Nickel in PDB 2ot7: Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9

The structure of Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9, PDB code: 2ot7 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)	20.00 / 2.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.209, 149.842, 57.470, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 24.1

The structure of Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9 (pdb code 2ot7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9, PDB code: 2ot7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9


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 JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:38.3 occ:1.00 O A:HOH612 2.0 24.1 1.0 O2 A:OGA500 2.1 37.3 1.0 OE2 A:GLU190 2.1 32.5 1.0 NE2 A:HIS276 2.1 35.9 1.0 O2' A:OGA500 2.1 41.9 1.0 NE2 A:HIS188 2.3 44.8 1.0 C1 A:OGA500 2.9 48.8 1.0 C2 A:OGA500 2.9 44.8 1.0 CE1 A:HIS276 3.0 36.3 1.0 CE1 A:HIS188 3.0 36.6 1.0 CD A:GLU190 3.1 35.1 1.0 CD2 A:HIS276 3.2 34.7 1.0 OE1 A:GLU190 3.4 34.2 1.0 CD2 A:HIS188 3.4 38.0 1.0 O1 A:OGA500 4.1 43.9 1.0 N1 A:OGA500 4.1 47.0 1.0 ND1 A:HIS276 4.2 35.2 1.0 OG A:SER196 4.2 38.0 1.0 ND1 A:HIS188 4.2 39.0 1.0 O A:HOH613 4.2 37.9 1.0 CG A:HIS276 4.3 35.4 1.0 CG A:HIS188 4.4 37.6 1.0 CG A:GLU190 4.4 34.0 1.0 O A:HOH532 4.5 30.9 1.0 CB A:SER196 4.8 29.4 1.0 CG2 A:THR270 4.8 33.0 1.0 C4 A:OGA500 4.9 44.3 1.0 OG1 A:THR270 4.9 31.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of JMJD2A Complexed with Histone H3 Peptide Monomethylated at LYS9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:39.9 occ:1.00 O B:HOH581 2.1 25.9 1.0 OE2 B:GLU190 2.1 40.2 1.0 O2 B:OGA500 2.2 43.1 1.0 O2' B:OGA500 2.2 40.2 1.0 NE2 B:HIS188 2.2 35.8 1.0 NE2 B:HIS276 2.2 37.0 1.0 C2 B:OGA500 2.9 37.4 1.0 C1 B:OGA500 2.9 47.4 1.0 CE1 B:HIS188 3.1 32.5 1.0 CD B:GLU190 3.1 40.1 1.0 CE1 B:HIS276 3.2 31.2 1.0 CD2 B:HIS188 3.2 29.5 1.0 CD2 B:HIS276 3.3 31.8 1.0 OE1 B:GLU190 3.5 41.2 1.0 O1 B:OGA500 4.1 45.7 1.0 N1 B:OGA500 4.1 43.2 1.0 OG B:SER196 4.2 41.7 1.0 ND1 B:HIS188 4.2 33.1 1.0 O D:HOH215 4.3 31.3 1.0 ND1 B:HIS276 4.3 32.6 1.0 CG B:HIS188 4.3 29.3 1.0 CG B:HIS276 4.4 33.2 1.0 CG B:GLU190 4.5 31.4 1.0 C4 B:OGA500 4.8 45.4 1.0 O B:HOH603 4.9 9.8 0.5 CB B:SER196 4.9 32.4 1.0 CG2 B:THR270 4.9 38.3 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