Zinc in PDB 5a7n: Crystal Structure of Human JMJD2A in Complex with Compound 43

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 43, PDB code: 5a7n was solved by R.Nowak, 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.Ortiz Torres, E.Williams, E.Riesebos, 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)	54.00 / 2.39
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.120, 149.760, 57.890, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 24.5

The structure of Crystal Structure of Human JMJD2A in Complex with Compound 43 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2A in Complex with Compound 43 (pdb code 5a7n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human JMJD2A in Complex with Compound 43, PDB code: 5a7n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human JMJD2A in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:37.8 occ:1.00 SG A:CYS306 2.1 35.9 1.0 NE2 A:HIS240 2.1 40.3 1.0 SG A:CYS234 2.3 35.2 1.0 SG A:CYS308 2.3 40.6 1.0 CE1 A:HIS240 3.0 35.6 1.0 CD2 A:HIS240 3.2 36.3 1.0 CB A:CYS306 3.3 34.6 1.0 CB A:CYS234 3.3 37.2 1.0 CB A:CYS308 3.6 45.5 1.0 N A:CYS308 3.6 53.7 1.0 CA A:CYS306 3.9 38.7 1.0 N A:SER307 4.0 39.9 1.0 CA A:CYS308 4.1 48.6 1.0 ND1 A:HIS240 4.1 34.4 1.0 C A:CYS306 4.2 41.5 1.0 CG A:HIS240 4.2 31.1 1.0 C A:CYS308 4.5 44.1 1.0 CA A:CYS234 4.6 41.9 1.0 N A:ARG309 4.6 50.5 1.0 O A:ALA236 4.7 35.3 1.0 CG A:ARG309 4.7 61.5 1.0 C A:SER307 4.7 55.2 1.0 CA A:PHE237 4.9 31.3 1.0 CD A:ARG309 4.9 60.7 1.0 CA A:SER307 4.9 47.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human JMJD2A in Complex with Compound 43


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human JMJD2A in Complex with Compound 43 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:36.4 occ:1.00 SG B:CYS306 2.1 36.8 1.0 NE2 B:HIS240 2.2 42.8 1.0 SG B:CYS234 2.2 40.9 1.0 SG B:CYS308 2.3 40.1 1.0 CE1 B:HIS240 3.1 33.5 1.0 CD2 B:HIS240 3.1 30.9 1.0 CB B:CYS306 3.3 41.6 1.0 CB B:CYS234 3.3 40.5 1.0 CB B:CYS308 3.6 42.1 1.0 N B:CYS308 3.6 50.7 1.0 CA B:CYS306 3.8 45.5 1.0 N B:SER307 3.9 51.2 1.0 CA B:CYS308 4.1 46.5 1.0 C B:CYS306 4.1 49.5 1.0 ND1 B:HIS240 4.2 32.1 1.0 CG B:HIS240 4.3 33.9 1.0 N B:ARG309 4.5 58.0 1.0 C B:CYS308 4.6 52.7 1.0 O B:ALA236 4.6 33.8 1.0 CA B:CYS234 4.7 48.5 1.0 CG B:ARG309 4.7 54.6 1.0 C B:SER307 4.7 60.0 1.0 CD B:ARG309 4.8 51.5 1.0 CA B:PHE237 4.8 36.6 1.0 NE B:ARG309 4.9 49.3 1.0 CA B:SER307 4.9 58.7 1.0 C B:ALA236 5.0 39.8 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