
PN H:NAD508 3.6 50.3 1.0
PA H:NAD508 3.7 43.8 1.0
O H:HOH3298 3.8 41.0 1.0
O3 H:NAD508 4.0 47.4 1.0
O H:HOH3450 4.1 46.9 1.0
CG1 H:ILE249 4.4 40.8 1.0
O2N H:NAD508 4.5 49.4 1.0
C5D H:NAD508 4.6 49.8 1.0
O5B H:NAD508 4.6 41.2 1.0
O5D H:NAD508 4.6 49.1 1.0
OG H:SER246 4.7 38.9 1.0
O1A H:NAD508 4.7 44.8 1.0
CD1 H:ILE249 4.8 40.4 1.0
C8A H:NAD508 4.9 37.8 1.0

Reference:

H.N.Larson, J.Zhou, Z.Chen, J.S.Stamler, H.Weiner, T.D.Hurley. Structural and Functional Consequences of Coenzyme Binding to the Inactive Asian Variant of Mitochondrial Aldehyde Dehydrogenase: Roles of Residues 475 and 487. J.Biol.Chem. V. 282 12940 2007.
ISSN: ISSN 0021-9258
PubMed: 17327228
DOI: 10.1074/JBC.M607959200
Page generated: Wed Aug 14 01:31:59 2024

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