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Chlorine in PDB 5jar: 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: 5jar 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) 46.33 / 2.11
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.767, 90.797, 51.348, 90.00, 111.76, 90.00
R / Rfree (%) 14.4 / 20.4

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 5jar). 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: 5jar:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5jar

Go back to Chlorine Binding Sites List in 5jar
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:21.4
occ:1.00
N A:ALA326 3.2 17.0 1.0
CD A:PRO325 3.6 18.5 1.0
CB A:ALA326 3.7 16.8 1.0
N A:PRO325 3.8 16.9 1.0
CD1 A:TYR324 3.8 19.7 1.0
CB A:TYR324 4.0 16.6 1.0
CA A:ALA326 4.0 16.7 1.0
CB A:PRO325 4.1 17.9 1.0
C A:PRO325 4.2 20.7 1.0
CA A:PRO325 4.2 15.9 1.0
C A:TYR324 4.3 19.7 1.0
CG A:PRO325 4.3 21.8 1.0
CG A:TYR324 4.4 18.0 1.0
CA A:TYR324 4.8 16.5 1.0
CE1 A:TYR324 4.9 16.8 1.0
O A:TYR324 5.0 19.2 1.0

Chlorine binding site 2 out of 2 in 5jar

Go back to Chlorine Binding Sites List in 5jar
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:Cl503

b:37.4
occ:1.00
O A:HOH1174 2.9 42.0 1.0
N A:HIS351 3.1 13.9 1.0
CB A:HIS351 3.6 14.4 1.0
CB A:VAL350 3.6 16.9 1.0
O A:HOH604 3.7 19.5 1.0
N A:PHE322 3.8 19.3 1.0
CA A:VAL350 3.8 14.9 1.0
CA A:PHE322 3.9 17.9 1.0
CB A:PHE322 3.9 17.2 1.0
CA A:HIS351 4.0 14.6 1.0
C A:VAL350 4.0 17.4 1.0
C A:TYR321 4.0 22.5 1.0
O A:TYR321 4.2 21.4 1.0
NZ A:LYS370 4.2 95.7 1.0
CG1 A:VAL350 4.3 17.9 1.0
CB A:TYR321 4.4 24.8 1.0
CD1 A:PHE322 4.7 16.9 1.0
CE A:LYS370 4.7 79.2 1.0
CG2 A:VAL350 4.8 15.8 1.0
CA A:TYR321 4.8 21.3 1.0
CG A:PHE322 4.8 16.4 1.0
O A:HOH804 4.9 47.0 1.0
CG A:HIS351 4.9 16.0 1.0
OG A:SER319 5.0 17.3 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: Sat Dec 12 11:52:42 2020

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