Sodium in PDB 5lz9: Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2

Enzymatic activity of Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2

All present enzymatic activity of Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2:
3.1.1.47;

Protein crystallography data

The structure of Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2, PDB code: 5lz9 was solved by A.Woolford, P.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	44.39 / 2.06
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	100.044, 91.332, 51.357, 90.00, 111.97, 90.00
*R / R_free (%)*	18.3 / 23.3

Other elements in 5lz9:

The structure of Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2 also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2 (pdb code 5lz9). 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 Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2, PDB code: 5lz9:

Sodium binding site 1 out of 1 in 5lz9

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Sodium Binding Sites List in 5lz9

Sodium binding site 1 out of 1 in the Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fragment-Based Inhibitors of Lipoprotein Associated Phospholipase A2 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na502 b:39.4 occ:0.50	O	A:HOH819	2.1	33.1	0.5
	O	A:GLU285	2.4	38.6	1.0
	O	A:HOH700	2.5	28.1	0.5
	C	A:GLU285	3.5	37.6	1.0
	O	A:HOH676	4.1	35.5	1.0
	CA	A:ASP286	4.1	35.1	1.0
	O	A:HOH761	4.1	33.3	1.0
	CB	A:ASP286	4.2	33.7	1.0
	N	A:ASP286	4.2	35.6	1.0
	CG	A:ASP286	4.5	34.8	1.0
	CA	A:GLU285	4.5	38.2	1.0
	CB	A:GLU285	4.7	39.9	1.0
	OG	A:SER230	4.7	31.3	1.0
	OD2	A:ASP286	4.8	35.5	1.0
	OD1	A:ASP286	5.0	36.2	1.0

Reference:

A.J.Woolford, P.J.Day, V.Beneton, V.Berdini, J.E.Coyle, Y.Dudit, P.Grondin, P.Huet, L.Y.Lee, E.S.Manas, R.L.Mcmenamin, C.W.Murray, L.W.Page, V.K.Patel, F.Potvain, S.J.Rich, Y.Sang, D.O.Somers, L.Trottet, Z.Wan, X.Zhang. Fragment-Based Approach to the Development of An Orally Bioavailable Lactam Inhibitor of Lipoprotein-Associated Phospholipase A2 (Lp-PLA2). J. Med. Chem. V. 59 10738 2016.
ISSN: ISSN 1520-4804
PubMed: 27933945
DOI: 10.1021/ACS.JMEDCHEM.6B01427

Page generated: Mon Oct 7 22:27:04 2024

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