Magnesium in PDB 5jal: Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening

Enzymatic activity of Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening

All present enzymatic activity of Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening:
3.1.1.47;

Protein crystallography data

The structure of Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening, PDB code: 5jal was solved by P.J.Day, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.90 / 2.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.663, 91.329, 51.422, 90.00, 111.79, 90.00
R / Rfree (%) 15.5 / 19.6

Other elements in 5jal:

The structure of Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening (pdb code 5jal). 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 Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening, PDB code: 5jal:

Magnesium binding site 1 out of 1 in 5jal

Go back to Magnesium Binding Sites List in 5jal
Magnesium binding site 1 out of 1 in the Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Exploitation of A Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-Pla2) Discovered Through X-Ray Fragment Screening within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:17.5
occ:0.50
 O A:HOH889 2.2 23.7 0.5
O A:GLU285 2.3 17.6 1.0
O A:HOH738 2.4 22.0 1.0
C A:GLU285 3.4 19.1 1.0
CA A:ASP286 4.0 15.0 1.0
CG A:GLU285 4.1 43.3 1.0
O A:HOH746 4.1 16.0 1.0
N A:ASP286 4.2 15.4 1.0
CB A:ASP286 4.2 14.7 1.0
O A:HOH808 4.2 16.5 1.0
CA A:GLU285 4.5 17.5 1.0
CB A:GLU285 4.5 19.7 1.0
CG A:ASP286 4.6 16.5 1.0
OE1 A:GLU285 4.6 32.7 1.0
OG A:SER230 4.7 21.9 1.0
CD A:GLU285 4.9 55.1 1.0
OD1 A:ASP286 4.9 18.2 1.0
OD2 A:ASP286 4.9 15.5 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: Mon Dec 14 20:33:06 2020

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