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Sodium in PDB 7a6q: Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound

Enzymatic activity of Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound

All present enzymatic activity of Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound:
1.2.1.36;

Protein crystallography data

The structure of Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound, PDB code: 7a6q was solved by E.L.M.Gelardi, S.Garavaglia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.32 / 2.95
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 83.162, 89.509, 158.646, 90, 90, 90
R / Rfree (%) 19.4 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound (pdb code 7a6q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound, PDB code: 7a6q:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7a6q

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Sodium binding site 1 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:97.8
occ:1.00
 O A:GLN208 2.6 77.8 1.0
O A:CYS52 2.9 91.2 1.0
N A:CYS52 3.4 77.8 1.0
C A:GLN208 3.5 66.1 1.0
OG1 A:THR51 3.6 92.2 1.0
OD1 A:ASP121 3.7 99.2 1.0
CA A:GLN208 3.7 55.6 1.0
C A:CYS52 3.8 82.7 1.0
O A:ASP121 3.8 86.2 1.0
CB A:GLN208 3.9 64.5 1.0
CA A:CYS52 4.1 87.6 1.0
C A:THR51 4.3 83.7 1.0
CA A:THR51 4.4 85.0 1.0
CB A:CYS52 4.5 106.5 1.0
CB A:THR51 4.5 90.7 1.0
CG A:GLN208 4.7 67.3 1.0
N A:THR209 4.7 64.9 1.0
CG A:ASP121 4.8 91.4 1.0
C A:ASP121 4.9 79.1 1.0
CG2 A:THR209 4.9 84.7 1.0
N A:ASN53 4.9 90.6 1.0

Sodium binding site 2 out of 6 in 7a6q

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Sodium binding site 2 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:56.7
occ:1.00
 OE1 A:GLU169 3.4 70.5 1.0
O B:SER456 4.2 66.0 1.0
NH2 A:ARG89 4.2 40.3 1.0
O B:ALA457 4.3 58.7 1.0
CD A:GLU169 4.3 52.5 1.0
CG B:GLU459 4.3 61.5 1.0
NH1 A:ARG89 4.7 53.7 1.0
C B:ALA457 4.8 46.7 1.0
OE2 A:GLU169 4.9 64.0 1.0
CZ A:ARG89 5.0 45.5 1.0
OE2 B:GLU459 5.0 69.7 1.0

Sodium binding site 3 out of 6 in 7a6q

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Sodium binding site 3 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:126.5
occ:1.00
 NA1 B:R2K604 0.0 126.5 1.0
O05 B:R2K604 1.9 101.6 1.0
O B:ASP121 3.1 90.5 1.0
C04 B:R2K604 3.3 108.3 1.0
O B:ILE357 3.4 122.5 1.0
CD1 B:ILE357 3.4 104.9 1.0
CB B:GLN208 3.6 70.6 1.0
CG B:PRO54 3.7 86.0 1.0
CG2 B:THR209 3.8 70.0 1.0
O B:GLN208 3.9 89.0 1.0
H032 B:R2K604 4.0 116.4 1.0
O07 B:R2K604 4.0 101.7 1.0
OD1 B:ASP358 4.1 129.9 1.0
C B:ASP121 4.1 75.7 1.0
CA B:THR122 4.1 88.1 1.0
C03 B:R2K604 4.2 97.0 1.0
CG B:GLN208 4.3 80.6 1.0
C B:GLN208 4.4 79.0 1.0
C B:ILE357 4.4 130.1 1.0
CD B:PRO54 4.4 86.6 1.0
CG1 B:ILE357 4.5 99.4 1.0
CA B:GLN208 4.5 68.6 1.0
N B:THR122 4.6 80.3 1.0
H031 B:R2K604 4.7 116.4 1.0
CG B:ASP358 4.7 134.1 1.0
CA B:ILE357 4.8 114.2 1.0
O B:CYS52 4.8 100.6 1.0
C B:THR122 4.9 86.9 1.0
CB B:PRO54 4.9 88.8 1.0
O B:THR122 5.0 70.7 1.0
CB B:THR122 5.0 84.7 1.0
CG2 B:THR122 5.0 80.8 1.0

Sodium binding site 4 out of 6 in 7a6q

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Sodium binding site 4 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:88.7
occ:1.00
 NA2 B:R2K604 0.0 88.7 1.0
O08 B:R2K604 1.9 114.3 1.0
C02 B:R2K604 3.3 113.4 1.0
CB B:GLU207 4.0 70.0 1.0
O01 B:R2K604 4.0 115.4 1.0
H032 B:R2K604 4.1 116.4 1.0
O B:ALA50 4.2 83.9 1.0
CZ B:PHE236 4.3 88.2 1.0
C03 B:R2K604 4.3 97.0 1.0
O B:GLU207 4.4 83.2 1.0
CE2 B:PHE236 4.4 90.7 1.0
C B:GLU207 4.4 72.4 1.0
N B:GLN208 4.6 64.2 1.0
CA B:GLN208 4.7 68.6 1.0
CG B:GLN208 4.8 80.6 1.0
OD2 B:ASP358 4.9 121.8 1.0
CA B:GLU207 4.9 62.2 1.0
H031 B:R2K604 4.9 116.4 1.0
CD2 B:PHE49 5.0 73.6 1.0

Sodium binding site 5 out of 6 in 7a6q

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Sodium binding site 5 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na606

b:67.0
occ:1.00
 O B:HIS168 3.6 51.1 1.0
NH2 B:ARG96 3.7 61.6 1.0
CG2 B:ILE151 4.6 37.5 1.0
O B:CYS197 4.6 45.7 1.0
CD B:PRO170 4.7 33.9 1.0
CZ B:ARG96 4.8 68.5 1.0
C B:HIS168 4.8 47.8 1.0
CB B:ILE151 4.8 45.1 1.0
O B:ILE151 4.9 49.0 1.0

Sodium binding site 6 out of 6 in 7a6q

Go back to Sodium Binding Sites List in 7a6q
Sodium binding site 6 out of 6 in the Crystal Structure of Human Aldehyde Dehydrogenase 1A3 in Complex with Selective NR6 Inhibitor Compound


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 1A3 in Complex with Selective NR6 Inhibitor Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:83.7
occ:1.00
 CD1 B:ILE425 3.1 88.0 1.0
NZ B:LYS453 4.0 99.4 1.0
CD B:LYS453 4.5 103.5 1.0
CG1 B:ILE425 4.6 87.9 1.0
CG B:LYS450 4.7 62.9 1.0
CE B:LYS453 4.9 99.2 1.0

Reference:

E.L.M.Gelardi, G.Colombo, F.Picarazzi, D.M.Ferraris, A.Mangione, G.Petrarolo, E.Aronica, M.Rizzi, M.Mori, C.La Motta, S.Garavaglia. A Selective Competitive Inhibitor of Aldehyde Dehydrogenase 1A3 Hinders Cancer Cell Growth, Invasiveness and Stemness in Vitro. Cancers (Basel) V. 13 2021.
ISSN: ESSN 2072-6694
PubMed: 33478031
DOI: 10.3390/CANCERS13020356
Page generated: Tue Oct 8 15:49:34 2024

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