Zinc in PDB 4d6s: Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole

The structure of Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole, PDB code: 4d6s was solved by T.Krojer, M.Vollmar, A.Bradley, L.Crawley, A.Szykowska, N.Burgess-Brown, C.Gileadi, C.Johansson, U.Oppermann, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.324 / 1.40
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.225, 71.225, 150.208, 90.00, 90.00, 90.00
R / Rfree (%)	13.92 / 16.39

The structure of Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole (pdb code 4d6s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole, PDB code: 4d6s:

Zinc binding site 1 out of 1 in the Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole


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 JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1338 b:17.8 occ:1.00 NE2 A:HIS244 2.1 17.3 1.0 SG A:CYS238 2.2 21.4 1.0 SG A:CYS310 2.3 21.5 1.0 SG A:CYS312 2.3 21.6 1.0 CE1 A:HIS244 3.0 16.3 1.0 CB A:CYS238 3.1 22.0 1.0 CD2 A:HIS244 3.1 15.5 1.0 CB A:CYS310 3.3 21.9 1.0 CB A:CYS312 3.3 25.4 1.0 N A:CYS312 3.8 31.6 1.0 CA A:CYS310 4.0 23.8 1.0 CA A:CYS312 4.0 29.4 1.0 ND1 A:HIS244 4.1 15.8 1.0 CG A:HIS244 4.2 14.7 1.0 CB A:GLU314 4.2 35.3 1.0 N A:GLU314 4.3 32.0 1.0 N A:SER311 4.4 36.0 1.0 N A:GLY313 4.4 32.8 1.0 CA A:CYS238 4.5 21.9 1.0 C A:CYS310 4.5 31.1 1.0 C A:CYS312 4.5 31.3 1.0 O A:HOH2326 4.7 35.6 1.0 N A:ALA315 4.7 31.1 1.0 O A:ALA240 4.8 16.8 1.0 CA A:PHE241 4.8 14.7 1.0 CA A:GLU314 4.8 33.6 1.0 CG A:GLU314 5.0 38.8 1.0 C A:SER311 5.0 36.5 1.0 C A:ALA240 5.0 16.7 1.0

T.Krojer, M.Vollmar, A.Bradley, L.Crawley, A.Szykowska, N.Burgess-Brown, C.Gileadi, C.Johansson, U.Oppermann, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Crystal Structure of Human JMJD2D in Complex with N-Oxalylglycine and Bound 5,6- Dimethylbenzimidazole To Be Published.