Zinc in PDB 5fwe: JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide, PDB code: 5fwe 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)	49.85 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.739, 149.400, 57.372, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 25.5

The structure of JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide (pdb code 5fwe). 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 Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide, PDB code: 5fwe:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1356 b:34.2 occ:1.00 SG A:CYS306 2.2 39.2 1.0 NE2 A:HIS240 2.2 40.8 1.0 SG A:CYS234 2.3 35.9 1.0 SG A:CYS308 2.3 44.5 1.0 CE1 A:HIS240 3.1 40.9 1.0 CB A:CYS234 3.1 43.5 1.0 CD2 A:HIS240 3.3 29.7 1.0 CB A:CYS306 3.4 32.0 1.0 N A:CYS308 3.5 55.8 1.0 CB A:CYS308 3.5 48.5 1.0 CA A:CYS306 3.9 35.8 1.0 N A:SER307 3.9 55.9 1.0 CA A:CYS308 4.0 57.4 1.0 C A:CYS306 4.2 42.0 1.0 ND1 A:HIS240 4.2 36.0 1.0 N A:ARG309 4.4 66.3 1.0 CG A:HIS240 4.4 32.0 1.0 O A:HOH2163 4.4 48.2 1.0 C A:CYS308 4.5 63.0 1.0 CA A:CYS234 4.5 49.6 1.0 C A:SER307 4.6 68.2 1.0 CG A:ARG309 4.7 64.5 1.0 O A:ALA236 4.7 32.1 1.0 CA A:PHE237 4.8 33.9 1.0 CA A:SER307 4.8 65.8 1.0 O A:HOH2133 4.9 39.8 1.0 CB A:ARG309 4.9 66.6 1.0 CD A:ARG309 4.9 60.3 1.0

Zinc binding site 2 out of 2 in the JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1357 b:29.4 occ:1.00 NE2 B:HIS240 2.0 36.1 1.0 SG B:CYS306 2.2 35.8 1.0 SG B:CYS234 2.3 33.0 1.0 SG B:CYS308 2.4 35.1 1.0 CE1 B:HIS240 3.0 31.7 1.0 CD2 B:HIS240 3.1 34.0 1.0 CB B:CYS234 3.2 35.8 1.0 CB B:CYS306 3.4 26.8 1.0 CB B:CYS308 3.6 40.8 1.0 N B:CYS308 3.6 46.7 1.0 CA B:CYS306 4.0 35.4 1.0 N B:SER307 4.0 44.9 1.0 CA B:CYS308 4.0 47.7 1.0 ND1 B:HIS240 4.1 29.4 1.0 CG B:HIS240 4.2 28.9 1.0 N B:ARG309 4.3 54.7 1.0 C B:CYS306 4.3 36.9 1.0 C B:CYS308 4.4 52.7 1.0 CA B:CYS234 4.6 51.1 1.0 O B:HOH2174 4.6 37.0 1.0 CG B:ARG309 4.7 65.7 1.0 C B:SER307 4.7 55.0 1.0 O B:HOH2173 4.7 45.1 1.0 O B:ALA236 4.7 23.4 1.0 CA B:PHE237 4.8 31.5 1.0 CD B:ARG309 4.9 64.2 1.0 NE B:ARG309 4.9 68.5 1.0 CA B:SER307 5.0 55.7 1.0 CB B:ARG309 5.0 64.8 1.0

L.J.Walport, R.J.Hopkinson, R.Chowdhury, R.Schiller, W.Ge, A.Kawamura, C.J.Schofield. Arginine Demethylation Is Catalysed By A Subset of Jmjc Histone Lysine Demethylases. Nat.Commun. V. 7 11974 2016.
ISSN: ESSN 2041-1723
PubMed: 27337104
DOI: 10.1038/NCOMMS11974