Nickel in PDB 5pkd: Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98), PDB code: 5pkd was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, M.Vollmar, J.Ng, A.Szykowska, N.Burgess-Brown, P.E.Brennan, O.Cox, 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)	29.36 / 1.55
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.338, 71.338, 150.219, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19

The structure of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98) also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Nickel atom in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98) (pdb code 5pkd). 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 Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98), PDB code: 5pkd:

Nickel binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of JMJD2D After Initial Refinement with No Ligand Modelled (Structure 98) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni402 b:11.6 occ:0.84 O2' A:OGA404 2.0 13.4 0.8 O2 A:OGA404 2.0 13.4 0.8 OE1 A:GLU194 2.0 14.2 1.0 NE2 A:HIS280 2.1 12.0 1.0 O A:HOH598 2.2 18.5 1.0 NE2 A:HIS192 2.2 15.5 1.0 C2 A:OGA404 2.7 15.2 0.8 C1 A:OGA404 2.8 14.1 0.8 CE1 A:HIS280 3.0 12.3 1.0 CE1 A:HIS192 3.1 16.5 1.0 CD A:GLU194 3.1 13.3 1.0 CD2 A:HIS280 3.2 11.8 1.0 CD2 A:HIS192 3.3 13.3 1.0 OE2 A:GLU194 3.4 14.1 1.0 O1 A:OGA404 4.0 14.0 0.8 N1 A:OGA404 4.0 16.7 0.8 OG A:SER200 4.1 9.0 0.6 ND1 A:HIS280 4.2 10.9 1.0 O A:HOH523 4.2 40.7 1.0 ND1 A:HIS192 4.2 15.4 1.0 O1 A:EDO412 4.3 34.9 1.0 CG A:HIS280 4.3 10.8 1.0 CG A:HIS192 4.4 12.9 1.0 CG A:GLU194 4.4 11.5 1.0 O A:HOH854 4.7 43.6 1.0 CB A:SER200 4.7 14.8 0.4 CB A:SER200 4.8 9.9 0.6 C4 A:OGA404 4.8 19.3 0.8 OG A:SER200 4.8 21.4 0.4 C1 A:EDO412 4.9 33.5 1.0 OG1 A:THR274 5.0 12.6 1.0

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123