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Calcium in PDB 5jap: 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: 5jap 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) 44.24 / 2.46
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.927, 90.661, 51.303, 90.00, 111.55, 90.00
R / Rfree (%) 17.3 / 24.6

Other elements in 5jap:

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:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 5jap). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium 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: 5jap:

Calcium binding site 1 out of 1 in 5jap

Go back to Calcium Binding Sites List in 5jap
Calcium 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 Calcium with other atoms in the Ca 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:Ca501

b:50.9
occ:0.50
 O A:HOH680 2.4 21.8 1.0
O A:GLU285 2.5 20.0 1.0
O A:HOH868 2.5 29.8 0.5
C A:GLU285 3.3 22.0 1.0
CB A:GLU285 4.0 23.8 1.0
CA A:GLU285 4.1 22.3 1.0
N A:ASP286 4.1 20.1 1.0
CA A:ASP286 4.2 19.7 1.0
O A:HOH792 4.2 22.4 1.0
O A:HOH607 4.3 3.0 0.5
CB A:ASP286 4.3 19.4 1.0
CG A:GLU285 4.5 39.8 1.0
OE1 A:GLU285 4.6 37.8 1.0
CG A:ASP286 4.6 25.9 1.0
OG A:SER230 4.7 32.1 1.0
OD1 A:ASP286 4.8 28.0 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: Wed Jul 9 07:05:15 2025

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