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Chlorine in PDB 5jao: 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: 5jao 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) 30.79 / 2.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.649, 90.931, 51.199, 90.00, 111.91, 90.00
R / Rfree (%) 15.6 / 21.3

Other elements in 5jao:

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:

Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 5jao). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where 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: 5jao:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5jao

Go back to Chlorine Binding Sites List in 5jao
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl502

b:29.1
occ:1.00
 O A:HOH1112 2.9 40.1 1.0
N A:HIS351 3.3 12.5 1.0
CB A:HIS351 3.7 13.2 1.0
O A:HOH615 3.7 15.1 1.0
CB A:VAL350 3.8 18.4 1.0
N A:PHE322 3.8 16.1 1.0
CA A:PHE322 3.8 15.1 1.0
NZ A:LYS370 3.9 90.8 1.0
C A:TYR321 3.9 18.9 1.0
CA A:VAL350 3.9 14.2 1.0
CB A:PHE322 4.0 14.7 1.0
CE A:LYS370 4.0 85.0 1.0
O A:TYR321 4.0 20.5 1.0
CA A:HIS351 4.1 12.9 1.0
C A:VAL350 4.1 15.7 1.0
CB A:TYR321 4.3 22.3 1.0
CG1 A:VAL350 4.3 19.9 1.0
CD1 A:PHE322 4.6 15.9 1.0
CA A:TYR321 4.6 18.6 1.0
CG A:PHE322 4.8 14.3 1.0
OG A:SER319 4.9 18.6 1.0
CG2 A:VAL350 5.0 18.0 1.0
CG A:HIS351 5.0 14.2 1.0

Chlorine binding site 2 out of 2 in 5jao

Go back to Chlorine Binding Sites List in 5jao
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl504

b:26.2
occ:0.81
 CL A:6HX504 0.0 26.2 0.8
C14 A:6HX504 1.7 21.6 0.8
C13 A:6HX504 2.7 20.4 0.8
C9 A:6HX504 2.7 20.5 0.8
H27 A:6HX504 2.8 19.8 0.8
H18 A:6HX504 2.9 20.0 0.8
C8 A:6HX504 3.1 16.4 0.8
CD1 A:LEU371 3.4 20.8 1.0
C2 A:6HX504 3.5 17.8 0.8
C1 A:6HX504 3.6 19.8 0.8
CD1 A:PHE357 3.8 21.6 1.0
C7 A:6HX504 3.9 18.7 0.8
CB A:ALA360 3.9 18.0 1.0
C12 A:6HX504 4.0 19.9 0.8
C10 A:6HX504 4.0 19.9 0.8
CG2 A:THR361 4.0 22.6 1.0
H23 A:6HX504 4.1 19.2 0.8
CB A:PHE357 4.1 17.8 1.0
H17 A:6HX504 4.2 20.3 0.8
O A:PHE357 4.2 15.2 1.0
H16 A:6HX504 4.2 19.1 0.8
O A:HOH1114 4.3 0.6 1.0
CG A:PHE357 4.3 19.5 1.0
CZ A:PHE125 4.4 23.7 1.0
CA A:PHE357 4.4 15.4 1.0
C3 A:6HX504 4.5 21.5 0.8
C11 A:6HX504 4.5 19.6 0.8
CG A:LEU371 4.6 21.7 1.0
CE1 A:PHE357 4.7 23.4 1.0
CD2 A:LEU371 4.7 20.9 1.0
H26 A:6HX504 4.7 18.4 0.8
CE2 A:PHE125 4.7 25.5 1.0
H24 A:6HX504 4.7 19.5 0.8
CE1 A:PHE125 4.8 24.4 1.0
C A:PHE357 4.8 16.6 1.0
C5 A:6HX504 4.8 20.1 0.8

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: Sat Dec 12 11:52:40 2020

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