Nickel in PDB 4v2v: JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa, PDB code: 4v2v was solved by R.Chowdhury, S.K.Madden, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.589 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.020, 149.910, 57.380, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.08

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Nickel atom in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa (pdb code 4v2v). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa, PDB code: 4v2v:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1357 b:28.4 occ:1.00 NE2 A:HIS276 2.1 23.7 1.0 OE2 A:GLU190 2.1 23.8 1.0 O A:HOH2127 2.2 37.0 1.0 O2' A:OGA1356 2.2 38.6 1.0 NE2 A:HIS188 2.3 25.9 1.0 O1 A:OGA1356 2.3 36.9 1.0 C2 A:OGA1356 3.0 42.5 1.0 C1 A:OGA1356 3.0 41.1 1.0 CE1 A:HIS276 3.1 24.3 1.0 CD2 A:HIS276 3.1 24.8 1.0 CE1 A:HIS188 3.1 26.9 1.0 CD A:GLU190 3.1 24.2 1.0 CD2 A:HIS188 3.3 24.6 1.0 OE1 A:GLU190 3.5 24.7 1.0 ND1 A:HIS276 4.2 24.1 1.0 O A:HOH2126 4.2 54.8 1.0 OG A:SER196 4.2 30.4 1.0 CG A:HIS276 4.2 22.6 1.0 O2 A:OGA1356 4.2 39.1 1.0 ND1 A:HIS188 4.2 26.7 1.0 N1 A:OGA1356 4.3 46.0 1.0 CG A:HIS188 4.3 23.1 1.0 O A:HOH2133 4.4 46.0 1.0 CG A:GLU190 4.5 19.7 1.0 CM2 C:M3L27 4.6 47.9 1.0 CG2 A:THR270 4.9 34.5 1.0 CB A:SER196 4.9 27.7 1.0 C4 A:OGA1356 5.0 46.7 1.0

Nickel binding site 2 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (25-29) Ark(ME3)Sa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1356 b:35.6 occ:1.00 OE2 B:GLU190 2.2 30.6 1.0 O2' B:OGA1355 2.2 35.9 1.0 NE2 B:HIS188 2.2 27.4 1.0 NE2 B:HIS276 2.2 19.9 1.0 O1 B:OGA1355 2.3 36.0 1.0 O B:HOH2122 2.5 39.9 1.0 C2 B:OGA1355 2.9 37.4 1.0 C1 B:OGA1355 3.0 38.3 1.0 CE1 B:HIS188 3.1 29.0 1.0 CE1 B:HIS276 3.1 19.7 1.0 CD B:GLU190 3.2 31.0 1.0 CD2 B:HIS188 3.2 27.4 1.0 CD2 B:HIS276 3.3 21.4 1.0 OE1 B:GLU190 3.5 28.4 1.0 N1 B:OGA1355 4.2 43.0 1.0 ND1 B:HIS188 4.2 29.7 1.0 O2 B:OGA1355 4.2 38.9 1.0 ND1 B:HIS276 4.3 20.1 1.0 CG B:HIS188 4.3 24.7 1.0 OG B:SER196 4.3 35.0 1.0 CG B:HIS276 4.4 20.6 1.0 O B:HOH2123 4.4 62.3 1.0 CG B:GLU190 4.5 27.9 1.0 CM2 D:M3L27 4.7 58.6 1.0 O B:HOH2128 4.8 46.2 1.0 C4 B:OGA1355 4.9 42.8 1.0 CB B:SER196 5.0 28.1 1.0

S.T.Williams, L.J.Walport, R.J.Hopkinson, S.K.Madden, R.Chowdhury, C.J.Schofield, A.Kawamura. Studies on the Catalytic Domains of Multiple Jmjc Oxygenases Using Peptide Substrates To Be Published.