Sodium in PDB 6y5m: Crystal Structure of Mouse Autotaxin in Complex with Compound 1A

All present enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with Compound 1A:
3.1.4.39;

The structure of Crystal Structure of Mouse Autotaxin in Complex with Compound 1A, PDB code: 6y5m was solved by M.Faller, F.Zink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.89 / 2.01
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.257, 61.199, 67.827, 87.55, 73.05, 80.76
R / Rfree (%)	16.5 / 19.5

The structure of Crystal Structure of Mouse Autotaxin in Complex with Compound 1A also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Crystal Structure of Mouse Autotaxin in Complex with Compound 1A (pdb code 6y5m). 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 Mouse Autotaxin in Complex with Compound 1A, PDB code: 6y5m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Mouse Autotaxin in Complex with Compound 1A


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 Mouse Autotaxin in Complex with Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na915 b:14.5 occ:1.00 OD1 A:ASN741 2.3 26.9 1.0 O A:HOH1160 2.4 31.3 1.0 OD1 A:ASN743 2.4 25.1 1.0 OD1 A:ASP739 2.4 22.9 1.0 O A:LEU745 2.4 25.7 1.0 OD1 A:ASP747 2.4 27.9 1.0 CG A:ASN743 3.3 26.2 1.0 CG A:ASN741 3.4 26.3 1.0 C A:LEU745 3.5 25.4 1.0 CG A:ASP739 3.5 24.6 1.0 CG A:ASP747 3.6 28.5 1.0 ND2 A:ASN743 3.9 26.5 1.0 ND2 A:ASN741 3.9 26.2 1.0 N A:ASP747 4.0 27.6 1.0 CA A:ASP739 4.0 23.9 1.0 N A:LEU745 4.1 23.9 1.0 CA A:ASP747 4.1 29.9 1.0 C A:ARG746 4.1 26.6 1.0 CA A:LEU745 4.2 24.8 1.0 CB A:ASP739 4.3 24.3 1.0 N A:ASN743 4.3 23.8 1.0 OE1 A:GLU751 4.3 40.4 1.0 O A:ARG746 4.3 25.6 1.0 OD2 A:ASP739 4.4 25.3 1.0 CB A:ASP747 4.4 29.0 1.0 O A:PHE738 4.4 25.2 1.0 C A:ASP739 4.5 23.4 1.0 N A:ASN741 4.5 24.7 1.0 CB A:LEU745 4.5 25.5 1.0 CB A:ASN743 4.5 24.6 1.0 OD2 A:ASP747 4.5 29.5 1.0 N A:ARG746 4.5 25.4 1.0 O A:HOH1386 4.7 33.7 1.0 CB A:ASN741 4.7 25.2 1.0 N A:TYR740 4.8 23.8 1.0 CA A:ASN743 4.8 24.0 1.0 CA A:ARG746 4.8 26.6 1.0 N A:TYR742 4.8 25.2 1.0 C A:ASN741 4.8 25.5 1.0 CA A:ASN741 4.9 25.1 1.0 N A:GLY744 4.9 23.9 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Mouse Autotaxin in Complex with Compound 1A


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 Mouse Autotaxin in Complex with Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na916 b:51.8 occ:1.00 OE1 A:GLU592 2.2 57.4 1.0 O A:HOH1090 2.7 41.6 1.0 OE2 A:GLU618 2.7 37.5 1.0 OH A:TYR613 3.1 44.0 1.0 CD A:GLU592 3.2 56.3 1.0 CG A:GLU592 3.5 48.1 1.0 CD2 A:LEU596 3.5 33.7 1.0 CD A:GLU618 3.6 37.3 1.0 CE1 A:TYR613 3.7 38.2 1.0 OE1 A:GLU618 3.8 37.4 1.0 CZ A:TYR613 3.8 40.5 1.0 CG2 A:ILE611 4.3 32.7 1.0 OE2 A:GLU592 4.4 58.9 1.0 CB A:ARG600 4.6 33.3 1.0 CE2 A:TYR552 4.7 42.3 1.0 OH A:TYR552 4.9 45.1 1.0 CG A:GLU618 4.9 33.7 1.0 CD1 A:TYR613 4.9 36.5 1.0 CB A:GLU592 5.0 41.9 1.0 CG A:LEU596 5.0 32.6 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Mouse Autotaxin in Complex with Compound 1A


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 Mouse Autotaxin in Complex with Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na917 b:48.3 occ:1.00 O A:HOH1287 2.2 42.8 1.0 O A:HOH1420 2.7 64.7 1.0 O A:ARG162 2.9 36.7 1.0 OG A:SER301 3.1 35.0 1.0 CG A:PRO164 3.8 29.4 1.0 CB A:SER301 3.9 30.0 1.0 C A:ARG162 3.9 37.4 1.0 N A:PRO164 4.1 28.8 1.0 CA A:SER301 4.1 27.1 1.0 CD A:PRO164 4.1 28.2 1.0 CA A:PRO164 4.3 27.5 1.0 CD1 A:PHE160 4.3 40.2 1.0 N A:ARG162 4.3 41.6 1.0 CB A:PRO164 4.4 28.6 1.0 C A:PRO163 4.5 30.2 1.0 O A:PRO300 4.6 27.0 1.0 CA A:ARG162 4.6 40.0 1.0 NE A:ARG299 4.6 38.4 1.0 NH2 A:ARG299 4.8 39.4 1.0 CB A:ARG162 4.8 41.0 1.0 N A:PRO163 4.9 35.2 1.0 N A:VAL161 4.9 44.5 1.0 O A:HOH1449 4.9 60.7 1.0 O A:PRO163 4.9 29.3 1.0 CE1 A:PHE160 5.0 40.6 1.0 N A:SER301 5.0 26.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Mouse Autotaxin in Complex with Compound 1A


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 Mouse Autotaxin in Complex with Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na918 b:38.6 occ:1.00 O A:TYR205 2.6 23.4 1.0 O A:HOH1004 2.6 25.4 1.0 O A:LEU432 2.7 22.0 1.0 O A:HOH1305 2.8 30.5 1.0 CD A:PRO222 3.4 19.6 1.0 C A:TYR205 3.6 22.0 1.0 N A:TYR205 3.7 20.3 1.0 O A:HIS433 3.8 22.6 1.0 CG A:PRO222 3.8 21.1 1.0 C A:LEU432 3.9 21.9 1.0 CA A:TYR205 4.1 20.9 1.0 CD1 A:TYR434 4.1 21.4 1.0 CB A:TYR205 4.1 20.7 1.0 CB A:VAL204 4.2 19.5 1.0 C A:HIS433 4.3 22.1 1.0 CB A:TYR434 4.4 22.0 1.0 N A:PRO222 4.4 20.6 1.0 CB A:PRO222 4.5 20.9 1.0 C A:VAL204 4.6 19.9 1.0 CD1 A:TYR221 4.7 20.7 1.0 CB A:HIS433 4.7 22.0 1.0 CG1 A:VAL204 4.7 20.8 1.0 CG A:TYR434 4.7 21.2 1.0 N A:TYR434 4.7 21.1 1.0 CB A:TYR221 4.8 19.4 1.0 CA A:TYR434 4.8 21.7 1.0 CA A:LEU432 4.8 22.1 1.0 N A:HIS433 4.8 21.1 1.0 N A:PRO206 4.8 22.0 1.0 CA A:VAL204 4.8 19.4 1.0 CA A:HIS433 4.8 22.0 1.0 CG2 A:VAL204 5.0 19.6 1.0

C.G.Thomson, D.Legrand, M.Dowling, D.Beattie, L.Elphick, M.Faller, M.Freeman, E.Hardaker, V.Head, R.Hemmig, J.Hill, A.Lister, D.Pascoe, S.Rieffel, B.Shresta, O.Steward, F.Zink. Development of Autotaxin Inhibitors: A Series of Tetrazole Cinnamides. Bioorg.Med.Chem.Lett. 27663 2020.
ISSN: ESSN 1464-3405
PubMed: 33160025
DOI: 10.1016/J.BMCL.2020.127663