Magnesium in PDB 5jad: Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening

Enzymatic activity of Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening

All present enzymatic activity of Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening:
3.1.1.47;

Protein crystallography data

The structure of Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening, PDB code: 5jad was solved by P.J.Day, A.J.-A.Woolford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	32.31 / 2.05
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	98.970, 91.029, 51.191, 90.00, 112.05, 90.00
*R / R_free (%)*	24.5 / 29.8

Other elements in 5jad:

The structure of Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening (pdb code 5jad). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening, PDB code: 5jad:

Magnesium binding site 1 out of 1 in 5jad

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Magnesium Binding Sites List in 5jad

Magnesium binding site 1 out of 1 in the Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Compound Binding to Human Lipoprotein-Associated Phospholipase A2 (Lp- PLA2)Discovered Through Fragment Screening within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg501 b:26.0 occ:0.50	O	A:GLU285	2.0	19.8	1.0
	O	A:HOH613	2.5	34.9	1.0
	C	A:GLU285	3.1	21.5	1.0
	O	A:HOH725	3.4	23.3	0.5
	CB	A:GLU285	3.9	19.1	1.0
	N	A:ASP286	4.0	19.3	1.0
	CA	A:GLU285	4.1	19.2	1.0
	CA	A:ASP286	4.1	18.6	1.0
	CB	A:ASP286	4.3	18.5	1.0
	CG	A:GLU285	4.4	29.1	1.0
	O	A:HOH708	4.4	21.5	1.0
	OE1	A:GLU285	4.4	33.1	1.0
	O	A:HOH637	4.6	21.9	1.0
	CG	A:ASP286	4.8	25.6	1.0
	OG	A:SER230	4.9	26.2	1.0
	CD	A:GLU285	4.9	52.7	1.0

Reference:

A.J.Woolford, J.E.Pero, S.Aravapalli, V.Berdini, J.E.Coyle, P.J.Day, A.M.Dodson, P.Grondin, F.P.Holding, L.Y.Lee, P.Li, E.S.Manas, J.Marino, A.C.Martin, B.W.Mccleland, R.L.Mcmenamin, C.W.Murray, C.E.Neipp, L.W.Page, V.K.Patel, F.Potvain, S.Rich, R.A.Rivero, K.Smith, D.O.Somers, L.Trottet, R.Velagaleti, G.Williams, R.Xie. Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered Through X-Ray Fragment Screening. J.Med.Chem. V. 59 5356 2016.
ISSN: ISSN 0022-2623
PubMed: 27167608
DOI: 10.1021/ACS.JMEDCHEM.6B00212

Page generated: Sun Sep 29 17:39:40 2024

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