Nickel in PDB 4d6q: Crystal Structure of Human JMJD2D in Complex with 2,4-Pdca

The structure of Crystal Structure of Human JMJD2D in Complex with 2,4-Pdca, PDB code: 4d6q 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)	33.435 / 1.29
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.910, 71.910, 151.060, 90.00, 90.00, 90.00
R / Rfree (%)	13.48 / 16.13

The structure of Crystal Structure of Human JMJD2D in Complex with 2,4-Pdca 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 2,4-Pdca (pdb code 4d6q). 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 2,4-Pdca, PDB code: 4d6q:

Nickel binding site 1 out of 1 in the Crystal Structure of Human JMJD2D in Complex with 2,4-Pdca


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 2,4-Pdca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1342 b:10.7 occ:0.65 OE2 A:GLU194 2.1 14.6 1.0 N1 A:PD21343 2.1 17.5 1.0 O22 A:PD21343 2.1 19.0 1.0 O A:HOH2287 2.2 22.5 1.0 NE2 A:HIS192 2.2 12.7 1.0 NE2 A:HIS280 2.3 12.0 1.0 C2 A:PD21343 2.9 19.4 1.0 C21 A:PD21343 3.0 20.7 1.0 CE1 A:HIS280 3.1 11.4 1.0 CE1 A:HIS192 3.1 13.5 1.0 CD A:GLU194 3.1 12.6 1.0 C6 A:PD21343 3.1 17.2 1.0 CD2 A:HIS192 3.3 12.1 1.0 CD2 A:HIS280 3.4 11.7 1.0 OE1 A:GLU194 3.5 14.8 1.0 O1 A:EDO1348 3.9 43.0 1.0 O A:HOH2293 4.1 50.6 1.0 O A:HOH2286 4.1 30.5 1.0 O21 A:PD21343 4.1 24.7 1.0 ND1 A:HIS192 4.2 12.9 1.0 ND1 A:HIS280 4.2 11.0 1.0 C3 A:PD21343 4.3 19.6 1.0 CG A:HIS192 4.4 11.7 1.0 CG A:HIS280 4.4 9.9 1.0 CG A:GLU194 4.4 11.4 1.0 C5 A:PD21343 4.4 18.1 1.0 OG A:SER200 4.5 10.8 0.7 C4 A:PD21343 4.9 19.2 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 2,4-Pdca To Be Published.