Nickel 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:

Zinc

(Zn)

1 atom

The binding sites of Nickel 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 Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Human JMJD2D in Complex with N- Oxalylglycine and Bound 5,6-Dimethylbenzimidazole, PDB code: 4d6s:

Nickel 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 Nickel with other atoms in the Ni 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:Ni1339 b:10.0 occ:0.66 OE2 A:GLU194 2.0 13.2 1.0 O2' A:OGA1341 2.1 18.6 1.0 O A:HOH2273 2.1 17.6 1.0 NE2 A:HIS280 2.2 12.5 1.0 O1 A:OGA1341 2.2 16.4 1.0 NE2 A:HIS192 2.2 13.8 1.0 C2 A:OGA1341 2.7 29.1 1.0 C1 A:OGA1341 2.8 17.3 1.0 CE1 A:HIS280 3.0 12.4 1.0 CD A:GLU194 3.1 10.6 1.0 CE1 A:HIS192 3.1 13.1 1.0 CD2 A:HIS280 3.3 10.6 1.0 CD2 A:HIS192 3.3 13.6 1.0 OE1 A:GLU194 3.4 13.1 1.0 O2 A:OGA1341 4.1 16.8 1.0 N1 A:OGA1341 4.1 22.4 1.0 ND1 A:HIS280 4.1 10.2 1.0 ND1 A:HIS192 4.2 13.0 1.0 OG A:SER200 4.3 11.1 0.8 CG A:HIS280 4.3 8.9 1.0 CG A:GLU194 4.4 10.1 1.0 CG A:HIS192 4.4 12.3 1.0 O2 A:EDO1343 4.4 42.5 1.0 C4 A:OGA1341 4.7 26.5 1.0 O A:HOH2332 4.8 42.8 1.0 CB A:SER200 4.8 10.7 0.2 OG A:SER200 4.8 10.9 0.2 CB A:SER200 4.9 10.4 0.8

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.