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Magnesium in PDB 4fr8: Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin

Enzymatic activity of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin

All present enzymatic activity of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin:
1.2.1.3;

Protein crystallography data

The structure of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin, PDB code: 4fr8 was solved by B.S.Lang, K.Gruber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.07 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.663, 175.916, 102.296, 90.00, 95.01, 90.00
R / Rfree (%) 13.2 / 16.7

Other elements in 4fr8:

The structure of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin (pdb code 4fr8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin, PDB code: 4fr8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4fr8

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Magnesium binding site 1 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:44.6
occ:1.00
 O1A A:NAD1001 2.6 34.0 1.0
O1N A:NAD1001 2.8 49.0 1.0
O A:HOH942 3.0 30.5 1.0
O A:HOH980 3.1 38.4 1.0
PA A:NAD1001 4.1 29.5 1.0
PN A:NAD1001 4.1 41.6 1.0
C8A A:NAD1001 4.2 22.1 1.0
N7A A:NAD1001 4.4 22.3 1.0
O3 A:NAD1001 4.7 39.3 1.0
O2N A:NAD1001 4.8 41.6 1.0
CG1 A:ILE249 4.8 28.1 1.0
O5B A:NAD1001 4.8 28.0 1.0
CD1 A:ILE249 4.8 28.7 1.0
O A:HOH731 4.9 28.7 1.0

Magnesium binding site 2 out of 8 in 4fr8

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Magnesium binding site 2 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:49.5
occ:1.00
 O1A B:ADP1001 2.1 27.8 1.0
O1B B:ADP1001 2.2 45.1 1.0
O B:HOH1328 3.4 29.8 1.0
PB B:ADP1001 3.5 57.5 1.0
PA B:ADP1001 3.5 28.7 1.0
O B:HOH1279 3.6 33.5 1.0
O2B B:ADP1001 3.8 42.6 1.0
O3A B:ADP1001 4.0 44.4 1.0
O B:HOH1479 4.0 30.2 1.0
O2A B:ADP1001 4.5 29.9 1.0
O5' B:ADP1001 4.5 29.7 1.0
CG1 B:ILE249 4.6 27.1 1.0
C8 B:ADP1001 4.6 21.8 1.0
O3B B:ADP1001 4.7 50.1 1.0
OG B:SER246 4.9 22.6 1.0
CD1 B:ILE249 4.9 28.3 1.0
N7 B:ADP1001 4.9 21.3 1.0

Magnesium binding site 3 out of 8 in 4fr8

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Magnesium binding site 3 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1002

b:54.6
occ:1.00
 O1N C:NAD1001 2.1 42.1 1.0
O1A C:NAD1001 2.2 36.8 1.0
O C:HOH1315 3.0 36.0 1.0
O C:HOH1461 3.3 33.0 1.0
PN C:NAD1001 3.5 49.4 1.0
PA C:NAD1001 3.6 29.5 1.0
O3 C:NAD1001 4.1 42.3 1.0
C8A C:NAD1001 4.1 22.1 1.0
CG1 C:ILE249 4.3 25.9 1.0
N7A C:NAD1001 4.3 22.7 1.0
CD1 C:ILE249 4.4 23.4 1.0
O2N C:NAD1001 4.4 34.4 1.0
O5B C:NAD1001 4.4 34.3 1.0
O5D C:NAD1001 4.7 50.3 1.0
C5D C:NAD1001 4.7 36.1 1.0
O2A C:NAD1001 4.7 27.5 1.0

Magnesium binding site 4 out of 8 in 4fr8

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Magnesium binding site 4 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:41.6
occ:1.00
 O1A D:NAD1001 2.3 24.7 1.0
O1N D:NAD1001 2.5 33.1 1.0
O D:HOH1415 3.0 29.7 1.0
PA D:NAD1001 3.7 26.5 1.0
PN D:NAD1001 3.8 41.4 1.0
C8A D:NAD1001 3.9 22.7 1.0
N7A D:NAD1001 4.1 20.6 1.0
O3 D:NAD1001 4.3 31.1 1.0
O2N D:NAD1001 4.3 35.3 1.0
O5B D:NAD1001 4.4 23.2 1.0
CG1 D:ILE249 4.5 23.5 1.0
CD1 D:ILE249 4.6 22.2 1.0
O2A D:NAD1001 4.9 23.7 1.0
O D:HOH1264 4.9 21.4 1.0

Magnesium binding site 5 out of 8 in 4fr8

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Magnesium binding site 5 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1002

b:38.9
occ:1.00
 O1B E:ADP1001 2.1 37.0 1.0
O1A E:ADP1001 2.3 33.8 1.0
O E:HOH1345 3.4 39.3 1.0
O E:HOH1335 3.5 28.7 1.0
PB E:ADP1001 3.6 48.9 1.0
PA E:ADP1001 3.7 28.4 1.0
O3A E:ADP1001 4.1 46.3 1.0
CG1 E:ILE249 4.3 25.9 1.0
O2B E:ADP1001 4.3 36.9 1.0
CD1 E:ILE249 4.5 21.5 1.0
C8 E:ADP1001 4.6 26.7 1.0
O3B E:ADP1001 4.6 38.1 1.0
O2A E:ADP1001 4.6 28.5 1.0
O5' E:ADP1001 4.6 31.2 1.0
N7 E:ADP1001 4.7 29.5 1.0
OG E:SER246 4.8 23.7 1.0

Magnesium binding site 6 out of 8 in 4fr8

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Magnesium binding site 6 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1002

b:52.0
occ:1.00
 O1A F:NAD1001 2.3 35.5 1.0
O1N F:NAD1001 2.4 47.4 1.0
O F:HOH1424 3.4 33.6 1.0
PA F:NAD1001 3.7 33.0 1.0
PN F:NAD1001 3.8 58.9 1.0
O F:HOH1368 3.9 33.6 1.0
CG1 F:ILE249 4.0 30.9 1.0
O3 F:NAD1001 4.3 45.8 1.0
CD1 F:ILE249 4.3 22.5 1.0
C8A F:NAD1001 4.4 25.9 1.0
N7A F:NAD1001 4.5 23.2 1.0
O2A F:NAD1001 4.6 29.2 1.0
O2N F:NAD1001 4.7 41.4 1.0
O5B F:NAD1001 4.7 32.8 1.0
C5D F:NAD1001 4.7 43.4 1.0
OG F:SER246 4.8 33.7 1.0
O5D F:NAD1001 4.9 52.0 1.0

Magnesium binding site 7 out of 8 in 4fr8

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Magnesium binding site 7 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1002

b:50.2
occ:1.00
 O1A G:ADP1001 2.2 31.5 1.0
O G:HOH1299 2.8 31.6 1.0
O1B G:ADP1001 3.6 32.8 1.0
PA G:ADP1001 3.7 30.1 1.0
C8 G:ADP1001 4.2 22.3 1.0
O5' G:ADP1001 4.4 31.8 1.0
PB G:ADP1001 4.4 54.5 1.0
O2B G:ADP1001 4.5 49.7 1.0
N7 G:ADP1001 4.5 25.6 1.0
O3A G:ADP1001 4.5 37.5 1.0
CG1 G:ILE249 4.6 20.4 1.0
O2A G:ADP1001 4.7 26.2 1.0
CD1 G:ILE249 4.8 25.8 1.0
O G:HOH1406 4.9 27.9 1.0

Magnesium binding site 8 out of 8 in 4fr8

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Magnesium binding site 8 out of 8 in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1002

b:45.6
occ:1.00
 O1A H:ADP1001 2.8 32.3 1.0
O H:HOH1300 3.0 29.1 1.0
O1B H:ADP1001 3.2 42.8 1.0
CG1 H:ILE249 4.0 24.9 1.0
CD1 H:ILE249 4.1 24.5 1.0
PA H:ADP1001 4.3 29.5 1.0
PB H:ADP1001 4.4 49.7 1.0
OG H:SER246 4.6 25.8 1.0
O2B H:ADP1001 4.7 45.8 1.0
O H:HOH1432 4.8 24.6 1.0
O3A H:ADP1001 4.8 44.6 1.0
N7 H:ADP1001 4.9 22.2 1.0
OE1 H:GLU248 4.9 56.8 1.0
OE2 H:GLU248 5.0 48.4 1.0
C8 H:ADP1001 5.0 20.9 1.0

Reference:

B.S.Lang, A.C.Gorren, G.Oberdorfer, M.V.Wenzl, C.M.Furdui, L.B.Poole, B.Mayer, K.Gruber. Vascular Bioactivation of Nitroglycerin By Aldehyde Dehydrogenase-2: Reaction Intermediates Revealed By Crystallography and Mass Spectrometry. J.Biol.Chem. V. 287 38124 2012.
ISSN: ISSN 0021-9258
PubMed: 22988236
DOI: 10.1074/JBC.M112.371716
Page generated: Fri Aug 16 15:15:10 2024

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