Atomistry » Magnesium » PDB 4fk1-4fs5 » 4fr8
Atomistry »
  Magnesium »
    PDB 4fk1-4fs5 »
      4fr8 »

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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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

Go back to Magnesium Binding Sites List in 4fr8
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: Mon Aug 11 13:01:34 2025

Last articles

Mg in 4JI0
Mg in 4JI2
Mg in 4JI3
Mg in 4JHD
Mg in 4JH6
Mg in 4JH8
Mg in 4JH7
Mg in 4JH3
Mg in 4JH5
Mg in 4JF2
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy