Zinc in PDB 2vd7: Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid, PDB code: 2vd7 was solved by S.S.Ng, F.Von Delft, E.S.Pilka, K.L.Kavanagh, M.A.Mcdonough, P.Savitsky, C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofield, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.63 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.285, 149.121, 57.566, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 21.9

The structure of Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid (pdb code 2vd7). 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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid, PDB code: 2vd7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid


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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:39.2 occ:1.00 NE2 A:HIS240 2.1 42.4 1.0 SG A:CYS306 2.2 43.7 1.0 SG A:CYS234 2.3 44.1 1.0 SG A:CYS308 2.4 49.3 1.0 CE1 A:HIS240 3.1 41.9 1.0 CD2 A:HIS240 3.1 40.3 1.0 CB A:CYS306 3.3 44.0 1.0 CB A:CYS234 3.4 47.1 1.0 CB A:CYS308 3.5 50.9 1.0 N A:CYS308 3.7 50.0 1.0 CA A:CYS306 3.9 44.2 1.0 N A:SER307 4.0 46.6 1.0 CA A:CYS308 4.1 51.6 1.0 ND1 A:HIS240 4.2 42.0 1.0 C A:CYS306 4.2 45.3 1.0 CG A:HIS240 4.3 41.8 1.0 N A:ARG309 4.3 56.5 1.0 CG A:ARG309 4.4 60.6 1.0 C A:CYS308 4.5 53.9 1.0 O A:HOH2116 4.6 41.6 1.0 O A:ALA236 4.6 40.9 1.0 CD A:ARG309 4.7 60.5 1.0 CA A:CYS234 4.7 47.4 1.0 C A:SER307 4.7 49.2 1.0 CA A:PHE237 4.9 40.1 1.0 CB A:ARG309 4.9 59.5 1.0 CA A:SER307 5.0 48.4 1.0 C A:ALA236 5.0 41.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid


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 JMJD2A Complexed with Inhibitor Pyridine-2,4- Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:39.4 occ:1.00 NE2 B:HIS240 2.1 42.2 1.0 SG B:CYS306 2.2 43.8 1.0 SG B:CYS234 2.3 46.4 1.0 SG B:CYS308 2.4 46.9 1.0 CE1 B:HIS240 3.0 43.1 1.0 CD2 B:HIS240 3.2 38.5 1.0 CB B:CYS234 3.2 48.0 1.0 CB B:CYS306 3.4 44.8 1.0 CB B:CYS308 3.6 51.7 1.0 N B:CYS308 3.7 51.3 1.0 CA B:CYS306 3.9 45.1 1.0 N B:SER307 3.9 48.5 1.0 CA B:CYS308 4.1 52.0 1.0 ND1 B:HIS240 4.1 41.6 1.0 C B:CYS306 4.2 46.7 1.0 CG B:HIS240 4.3 42.0 1.0 N B:ARG309 4.3 56.5 1.0 CA B:CYS234 4.5 47.9 1.0 C B:CYS308 4.5 54.3 1.0 O B:HOH2125 4.6 35.6 1.0 O B:ALA236 4.6 42.4 1.0 C B:SER307 4.8 51.0 1.0 CD B:ARG309 4.8 60.7 1.0 CA B:PHE237 4.9 39.2 1.0 CA B:SER307 4.9 50.0 1.0 CG B:ARG309 4.9 59.9 1.0 NE B:ARG309 5.0 63.0 1.0 C B:ALA236 5.0 42.2 1.0

N.R.Rose, S.S.Ng, J.Mecinovic, B.M.Lienard, S.H.Bello, Z.Sun, M.A.Mcdonough, U.Oppermann, C.J.Schofield. Inhibitor Scaffolds For 2-Oxoglutarate-Dependent Histone Lysine Demethylases. J. Med. Chem. V. 51 7053 2008.
ISSN: ISSN 1520-4804
PubMed: 18942826
DOI: 10.1021/JM800936S