Nickel in PDB 6h8p: JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer), PDB code: 6h8p was solved by R.Chowdhury, L.J.Walport, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.44 / 1.98
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.722, 150.146, 57.601, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.2

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) also contains other interesting chemical elements:

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

The binding sites of Nickel atom in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) (pdb code 6h8p). 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/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer), PDB code: 6h8p:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:32.1 occ:1.00 OE2 A:GLU190 2.0 38.4 1.0 O2 A:OGA504 2.0 43.5 1.0 NE2 A:HIS188 2.1 35.6 1.0 NE2 A:HIS276 2.1 32.8 1.0 O2' A:OGA504 2.1 41.1 1.0 O A:HOH713 2.4 42.7 1.0 C1 A:OGA504 2.7 46.9 1.0 C2 A:OGA504 2.7 47.8 1.0 CE1 A:HIS188 2.9 31.9 1.0 CE1 A:HIS276 3.1 28.4 1.0 HE1 A:HIS188 3.1 38.3 1.0 CD2 A:HIS188 3.1 31.3 1.0 CD A:GLU190 3.2 33.4 1.0 CD2 A:HIS276 3.2 27.4 1.0 HE1 A:HIS276 3.2 34.1 1.0 HD2 A:HIS276 3.4 32.9 1.0 HD2 A:HIS188 3.4 37.5 1.0 HM22 C:M3L26 3.5 93.0 1.0 OE1 A:GLU190 3.6 34.3 1.0 HG A:SER196 3.7 50.0 1.0 O1 A:OGA504 3.9 49.9 1.0 N1 A:OGA504 4.0 58.8 1.0 ND1 A:HIS188 4.1 31.2 1.0 HG21 A:THR270 4.1 45.8 1.0 ND1 A:HIS276 4.2 27.7 1.0 CG A:HIS188 4.2 30.5 1.0 HM23 C:M3L26 4.2 93.0 1.0 CG A:HIS276 4.3 26.1 1.0 CM2 C:M3L26 4.4 77.5 1.0 HG2 A:GLU190 4.4 39.3 1.0 O A:HOH730 4.4 64.9 1.0 CG A:GLU190 4.4 32.8 1.0 HG1 A:THR270 4.5 44.5 1.0 OG A:SER196 4.5 41.7 1.0 H4C1 A:OGA504 4.5 80.0 1.0 HZ3 A:TRP208 4.6 40.5 1.0 H1 A:OGA504 4.6 70.5 1.0 HA A:GLU190 4.7 36.6 1.0 O A:HOH694 4.8 50.5 1.0 C4 A:OGA504 4.8 66.7 1.0 HB3 A:SER196 4.8 44.4 1.0 HD1 A:HIS188 4.8 37.5 1.0 HD2 A:PHE185 4.9 36.0 1.0 HE2 C:M3L26 4.9 91.2 1.0 HZ3 A:LYS241 4.9 0.2 1.0 HG3 A:GLU190 4.9 39.3 1.0 H4C2 A:OGA504 4.9 80.0 1.0 HD1 A:HIS276 5.0 33.2 1.0 HM21 C:M3L26 5.0 93.0 1.0

Nickel binding site 2 out of 2 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Histone H1.4(18-32)K26ME3 Peptide (15-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:40.7 occ:1.00 O2 B:OGA504 1.8 82.1 1.0 NE2 B:HIS276 2.1 36.5 1.0 O2' B:OGA504 2.1 83.3 1.0 NE2 B:HIS188 2.2 37.4 1.0 OE2 B:GLU190 2.2 37.6 1.0 O B:HOH677 2.2 44.5 1.0 C1 B:OGA504 2.5 90.0 1.0 C2 B:OGA504 2.7 91.7 1.0 CE1 B:HIS188 3.0 32.2 1.0 CE1 B:HIS276 3.0 31.6 1.0 HE1 B:HIS188 3.1 38.7 1.0 CD2 B:HIS276 3.1 30.9 1.0 HE1 B:HIS276 3.1 37.9 1.0 CD B:GLU190 3.2 30.5 1.0 CD2 B:HIS188 3.2 30.8 1.0 HD2 B:HIS276 3.3 37.2 1.0 HD2 B:HIS188 3.5 37.0 1.0 OE1 B:GLU190 3.5 30.9 1.0 HM22 D:M3L26 3.5 86.0 1.0 HG B:SER196 3.7 47.0 1.0 O1 B:OGA504 3.8 89.3 1.0 N1 B:OGA504 4.0 95.0 1.0 O B:HOH669 4.0 50.6 1.0 O B:HOH627 4.1 62.9 1.0 ND1 B:HIS276 4.1 30.5 1.0 ND1 B:HIS188 4.1 31.6 1.0 HG21 B:THR270 4.1 40.1 1.0 CG B:HIS276 4.2 29.1 1.0 CG B:HIS188 4.3 29.4 1.0 CG B:GLU190 4.5 26.5 1.0 OG B:SER196 4.5 39.2 1.0 HG2 B:GLU190 4.5 31.8 1.0 H4C2 B:OGA504 4.6 0.7 1.0 CM2 D:M3L26 4.6 71.6 1.0 H1 B:OGA504 4.6 0.0 1.0 HA B:GLU190 4.7 33.7 1.0 HZ3 B:TRP208 4.7 40.8 1.0 C4 B:OGA504 4.8 98.0 1.0 HZ3 B:LYS241 4.8 83.0 1.0 HB3 B:SER196 4.8 40.4 1.0 HD2 B:PHE185 4.8 38.3 1.0 HE2 D:M3L26 4.8 86.0 1.0 HD1 B:HIS188 4.9 38.0 1.0 H4C1 B:OGA504 4.9 0.7 1.0 HM23 D:M3L26 4.9 86.0 1.0 HD1 B:HIS276 4.9 36.6 1.0 HM21 D:M3L26 4.9 86.0 1.0

L.J.Walport, R.J.Hopkinson, R.Chowdhury, Y.Zhang, J.Bonnici, R.Schiller, A.Kawamura, C.J.Schofield. Mechanistic and Structural Studies of Kdm-Catalysed Demethylation of Histone 1 Isotype 4 at Lysine 26. Febs Lett. V. 592 3264 2018.
ISSN: ISSN 1873-3468
PubMed: 30156264
DOI: 10.1002/1873-3468.13231