Nickel in PDB 2oq7: The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine

All present enzymatic activity of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine:
1.14.11.27;

The structure of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine, PDB code: 2oq7 was solved by K.L.Kavanagh, S.S.Ng, E.Pilka, M.A.Mcdonough, P.Savitsky, F.Von Delft, C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofield, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.120, 148.531, 57.333, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.8

The structure of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine (pdb code 2oq7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine, PDB code: 2oq7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:33.7 occ:1.00 O A:HOH653 1.8 21.6 1.0 NE2 A:HIS276 1.9 25.1 1.0 O2 A:OGA601 2.1 29.2 1.0 OE1 A:GLU190 2.2 28.6 1.0 O2' A:OGA601 2.2 33.3 1.0 NE2 A:HIS188 2.3 30.2 1.0 CE1 A:HIS276 2.8 38.3 1.0 C1 A:OGA601 2.9 48.8 1.0 C2 A:OGA601 2.9 35.3 1.0 CD2 A:HIS276 3.1 32.1 1.0 CE1 A:HIS188 3.1 24.5 1.0 CD A:GLU190 3.1 32.9 1.0 CD2 A:HIS188 3.3 35.7 1.0 OE2 A:GLU190 3.4 31.0 1.0 ND1 A:HIS276 4.0 33.5 1.0 O1 A:OGA601 4.1 34.5 1.0 CG A:HIS276 4.1 27.9 1.0 OG A:SER196 4.1 31.6 1.0 N1 A:OGA601 4.2 53.9 1.0 ND1 A:HIS188 4.2 36.9 1.0 O A:HOH642 4.3 38.4 1.0 CG A:HIS188 4.4 26.3 1.0 CG A:GLU190 4.5 31.4 1.0 NZ A:LYS241 4.7 28.4 0.5 CB A:SER196 4.8 30.6 1.0 C4 A:OGA601 4.8 34.3 1.0

Nickel binding site 2 out of 2 in the The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of JMJD2A Complexed with Ni and N-Oxalylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:36.0 occ:1.00 O B:HOH678 2.0 19.1 1.0 NE2 B:HIS276 2.0 32.8 1.0 NE2 B:HIS188 2.1 31.4 1.0 O2 B:OGA601 2.2 31.3 1.0 OE1 B:GLU190 2.2 38.5 1.0 O2' B:OGA601 2.3 33.6 1.0 CE1 B:HIS276 2.9 32.1 1.0 C1 B:OGA601 3.0 54.0 1.0 C2 B:OGA601 3.0 30.9 1.0 CE1 B:HIS188 3.0 33.1 1.0 CD2 B:HIS276 3.1 34.2 1.0 CD B:GLU190 3.2 38.1 1.0 CD2 B:HIS188 3.2 35.5 1.0 OE2 B:GLU190 3.5 31.8 1.0 ND1 B:HIS276 4.0 33.1 1.0 ND1 B:HIS188 4.1 26.5 1.0 CG B:HIS276 4.2 28.1 1.0 O1 B:OGA601 4.2 41.5 1.0 OG B:SER196 4.2 40.6 1.0 N1 B:OGA601 4.2 51.5 1.0 CG B:HIS188 4.3 31.0 1.0 CG B:GLU190 4.5 30.4 1.0 CB B:SER196 4.9 34.5 1.0 C4 B:OGA601 4.9 44.4 1.0

S.S.Ng, K.L.Kavanagh, M.A.Mcdonough, D.Butler, E.S.Pilka, B.M.Lienard, J.E.Bray, P.Savitsky, O.Gileadi, F.Von Delft, N.R.Rose, J.Offer, J.C.Scheinost, T.Borowski, M.Sundstrom, C.J.Schofield, U.Oppermann. Crystal Structures of Histone Demethylase JMJD2A Reveal Basis For Substrate Specificity. Nature V. 448 87 2007.
ISSN: ISSN 0028-0836
PubMed: 17589501
DOI: 10.1038/NATURE05971