Sodium in PDB 5m0s: Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

Enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

All present enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors:
3.1.4.39;

Protein crystallography data

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0s was solved by W.-J.Keune, T.Heidebrecht, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	75.29 / 2.10
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	62.826, 88.857, 77.293, 90.00, 103.08, 90.00
*R / R_free (%)*	23.8 / 28.6

Other elements in 5m0s:

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iodine	(I)	13 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0s:

Sodium binding site 1 out of 1 in 5m0s

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Sodium Binding Sites List in 5m0s

Sodium binding site 1 out of 1 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na926 b:59.1 occ:1.00	O	A:MET675	2.6	50.0	1.0
	O	A:TYR669	2.7	54.6	1.0
	O	A:ASP672	2.9	53.3	1.0
	C	A:MET675	3.5	49.0	1.0
	C	A:TYR669	3.8	54.9	1.0
	C	A:ASP672	4.0	53.8	1.0
	N	A:SER676	4.1	48.3	1.0
	CA	A:SER676	4.2	48.7	1.0
	N	A:MET675	4.4	49.5	1.0
	CA	A:MET675	4.6	48.5	1.0
	O	A:LYS673	4.6	53.9	1.0
	O	A:LYS670	4.6	58.1	1.0
	C	A:LYS673	4.6	53.6	1.0
	CA	A:LYS673	4.7	54.9	1.0
	N	A:LYS670	4.7	56.3	1.0
	CA	A:TYR669	4.7	53.6	1.0
	CA	A:LYS670	4.8	57.7	1.0
	CB	A:SER676	4.8	49.0	1.0
	N	A:LYS673	4.8	54.4	1.0
	C	A:LYS670	5.0	57.9	1.0
	CB	A:TYR669	5.0	53.2	1.0

Reference:

W.J.Keune, F.Potjewyd, T.Heidebrecht, F.Salgado-Polo, S.J.Macdonald, L.Chelvarajan, A.Abdel Latif, S.Soman, A.J.Morris, A.J.Watson, C.Jamieson, A.Perrakis. Rational Design of Autotaxin Inhibitors By Structural Evolution of Endogenous Modulators. J. Med. Chem. V. 60 2006 2017.
ISSN: ISSN 1520-4804
PubMed: 28165241
DOI: 10.1021/ACS.JMEDCHEM.6B01743

Page generated: Mon Oct 7 22:27:56 2024

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