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Sodium 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:

Magnesium (Mg) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Thionitrate Intermediate of Human Aldehyde Dehydrogenase-2, PDB code: 4fqf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4fqf

Go back to Sodium Binding Sites List in 4fqf
Sodium 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 Sodium with other atoms in the Na 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:Na705

b:21.5
occ:1.00
 O A:GLN196 2.2 17.6 1.0
OD1 A:ASP109 2.4 19.5 1.0
O A:ASP109 2.6 14.9 1.0
O A:VAL40 2.7 21.5 1.0
O A:HOH816 2.9 19.8 1.0
O A:HOH827 3.0 20.5 1.0
OG1 A:THR39 3.1 18.3 1.0
C A:GLN196 3.4 18.3 1.0
CG A:ASP109 3.4 17.4 1.0
C A:ASP109 3.5 17.7 1.0
C A:VAL40 3.7 20.8 1.0
N A:VAL40 3.8 18.3 1.0
CA A:ASP109 3.8 11.7 1.0
CB A:ASP109 4.1 14.1 1.0
CA A:GLN196 4.2 17.4 1.0
CA A:VAL40 4.3 18.4 1.0
OD2 A:ASP109 4.3 16.2 1.0
CG2 A:THR197 4.4 15.6 1.0
N A:THR197 4.4 17.3 1.0
CA A:THR197 4.5 15.7 1.0
CB A:THR39 4.5 15.4 1.0
CD A:PRO42 4.6 17.1 1.0
C A:THR39 4.6 20.0 1.0
CB A:GLN196 4.7 18.7 1.0
N A:ASN110 4.7 20.3 1.0
N A:ASN41 4.8 20.1 1.0
CA A:THR39 4.9 18.1 1.0

Sodium binding site 2 out of 4 in 4fqf

Go back to Sodium Binding Sites List in 4fqf
Sodium 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 Sodium with other atoms in the Na 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:Na706

b:23.5
occ:1.00
 O B:GLN196 2.4 14.4 1.0
O B:VAL40 2.5 12.3 1.0
O B:ASP109 2.5 16.4 1.0
OD1 B:ASP109 2.7 11.1 1.0
O B:HOH2354 2.7 28.1 1.0
O B:HOH2353 3.0 20.6 1.0
OG1 B:THR39 3.3 18.2 1.0
C B:ASP109 3.6 18.2 1.0
C B:VAL40 3.6 17.4 1.0
C B:GLN196 3.6 14.8 1.0
CG B:ASP109 3.6 16.8 1.0
N B:VAL40 3.7 15.8 1.0
CA B:ASP109 4.0 13.9 1.0
CA B:VAL40 4.2 14.6 1.0
CD B:PRO42 4.3 13.0 1.0
CB B:ASP109 4.4 13.2 1.0
CA B:GLN196 4.4 16.6 1.0
OD2 B:ASP109 4.4 17.7 1.0
CG2 B:THR197 4.5 11.3 1.0
C B:THR39 4.6 14.0 1.0
CB B:THR39 4.6 14.9 1.0
N B:THR197 4.6 13.3 1.0
N B:ASN41 4.7 16.1 1.0
CA B:THR197 4.7 14.1 1.0
CB B:GLN196 4.8 17.2 1.0
N B:ASN110 4.8 16.1 1.0
CB B:VAL40 4.9 16.2 1.0
CA B:THR39 4.9 19.3 1.0
CD1 B:ILE48 5.0 14.3 1.0

Sodium binding site 3 out of 4 in 4fqf

Go back to Sodium Binding Sites List in 4fqf
Sodium 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 Sodium with other atoms in the Na 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:Na705

b:24.1
occ:1.00
 O C:GLN196 2.2 16.6 1.0
OD1 C:ASP109 2.4 20.3 1.0
O C:ASP109 2.5 15.9 1.0
O C:HOH934 2.8 22.5 1.0
O C:VAL40 2.8 22.0 1.0
OG1 C:THR39 3.1 16.8 1.0
O C:HOH802 3.2 16.5 1.0
CG C:ASP109 3.2 20.4 1.0
C C:GLN196 3.4 18.9 1.0
C C:ASP109 3.4 20.9 1.0
CA C:ASP109 3.8 16.6 1.0
N C:VAL40 3.9 18.8 1.0
OD2 C:ASP109 3.9 21.4 1.0
C C:VAL40 3.9 18.9 1.0
CB C:ASP109 4.1 16.7 1.0
CG2 C:THR197 4.2 17.5 1.0
CA C:GLN196 4.3 18.2 1.0
N C:THR197 4.3 16.4 1.0
CA C:THR197 4.4 17.4 1.0
CB C:THR39 4.4 16.1 1.0
CA C:VAL40 4.5 18.4 1.0
CD C:PRO42 4.6 17.4 1.0
N C:ASN110 4.6 17.7 1.0
C C:THR39 4.7 16.8 1.0
CB C:GLN196 4.8 16.9 1.0
CA C:THR39 4.9 19.8 1.0
CB C:THR197 5.0 19.8 1.0

Sodium binding site 4 out of 4 in 4fqf

Go back to Sodium Binding Sites List in 4fqf
Sodium 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 Sodium with other atoms in the Na 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:Na705

b:30.7
occ:1.00
 O D:GLN196 2.2 25.1 1.0
OD1 D:ASP109 2.4 27.6 1.0
O D:ASP109 2.5 24.2 1.0
O D:VAL40 2.7 29.3 1.0
O D:HOH926 2.9 28.7 1.0
OG1 D:THR39 3.0 27.2 1.0
O D:HOH918 3.1 27.1 1.0
CG D:ASP109 3.4 24.3 1.0
C D:GLN196 3.4 21.0 1.0
C D:ASP109 3.5 28.3 1.0
N D:VAL40 3.8 28.6 1.0
C D:VAL40 3.8 29.8 1.0
CA D:ASP109 3.9 20.3 1.0
OD2 D:ASP109 4.1 24.5 1.0
CB D:ASP109 4.2 22.8 1.0
CA D:GLN196 4.3 22.9 1.0
CB D:THR39 4.3 28.5 1.0
CA D:VAL40 4.4 28.2 1.0
CG2 D:THR197 4.4 22.9 1.0
N D:THR197 4.4 22.1 1.0
CD D:PRO42 4.4 22.4 1.0
CA D:THR197 4.5 21.6 1.0
C D:THR39 4.5 27.7 1.0
N D:ASN110 4.7 25.2 1.0
CA D:THR39 4.8 29.9 1.0
CB D:GLN196 4.8 21.4 1.0
N D:ASN41 4.9 29.1 1.0
CG2 D:THR39 5.0 21.6 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 Oct 7 15:27:31 2024

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