Chlorine in PDB 5a7q: Crystal Structure of Human JMJD2A in Complex with Compound 30

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 30, PDB code: 5a7q was solved by S.Velupillai, T.Krojer, C.Gileadi, C.Johansson, M.Korczynska, D.D.Le, N.Younger, E.Gregori-Puigjane, A.Tumber, E.Iwasa, S.B.Pollock, I.Ortiztorres, J.Kopec, S.Dixon-Clarke, A.Mackenzie, R.Nowak, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, B.K.Shoichet, D.G.Fujimori, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.73 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.194, 149.080, 57.627, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 23.1

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 30 also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Zinc	(Zn)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human JMJD2A in Complex with Compound 30 (pdb code 5a7q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human JMJD2A in Complex with Compound 30, PDB code: 5a7q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Human JMJD2A in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human JMJD2A in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1358 b:64.6 occ:1.00 N A:LEU238 3.2 27.6 1.0 CB A:LEU238 3.3 27.6 1.0 C A:ALA236 3.3 30.3 1.0 CA A:ALA236 3.4 36.7 1.0 O A:HOH2117 3.4 73.0 1.0 N A:PHE237 3.5 28.8 1.0 CG A:LEU238 3.5 28.2 1.0 O A:HOH2118 3.7 48.2 1.0 CA A:LEU238 3.8 26.8 1.0 O A:ALA236 3.9 30.2 1.0 CD1 A:LEU238 3.9 26.7 1.0 CB A:ALA236 4.0 31.1 1.0 OH A:TYR275 4.1 29.4 1.0 C A:PHE237 4.2 29.3 1.0 CA A:PHE237 4.4 33.0 1.0 CD1 A:PHE237 4.5 34.4 1.0 N A:ARG239 4.5 27.5 1.0 N A:ALA236 4.5 37.0 1.0 C A:LEU238 4.7 28.8 1.0 O A:GLU235 4.7 52.8 1.0 O A:HOH2112 4.8 55.0 1.0 O A:HOH2088 4.8 45.5 1.0 CE1 A:PHE237 4.9 33.5 1.0 CD2 A:LEU238 4.9 20.8 1.0 CG A:GLU220 4.9 29.2 1.0 OE2 A:GLU220 4.9 36.8 1.0 CD A:GLU220 4.9 39.5 1.0 CG A:PHE237 4.9 33.5 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Human JMJD2A in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human JMJD2A in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1359 b:76.2 occ:1.00 OG A:SER288 3.0 49.1 1.0 O A:GLY170 3.2 35.0 1.0 OH A:TYR177 3.5 50.8 1.0 CB A:SER288 4.1 45.0 1.0 C A:GLY170 4.1 36.2 1.0 O17 A:KCH1356 4.2 33.0 1.0 CA A:THR289 4.2 29.9 1.0 C A:SER288 4.2 29.9 1.0 N A:THR289 4.2 30.3 1.0 C05 A:KCH1356 4.3 38.6 1.0 O A:SER288 4.3 38.0 1.0 C04 A:KCH1356 4.3 43.7 1.0 CA A:GLY170 4.5 30.1 1.0 C A:THR289 4.5 32.2 1.0 CZ A:TYR177 4.5 44.3 1.0 CE1 A:TYR177 4.6 46.6 1.0 OD1 A:ASN290 4.6 35.2 1.0 OE1 A:GLU190 4.7 27.2 1.0 CD2 A:TYR175 4.8 42.3 1.0 O A:HOH2061 4.8 50.8 1.0 CB A:TYR175 4.8 40.9 1.0 O A:THR289 4.8 31.5 1.0 CA A:SER288 4.8 35.2 1.0 C06 A:KCH1356 4.9 51.8 1.0 N A:ASN290 5.0 28.4 1.0 C03 A:KCH1356 5.0 44.8 1.0 CG A:ASN290 5.0 34.1 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Human JMJD2A in Complex with Compound 30


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human JMJD2A in Complex with Compound 30 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1359 b:88.9 occ:1.00 OG B:SER288 3.2 65.0 1.0 O B:GLY170 3.3 48.1 1.0 OH B:TYR177 3.6 64.8 1.0 C05 B:KCH1357 4.2 54.7 1.0 C04 B:KCH1357 4.2 59.9 1.0 CB B:SER288 4.2 50.3 1.0 O17 B:KCH1357 4.2 38.8 1.0 C B:GLY170 4.3 60.7 1.0 C B:SER288 4.3 38.6 1.0 CA B:THR289 4.3 42.1 1.0 N B:THR289 4.3 37.1 1.0 CD2 B:TYR175 4.4 68.0 1.0 O B:SER288 4.4 38.4 1.0 CZ B:TYR177 4.5 51.5 1.0 CE1 B:TYR177 4.5 49.5 1.0 O B:HOH2088 4.5 57.4 1.0 OD1 B:ASN290 4.5 45.0 1.0 CA B:GLY170 4.5 62.8 1.0 C B:THR289 4.6 40.3 1.0 CB B:TYR175 4.7 46.1 1.0 OE1 B:GLU190 4.8 31.9 1.0 C06 B:KCH1357 4.8 59.4 1.0 C03 B:KCH1357 4.8 61.8 1.0 O B:HOH2106 4.8 49.6 1.0 CG B:TYR175 4.9 52.5 1.0 CA B:SER288 4.9 37.6 1.0 O B:THR289 5.0 42.1 1.0

M.Korczynska, D.D.Le, N.Younger, E.Gregori-Puigjane, A.Tumber, T.Krojer, S.Velupillai, C.Gileadi, R.P.Nowak, E.Iwasa, S.B.Pollock, I.Ortiz Torres, U.Oppermann, B.K.Shoichet, D.G.Fujimori. Docking and Linking of Fragments to Discover Jumonji Histone Demethylase Inhibitors. J.Med.Chem. V. 59 1580 2016.
ISSN: ISSN 0022-2623
PubMed: 26699912
DOI: 10.1021/ACS.JMEDCHEM.5B01527