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Magnesium in PDB 4fqf: Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2

Enzymatic activity of Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2

All present enzymatic activity of Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2:
1.2.1.3;

Protein crystallography data

The structure of Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2, PDB code: 4fqf 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) 19.80 / 2.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 136.862, 148.431, 176.005, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.9

Other elements in 4fqf:

The structure of Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 (pdb code 4fqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2, PDB code: 4fqf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4fqf

Go back to Magnesium Binding Sites List in 4fqf
Magnesium binding site 1 out of 4 in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2


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 A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:50.9
occ:1.00
 O A:HOH1018 2.6 33.4 1.0
O1N A:NAD702 2.7 32.3 1.0
O1A A:NAD702 2.9 26.3 1.0
PN A:NAD702 4.1 30.3 1.0
PA A:NAD702 4.3 16.8 1.0
C8A A:NAD702 4.7 15.4 1.0
O3 A:NAD702 4.7 26.0 1.0
O A:HOH886 4.8 24.6 1.0
N7A A:NAD702 4.8 17.7 1.0
O2N A:NAD702 4.9 31.2 1.0

Magnesium binding site 2 out of 4 in 4fqf

Go back to Magnesium Binding Sites List in 4fqf
Magnesium binding site 2 out of 4 in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2


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 A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg704

b:35.5
occ:1.00
 O1A B:NAD703 2.2 25.7 1.0
O1N B:NAD703 2.5 25.6 1.0
O B:HOH2197 3.0 29.5 1.0
O B:HOH2226 3.0 33.5 1.0
PA B:NAD703 3.6 18.0 1.0
PN B:NAD703 3.8 27.2 1.0
O3 B:NAD703 4.0 25.1 1.0
CG1 B:ILE249 4.3 16.8 1.0
C8A B:NAD703 4.5 14.8 1.0
CD1 B:ILE249 4.6 18.0 1.0
O2A B:NAD703 4.6 23.2 1.0
C5D B:NAD703 4.6 25.7 1.0
N7A B:NAD703 4.6 20.9 1.0
O5B B:NAD703 4.7 17.6 1.0
O5D B:NAD703 4.8 26.8 1.0
O2N B:NAD703 4.9 29.0 1.0

Magnesium binding site 3 out of 4 in 4fqf

Go back to Magnesium Binding Sites List in 4fqf
Magnesium binding site 3 out of 4 in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2


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 A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:41.4
occ:1.00
 O1A C:NAD703 2.4 24.9 1.0
O1N C:NAD703 2.4 37.6 1.0
O C:HOH922 3.4 29.2 1.0
PA C:NAD703 3.9 19.7 1.0
PN C:NAD703 3.9 36.8 1.0
O3 C:NAD703 4.3 30.6 1.0
CG1 C:ILE249 4.4 24.4 1.0
C8A C:NAD703 4.5 16.9 1.0
N7A C:NAD703 4.6 17.3 1.0
CD1 C:ILE249 4.6 19.3 1.0
C5D C:NAD703 4.8 31.0 1.0
O2A C:NAD703 4.8 22.3 1.0
O5B C:NAD703 4.8 24.9 1.0
O2N C:NAD703 4.9 35.0 1.0
O5D C:NAD703 4.9 31.5 1.0

Magnesium binding site 4 out of 4 in 4fqf

Go back to Magnesium Binding Sites List in 4fqf
Magnesium binding site 4 out of 4 in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2


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 A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:35.4
occ:1.00
 O1A D:NAD702 2.2 28.8 1.0
O1N D:NAD702 2.3 31.9 1.0
PN D:NAD702 3.6 35.6 1.0
PA D:NAD702 3.6 25.6 1.0
O3 D:NAD702 4.1 32.4 1.0
C8A D:NAD702 4.2 20.4 1.0
N7A D:NAD702 4.4 23.1 1.0
CG1 D:ILE249 4.4 28.5 1.0
O2N D:NAD702 4.5 33.2 1.0
O5B D:NAD702 4.5 20.1 1.0
O2A D:NAD702 4.7 29.6 1.0
CD1 D:ILE249 4.7 21.8 1.0
O5D D:NAD702 4.8 40.6 1.0
C5D D:NAD702 4.9 38.8 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 Dec 14 15:38:48 2020

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