Zinc 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:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:36.8 occ:1.00 NE2 A:HIS240 2.2 46.6 1.0 SG A:CYS306 2.2 45.4 1.0 SG A:CYS234 2.3 41.7 1.0 SG A:CYS308 2.3 45.9 1.0 H A:CYS308 2.7 71.0 1.0 HB2 A:CYS234 3.0 58.4 1.0 CE1 A:HIS240 3.1 43.8 1.0 HE1 A:HIS240 3.2 52.6 1.0 CD2 A:HIS240 3.2 41.9 1.0 CB A:CYS234 3.2 48.6 1.0 HG3 A:ARG309 3.3 69.5 0.5 CB A:CYS306 3.4 40.0 1.0 HD2 A:HIS240 3.4 50.3 1.0 HB2 A:CYS306 3.5 48.0 1.0 HG3 A:ARG309 3.5 69.6 0.5 H A:SER307 3.5 65.9 1.0 HA A:CYS306 3.5 49.1 1.0 N A:CYS308 3.5 59.2 1.0 CB A:CYS308 3.6 48.2 1.0 HB3 A:CYS308 3.6 57.9 1.0 HB3 A:CYS234 3.7 58.4 1.0 HA A:PHE237 3.9 43.2 1.0 CA A:CYS306 3.9 40.9 1.0 N A:SER307 3.9 54.9 1.0 H A:ARG309 4.0 66.9 0.5 H A:ARG309 4.0 66.9 0.5 CA A:CYS308 4.1 52.6 1.0 C A:CYS306 4.2 44.8 1.0 HB3 A:CYS306 4.2 48.0 1.0 ND1 A:HIS240 4.2 42.2 1.0 CG A:ARG309 4.3 57.9 0.5 CG A:HIS240 4.3 40.8 1.0 N A:ARG309 4.4 55.7 0.5 HB2 A:CYS308 4.4 57.9 1.0 N A:ARG309 4.4 55.7 0.5 HD2 A:ARG309 4.4 73.8 0.5 CG A:ARG309 4.4 58.0 0.5 C A:CYS308 4.5 53.8 1.0 H A:ALA236 4.5 49.1 1.0 CA A:CYS234 4.6 53.6 1.0 HA A:CYS234 4.6 64.4 1.0 C A:SER307 4.6 75.1 1.0 HG2 A:ARG309 4.6 69.5 0.5 HB2 A:ARG309 4.7 68.7 0.5 HB2 A:ARG309 4.7 68.7 0.5 O A:ALA236 4.7 33.8 1.0 O A:HOH790 4.8 48.0 1.0 CA A:PHE237 4.8 36.0 1.0 CD A:ARG309 4.8 61.5 0.5 CA A:SER307 4.9 69.0 1.0 HA A:CYS308 4.9 63.1 1.0 HE A:ARG309 5.0 78.7 0.5 C A:ALA236 5.0 32.7 1.0 HD1 A:HIS240 5.0 50.7 1.0 CB A:ARG309 5.0 57.2 0.5 NE A:ARG309 5.0 65.6 0.5

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:38.1 occ:1.00 NE2 B:HIS240 2.0 36.0 1.0 SG B:CYS234 2.2 37.1 1.0 SG B:CYS306 2.2 37.6 1.0 SG B:CYS308 2.3 37.8 1.0 H B:CYS308 2.8 51.9 1.0 HB2 B:CYS234 2.9 46.9 1.0 CE1 B:HIS240 3.0 33.9 1.0 CD2 B:HIS240 3.1 34.7 1.0 HE1 B:HIS240 3.1 40.7 1.0 CB B:CYS234 3.1 39.1 1.0 HD2 B:HIS240 3.3 41.6 1.0 CB B:CYS306 3.3 38.8 1.0 HB2 B:CYS306 3.3 46.5 1.0 HB3 B:CYS308 3.4 45.9 1.0 CB B:CYS308 3.4 38.2 1.0 HA B:CYS306 3.5 45.8 1.0 HB3 B:CYS234 3.6 46.9 1.0 H B:SER307 3.6 54.6 1.0 N B:CYS308 3.6 43.3 1.0 CA B:CYS306 3.9 38.1 1.0 HA B:PHE237 3.9 37.6 1.0 CA B:CYS308 4.0 40.0 1.0 N B:SER307 4.0 45.5 1.0 ND1 B:HIS240 4.1 33.9 1.0 H B:ARG309 4.1 56.8 1.0 HB3 B:CYS306 4.1 46.5 1.0 CG B:HIS240 4.2 32.6 1.0 C B:CYS306 4.2 41.0 1.0 HD2 B:ARG309 4.3 97.9 1.0 HB2 B:CYS308 4.3 45.9 1.0 HG3 B:ARG309 4.3 88.6 1.0 HB2 B:ARG309 4.3 74.5 1.0 N B:ARG309 4.4 47.3 1.0 C B:CYS308 4.4 43.4 1.0 CA B:CYS234 4.5 38.2 1.0 HA B:CYS234 4.5 45.9 1.0 H B:ALA236 4.5 42.9 1.0 O B:HOH802 4.6 44.4 1.0 O B:ALA236 4.6 25.2 1.0 C B:SER307 4.7 53.4 1.0 CA B:PHE237 4.9 31.3 1.0 CG B:ARG309 4.9 73.8 1.0 HA B:CYS308 4.9 48.1 1.0 HD1 B:HIS240 4.9 40.7 1.0 O B:HOH813 4.9 58.1 1.0 CD B:ARG309 4.9 81.5 1.0 CA B:SER307 4.9 55.5 1.0 C B:ALA236 4.9 27.6 1.0 CB B:ARG309 4.9 62.1 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