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Sodium 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:

Magnesium (Mg) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Aldehyde Dehydrogenase-2 in Complex with Nitroglycerin, PDB code: 4fr8:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na605

b:27.5
occ:1.00
 O A:HOH1042 2.0 30.5 1.0
O A:GLN196 2.2 22.7 1.0
O A:ASP109 2.5 24.1 1.0
OD1 A:ASP109 2.6 19.0 1.0
O A:VAL40 2.7 22.0 1.0
O A:HOH806 2.8 28.7 1.0
OG1 A:THR39 3.1 25.6 1.0
C A:GLN196 3.4 22.6 1.0
CG A:ASP109 3.6 24.7 1.0
C A:ASP109 3.6 22.1 1.0
N A:VAL40 3.7 24.6 1.0
C A:VAL40 3.7 24.8 1.0
CA A:ASP109 4.1 17.0 1.0
CA A:GLN196 4.2 21.7 1.0
CA A:VAL40 4.3 21.9 1.0
OD2 A:ASP109 4.4 20.3 1.0
N A:THR197 4.4 20.6 1.0
CB A:THR39 4.4 20.2 1.0
CB A:ASP109 4.4 19.1 1.0
C A:THR39 4.4 24.7 1.0
CG2 A:THR197 4.4 18.2 1.0
CD A:PRO42 4.5 21.3 1.0
CA A:THR197 4.5 22.4 1.0
CB A:GLN196 4.6 21.0 1.0
CA A:THR39 4.7 25.5 1.0
N A:ASN110 4.8 20.2 1.0
N A:ASN41 4.9 18.3 1.0
O A:VAL345 5.0 21.7 1.0
CB A:VAL40 5.0 26.6 1.0

Sodium binding site 2 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1004

b:23.2
occ:1.00
 OD1 B:ASP109 2.3 22.2 1.0
O B:HOH1414 2.3 20.0 1.0
O B:GLN196 2.5 24.4 1.0
O B:ASP109 2.5 21.8 1.0
O B:VAL40 2.6 20.2 1.0
OG1 B:THR39 2.8 20.4 1.0
CG B:ASP109 3.3 23.1 1.0
O B:HOH1477 3.4 27.1 1.0
C B:ASP109 3.5 16.9 1.0
N B:VAL40 3.6 20.2 1.0
C B:VAL40 3.6 21.8 1.0
C B:GLN196 3.7 21.6 1.0
CA B:ASP109 3.8 13.7 1.0
OD2 B:ASP109 4.1 16.0 1.0
CB B:ASP109 4.1 19.8 1.0
CB B:THR39 4.2 20.0 1.0
CA B:VAL40 4.2 22.5 1.0
C B:THR39 4.3 21.0 1.0
CD B:PRO42 4.5 17.0 1.0
CA B:THR39 4.6 21.9 1.0
CA B:GLN196 4.6 19.2 1.0
N B:THR197 4.6 19.1 1.0
CG2 B:THR197 4.7 15.0 1.0
CA B:THR197 4.7 19.5 1.0
CD1 B:ILE48 4.7 17.6 1.0
N B:ASN41 4.7 21.3 1.0
N B:ASN110 4.7 22.3 1.0
CG2 B:THR39 4.9 20.3 1.0
CB B:VAL40 5.0 19.5 1.0

Sodium binding site 3 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1004

b:25.6
occ:1.00
 O C:HOH1438 2.2 21.4 1.0
O C:VAL40 2.4 21.7 1.0
O C:GLN196 2.4 19.0 1.0
O C:ASP109 2.4 18.6 1.0
OD1 C:ASP109 2.6 15.8 1.0
OG1 C:THR39 3.0 20.2 1.0
O C:HOH1138 3.3 24.0 1.0
C C:ASP109 3.5 17.2 1.0
C C:VAL40 3.5 22.8 1.0
N C:VAL40 3.6 24.7 1.0
CG C:ASP109 3.6 20.5 1.0
C C:GLN196 3.7 21.4 1.0
CA C:ASP109 3.8 14.8 1.0
CA C:VAL40 4.1 21.1 1.0
CB C:ASP109 4.3 16.6 1.0
CD C:PRO42 4.4 15.9 1.0
CB C:THR39 4.4 23.7 1.0
C C:THR39 4.4 17.4 1.0
OD2 C:ASP109 4.5 19.7 1.0
CA C:GLN196 4.5 21.6 1.0
N C:THR197 4.6 18.7 1.0
N C:ASN41 4.6 21.2 1.0
CG2 C:THR197 4.6 12.6 1.0
N C:ASN110 4.7 18.0 1.0
CA C:THR39 4.7 25.0 1.0
CA C:THR197 4.7 18.4 1.0
CB C:VAL40 4.8 26.7 1.0
O C:VAL345 4.8 21.1 1.0
CD1 C:ILE48 4.9 15.8 1.0
CA C:ASN41 5.0 22.4 1.0

Sodium binding site 4 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1004

b:25.1
occ:1.00
 O D:GLN196 2.4 16.8 1.0
O D:ASP109 2.5 17.5 1.0
OD1 D:ASP109 2.5 13.8 1.0
O D:VAL40 2.5 15.9 1.0
O D:HOH1296 2.6 17.4 1.0
OG1 D:THR39 2.9 19.1 1.0
O D:HOH1260 3.1 17.5 1.0
CG D:ASP109 3.4 16.2 1.0
C D:ASP109 3.4 13.6 1.0
C D:GLN196 3.6 13.5 1.0
N D:VAL40 3.6 18.0 1.0
C D:VAL40 3.6 14.7 1.0
CA D:ASP109 3.7 12.8 1.0
CB D:ASP109 4.1 15.7 1.0
OD2 D:ASP109 4.1 18.7 1.0
CA D:VAL40 4.2 15.0 1.0
CB D:THR39 4.2 14.7 1.0
CD D:PRO42 4.4 14.8 1.0
C D:THR39 4.4 14.7 1.0
CA D:GLN196 4.4 15.6 1.0
O D:HOH1350 4.5 17.0 1.0
N D:THR197 4.6 15.0 1.0
CD1 D:ILE48 4.6 10.6 1.0
CA D:THR39 4.7 16.5 1.0
N D:ASN110 4.7 14.5 1.0
N D:ASN41 4.7 16.9 1.0
CA D:THR197 4.7 17.0 1.0
CG2 D:THR197 4.8 12.9 1.0
CB D:GLN196 4.9 17.0 1.0
CB D:VAL40 4.9 16.0 1.0
CG2 D:THR39 5.0 15.2 1.0

Sodium binding site 5 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:28.5
occ:1.00
 OD1 E:ASP109 1.9 22.3 1.0
O E:GLN196 2.4 21.9 1.0
OG1 E:THR39 2.5 23.0 1.0
O E:VAL40 2.7 25.4 1.0
O E:ASP109 2.7 22.5 1.0
CG E:ASP109 2.9 26.0 1.0
O E:HOH1249 3.3 34.2 1.0
C E:ASP109 3.5 22.4 1.0
C E:GLN196 3.6 22.7 1.0
N E:VAL40 3.6 21.0 1.0
CA E:ASP109 3.6 22.4 1.0
OD2 E:ASP109 3.7 23.0 1.0
C E:VAL40 3.7 25.4 1.0
CB E:ASP109 3.8 21.1 1.0
O E:HOH1324 3.8 23.8 1.0
CB E:THR39 3.9 23.2 1.0
C E:THR39 4.1 20.2 1.0
CA E:VAL40 4.3 25.1 1.0
CA E:THR39 4.4 23.5 1.0
CD1 E:ILE48 4.5 19.9 1.0
N E:THR197 4.5 22.7 1.0
CA E:THR197 4.5 20.3 1.0
CA E:GLN196 4.6 25.8 1.0
CG2 E:THR39 4.6 22.7 1.0
CG2 E:THR197 4.7 17.4 1.0
N E:ASN110 4.8 21.8 1.0
N E:ASN41 4.8 23.5 1.0
CD E:PRO42 4.8 24.5 1.0
O E:THR39 4.9 20.1 1.0
CD E:PRO198 5.0 19.0 1.0

Sodium binding site 6 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:27.8
occ:1.00
 O F:ASP109 2.3 21.9 1.0
O F:HOH1423 2.4 34.9 1.0
OD1 F:ASP109 2.5 26.0 1.0
O F:GLN196 2.5 28.7 1.0
O F:VAL40 2.6 28.9 1.0
OG1 F:THR39 2.9 19.4 1.0
C F:ASP109 3.3 21.4 1.0
O F:HOH1180 3.3 29.9 1.0
CG F:ASP109 3.4 27.0 1.0
C F:VAL40 3.6 26.4 1.0
CA F:ASP109 3.7 21.6 1.0
C F:GLN196 3.7 26.5 1.0
N F:VAL40 3.8 25.4 1.0
CB F:ASP109 4.1 26.2 1.0
OD2 F:ASP109 4.2 23.3 1.0
CB F:THR39 4.3 24.4 1.0
CA F:VAL40 4.3 25.9 1.0
CD F:PRO42 4.4 21.3 1.0
C F:THR39 4.4 21.1 1.0
N F:ASN110 4.5 22.0 1.0
CG2 F:THR197 4.6 15.7 1.0
CA F:GLN196 4.6 23.2 1.0
N F:ASN41 4.7 25.0 1.0
N F:THR197 4.7 21.3 1.0
CA F:THR197 4.7 23.7 1.0
CA F:THR39 4.8 27.8 1.0
CD1 F:ILE48 4.9 21.4 1.0
O F:VAL345 5.0 26.8 1.0

Sodium binding site 7 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:27.8
occ:1.00
 O G:HOH1219 2.4 26.0 1.0
O G:GLN196 2.4 23.8 1.0
O G:VAL40 2.5 26.6 1.0
O G:ASP109 2.6 22.8 1.0
OG1 G:THR39 3.0 23.6 1.0
OD1 G:ASP109 3.1 28.5 1.0
C G:ASP109 3.6 21.2 1.0
C G:VAL40 3.6 27.6 1.0
C G:GLN196 3.6 22.6 1.0
CG G:ASP109 3.6 27.9 1.0
N G:VAL40 3.7 28.8 1.0
O G:HOH1236 3.8 28.4 1.0
CA G:ASP109 3.9 22.4 1.0
CA G:VAL40 4.2 27.0 1.0
OD2 G:ASP109 4.3 22.9 1.0
CB G:ASP109 4.3 24.0 1.0
CB G:THR39 4.3 26.9 1.0
C G:THR39 4.4 28.5 1.0
CA G:GLN196 4.4 22.0 1.0
CD G:PRO42 4.5 21.4 1.0
CG2 G:THR197 4.6 16.4 1.0
N G:THR197 4.6 20.9 1.0
N G:ASN41 4.7 25.5 1.0
CA G:THR39 4.7 31.1 1.0
CA G:THR197 4.7 22.5 1.0
N G:ASN110 4.7 24.1 1.0
CB G:VAL40 4.8 23.3 1.0
CD1 G:ILE48 4.9 26.2 1.0
CB G:GLN196 4.9 19.0 1.0
O G:VAL345 5.0 25.1 1.0

Sodium binding site 8 out of 8 in 4fr8

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Sodium 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 Sodium with other atoms in the Na 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:Na1003

b:15.2
occ:1.00
 O H:GLN196 2.4 13.0 1.0
O H:VAL40 2.4 16.1 1.0
O H:HOH1280 2.5 22.5 1.0
O H:ASP109 2.5 16.0 1.0
OD1 H:ASP109 2.5 15.6 1.0
OG1 H:THR39 3.1 19.6 1.0
O H:HOH1179 3.3 18.3 1.0
C H:ASP109 3.4 15.6 1.0
CG H:ASP109 3.4 18.4 1.0
C H:VAL40 3.5 20.1 1.0
C H:GLN196 3.6 13.3 1.0
N H:VAL40 3.7 17.1 1.0
CA H:ASP109 3.7 15.9 1.0
CB H:ASP109 4.1 15.7 1.0
CA H:VAL40 4.2 16.9 1.0
OD2 H:ASP109 4.3 17.9 1.0
CD H:PRO42 4.4 12.8 1.0
CB H:THR39 4.4 20.9 1.0
CA H:GLN196 4.5 17.3 1.0
C H:THR39 4.5 17.6 1.0
N H:THR197 4.5 14.9 1.0
CG2 H:THR197 4.6 10.3 1.0
CA H:THR197 4.6 13.2 1.0
N H:ASN41 4.6 16.4 1.0
O H:HOH1319 4.6 23.0 1.0
N H:ASN110 4.7 17.7 1.0
CD1 H:ILE48 4.7 16.4 1.0
CA H:THR39 4.8 18.3 1.0
CA H:ASN41 4.9 17.5 1.0
CB H:VAL40 5.0 21.2 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 15:27:32 2024

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