Nickel 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:

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

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the JMJD2A Complexed with Ni(II), Nog and Histone H4(1-15)R3ME2S Peptide, PDB code: 5fwe:
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 H4(1-15)R3ME2S Peptide


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 H4(1-15)R3ME2S Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1355 b:31.4 occ:1.00 OE2 A:GLU190 2.0 25.1 1.0 NE2 A:HIS188 2.1 24.7 1.0 O2' A:OGA1358 2.2 22.6 1.0 O2 A:OGA1358 2.3 24.4 1.0 O A:HOH2102 2.3 28.9 1.0 NE2 A:HIS276 2.3 28.6 1.0 C2 A:OGA1358 2.9 25.8 1.0 C1 A:OGA1358 2.9 25.5 1.0 CE1 A:HIS188 3.1 27.0 1.0 CD A:GLU190 3.1 30.0 1.0 CD2 A:HIS188 3.1 30.4 1.0 CE1 A:HIS276 3.2 27.1 1.0 CD2 A:HIS276 3.3 26.3 1.0 OE1 A:GLU190 3.4 27.8 1.0 O A:HOH2103 3.7 53.1 1.0 O1 A:OGA1358 4.1 29.3 1.0 N1 A:OGA1358 4.2 28.0 1.0 ND1 A:HIS188 4.2 29.5 1.0 CG A:HIS188 4.2 26.2 1.0 O A:HOH2104 4.3 52.0 1.0 OG A:SER196 4.3 40.5 1.0 ND1 A:HIS276 4.3 28.0 1.0 CG A:GLU190 4.4 31.6 1.0 CG A:HIS276 4.4 28.6 1.0 C4 A:OGA1358 4.8 30.4 1.0 CB A:SER196 4.9 32.4 1.0 CG2 A:THR270 5.0 31.5 1.0

Nickel 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 Nickel with other atoms in the Ni 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:Ni1356 b:31.3 occ:1.00 OE2 B:GLU190 2.0 40.4 1.0 NE2 B:HIS276 2.0 28.6 1.0 NE2 B:HIS188 2.2 37.3 1.0 O2' B:OGA1359 2.2 28.6 1.0 O B:HOH2112 2.2 35.0 1.0 O2 B:OGA1359 2.2 30.3 1.0 C2 B:OGA1359 2.9 32.9 1.0 C1 B:OGA1359 2.9 32.9 1.0 CE1 B:HIS276 3.0 22.3 1.0 CE1 B:HIS188 3.0 30.4 1.0 CD B:GLU190 3.1 21.8 1.0 CD2 B:HIS276 3.1 22.0 1.0 CD2 B:HIS188 3.2 20.4 1.0 OE1 B:GLU190 3.5 22.3 1.0 CQ1 D:2MR3 3.9 45.8 0.3 O1 B:OGA1359 4.1 31.6 1.0 ND1 B:HIS276 4.1 27.2 1.0 ND1 B:HIS188 4.1 27.4 1.0 CQ1 D:2MR3 4.2 55.8 0.3 CG B:HIS276 4.2 23.4 1.0 N1 B:OGA1359 4.2 33.0 1.0 OG B:SER196 4.2 32.2 1.0 CG B:HIS188 4.3 24.9 1.0 O B:HOH2113 4.3 41.6 1.0 CG B:GLU190 4.4 28.7 1.0 O B:HOH2114 4.4 47.9 1.0 CB B:SER196 4.8 26.6 1.0 C4 B:OGA1359 4.8 34.9 1.0 CG2 B:THR270 4.9 27.9 1.0 OG1 B:THR270 4.9 34.5 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