Nickel in PDB 4v2w: JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35)

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35), PDB code: 4v2w was solved by R.Chowdhury, D.Zafred, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.072 / 1.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.711, 149.740, 57.508, 90.00, 90.00, 90.00
R / Rfree (%)	17.24 / 20.82

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35) (pdb code 4v2w). 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 (16-35), PDB code: 4v2w:
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 (16-35)


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 (16-35) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:32.3 occ:1.00 OE2 A:GLU190 2.1 33.3 1.0 NE2 A:HIS188 2.2 27.1 1.0 NE2 A:HIS276 2.2 23.6 1.0 O2' A:OGA601 2.2 39.6 1.0 O1 A:OGA601 2.3 37.6 1.0 O A:HOH2152 2.3 36.4 1.0 C2 A:OGA601 2.9 42.8 1.0 C1 A:OGA601 2.9 42.6 1.0 CE1 A:HIS276 3.0 24.6 1.0 HE1 A:HIS276 3.1 29.5 1.0 CE1 A:HIS188 3.1 28.8 1.0 CD A:GLU190 3.1 31.9 1.0 CD2 A:HIS188 3.2 28.0 1.0 CD2 A:HIS276 3.3 24.2 1.0 HE1 A:HIS188 3.3 34.5 1.0 HD2 A:HIS188 3.4 33.6 1.0 OE1 A:GLU190 3.5 31.2 1.0 HD2 A:HIS276 3.5 29.0 1.0 HG A:SER196 3.5 41.4 1.0 HM22 C:M3L27 3.7 0.1 1.0 HG22 A:THR270 4.1 36.0 1.0 O A:HOH2189 4.1 62.7 1.0 O2 A:OGA601 4.1 44.0 1.0 N1 A:OGA601 4.2 47.1 1.0 ND1 A:HIS276 4.2 24.8 1.0 ND1 A:HIS188 4.2 27.6 1.0 CG A:HIS188 4.3 27.3 1.0 O A:HOH2153 4.3 52.3 1.0 CG A:HIS276 4.3 23.7 1.0 OG A:SER196 4.3 34.5 1.0 HG2 A:GLU190 4.5 38.4 1.0 CG A:GLU190 4.5 32.0 1.0 HZ3 A:TRP208 4.5 34.2 1.0 HZ1 A:LYS241 4.6 75.8 1.0 CM2 C:M3L27 4.6 98.4 1.0 HB3 A:SER196 4.7 35.4 1.0 HA A:GLU190 4.7 36.5 1.0 HM23 C:M3L27 4.7 0.1 1.0 1H4 A:OGA601 4.7 61.4 1.0 HD2 A:PHE185 4.9 38.4 1.0 O A:HOH2158 4.9 51.3 1.0 C4 A:OGA601 4.9 51.1 1.0 H1 A:OGA601 4.9 56.5 1.0 HE3 C:M3L27 4.9 0.2 1.0 HG3 A:GLU190 4.9 38.4 1.0 CB A:SER196 5.0 29.5 1.0 CG2 A:THR270 5.0 30.0 1.0 HM11 C:M3L27 5.0 0.9 1.0

Nickel binding site 2 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H3K27ME3 Peptide (16-35)


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 (16-35) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:30.1 occ:1.00 OE2 B:GLU190 2.1 26.9 1.0 NE2 B:HIS276 2.1 25.1 1.0 O1 B:OGA601 2.2 27.3 0.8 NE2 B:HIS188 2.2 25.5 1.0 O2' B:OGA601 2.2 26.2 0.8 O B:HOH2137 2.3 31.0 1.0 C1 B:OGA601 2.8 34.7 0.8 C2 B:OGA601 2.9 34.6 0.8 CE1 B:HIS188 3.0 27.6 1.0 CE1 B:HIS276 3.1 25.1 1.0 CD B:GLU190 3.1 26.9 1.0 CD2 B:HIS276 3.1 26.1 1.0 HE1 B:HIS188 3.2 33.1 1.0 CD2 B:HIS188 3.2 24.2 1.0 HE1 B:HIS276 3.2 30.1 1.0 HD2 B:HIS276 3.3 31.3 1.0 HD2 B:HIS188 3.4 29.1 1.0 OE1 B:GLU190 3.4 26.3 1.0 HG B:SER196 3.5 37.2 1.0 O B:HOH2136 4.0 57.2 1.0 HG22 B:THR270 4.0 35.8 1.0 O2 B:OGA601 4.1 37.3 0.8 O B:HOH2135 4.2 53.8 1.0 ND1 B:HIS188 4.2 26.1 1.0 N1 B:OGA601 4.2 42.1 0.8 ND1 B:HIS276 4.2 25.2 1.0 OG B:SER196 4.3 31.0 1.0 CG B:HIS276 4.3 25.1 1.0 CG B:HIS188 4.3 24.1 1.0 CG B:GLU190 4.4 24.4 1.0 HG2 B:GLU190 4.4 29.3 1.0 HZ3 B:TRP208 4.5 34.0 1.0 O B:HOH2142 4.5 68.1 1.0 HE2 B:LYS241 4.6 57.2 1.0 HB3 B:SER196 4.7 32.0 1.0 HA B:GLU190 4.8 28.1 1.0 1H4 B:OGA601 4.8 55.3 0.8 C4 B:OGA601 4.9 46.1 0.8 HG3 B:GLU190 4.9 29.3 1.0 CG2 B:THR270 4.9 29.8 1.0 H1 B:OGA601 4.9 50.5 0.8 HD2 B:PHE185 4.9 33.4 1.0 CB B:SER196 4.9 26.6 1.0 2H4 B:OGA601 5.0 55.3 0.8 OG1 B:THR270 5.0 28.0 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.