Nickel in PDB 5ly2: JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer), PDB code: 5ly2 was solved by R.Chowdhury, S.K.Madden, R.Hopkinson, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.67 / 2.43
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.306, 103.747, 142.367, 90.00, 99.14, 90.00
R / Rfree (%)	21.9 / 24.5

The structure of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	4 atoms

The binding sites of Nickel atom in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) (pdb code 5ly2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer), PDB code: 5ly2:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-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 Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:38.1 occ:1.00 O2' A:OGA503 2.0 36.4 1.0 OE2 A:GLU190 2.1 38.8 1.0 NE2 A:HIS188 2.1 32.9 1.0 O1 A:OGA503 2.3 37.2 1.0 O A:HOH663 2.4 43.2 1.0 NE2 A:HIS276 2.4 34.2 1.0 C2 A:OGA503 2.8 39.1 1.0 C1 A:OGA503 2.9 38.9 1.0 CE1 A:HIS188 3.0 33.2 1.0 CD A:GLU190 3.1 36.6 1.0 CE1 A:HIS276 3.2 33.5 1.0 CD2 A:HIS188 3.2 34.2 1.0 OE1 A:GLU190 3.4 36.9 1.0 CD2 A:HIS276 3.5 34.1 1.0 N1 A:OGA503 4.1 37.0 1.0 O2 A:OGA503 4.1 36.6 1.0 ND1 A:HIS188 4.1 31.6 1.0 CG A:HIS188 4.3 30.3 1.0 ND1 A:HIS276 4.4 34.4 1.0 CG A:GLU190 4.5 35.9 1.0 CG A:HIS276 4.5 32.8 1.0 OG A:SER196 4.6 39.0 1.0 CM2 E:M3L6 4.6 43.2 1.0 C4 A:OGA503 4.7 39.5 1.0 CB A:SER196 4.9 33.3 1.0

Nickel binding site 2 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-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 Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni402 b:40.4 occ:1.00 O1 B:OGA405 2.1 42.5 1.0 OE2 B:GLU190 2.1 35.6 1.0 NE2 B:HIS188 2.1 31.8 1.0 O2' B:OGA405 2.2 41.8 1.0 NE2 B:HIS276 2.4 35.3 1.0 O B:HOH545 2.4 43.8 1.0 C1 B:OGA405 2.8 43.9 1.0 C2 B:OGA405 2.9 42.5 1.0 CE1 B:HIS188 2.9 31.8 1.0 CD B:GLU190 3.1 34.7 1.0 CE1 B:HIS276 3.2 34.3 1.0 CD2 B:HIS188 3.3 33.1 1.0 OE1 B:GLU190 3.4 37.6 1.0 CD2 B:HIS276 3.5 34.5 1.0 O2 B:OGA405 4.0 45.3 1.0 ND1 B:HIS188 4.1 32.5 1.0 CM1 F:M3L6 4.1 57.5 1.0 N1 B:OGA405 4.2 45.2 1.0 CG B:HIS188 4.3 33.4 1.0 ND1 B:HIS276 4.4 33.5 1.0 CG B:GLU190 4.5 36.0 1.0 OG B:SER196 4.5 41.5 1.0 CG B:HIS276 4.5 33.5 1.0 NZ B:LYS241 4.9 44.7 1.0 C4 B:OGA405 4.9 46.9 1.0 CG2 B:THR270 4.9 37.1 1.0 CB B:SER196 4.9 37.6 1.0

Nickel binding site 3 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:38.0 occ:1.00 OE2 C:GLU190 2.1 30.2 1.0 O2' C:OGA504 2.2 43.0 1.0 NE2 C:HIS188 2.2 31.6 1.0 O C:HOH641 2.3 41.2 1.0 O1 C:OGA504 2.3 38.6 1.0 NE2 C:HIS276 2.4 31.1 1.0 C2 C:OGA504 2.9 44.6 1.0 C1 C:OGA504 3.0 42.6 1.0 CE1 C:HIS188 3.0 30.7 1.0 CD C:GLU190 3.1 30.5 1.0 CE1 C:HIS276 3.3 28.0 1.0 CD2 C:HIS188 3.3 30.5 1.0 CD2 C:HIS276 3.3 30.1 1.0 OE1 C:GLU190 3.5 30.5 1.0 O C:HOH693 4.1 40.4 1.0 ND1 C:HIS188 4.2 31.1 1.0 N1 C:OGA504 4.2 45.8 1.0 O2 C:OGA504 4.2 42.7 1.0 OG C:SER196 4.3 31.6 1.0 CG C:HIS188 4.4 30.6 1.0 ND1 C:HIS276 4.4 29.9 1.0 CG C:HIS276 4.4 28.7 1.0 CG C:GLU190 4.5 29.3 1.0 CB C:SER196 4.8 31.6 1.0 C4 C:OGA504 4.9 46.4 1.0

Nickel binding site 4 out of 4 in the JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of JMJD2A/ KDM4A Complexed with Ni(II), Nog and Macrocyclic Peptide Inhibitor CP2_R6KME3 (13-Mer) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni402 b:42.3 occ:1.00 NE2 D:HIS188 2.1 34.0 1.0 OE2 D:GLU190 2.2 39.7 1.0 O2' D:OGA405 2.2 48.8 1.0 O D:HOH528 2.3 41.6 1.0 NE2 D:HIS276 2.3 35.4 1.0 O2 D:OGA405 2.4 44.4 1.0 CE1 D:HIS188 2.9 31.6 1.0 C2 D:OGA405 3.0 49.3 1.0 C1 D:OGA405 3.1 48.2 1.0 CD2 D:HIS276 3.1 31.1 1.0 CD2 D:HIS188 3.2 35.6 1.0 CD D:GLU190 3.2 39.7 1.0 CE1 D:HIS276 3.5 32.3 1.0 OE1 D:GLU190 3.7 40.5 1.0 ND1 D:HIS188 4.1 32.7 1.0 CG D:HIS188 4.2 34.5 1.0 N1 D:OGA405 4.2 49.2 1.0 O1 D:OGA405 4.3 48.1 1.0 CG D:HIS276 4.3 29.6 1.0 ND1 D:HIS276 4.5 29.1 1.0 OG D:SER196 4.5 44.7 1.0 CG D:GLU190 4.5 39.1 1.0 CG2 D:THR270 4.9 35.1 1.0 C4 D:OGA405 4.9 49.9 1.0 CB D:SER196 4.9 38.5 1.0

A.Kawamura, M.Munzel, T.Kojima, C.Yapp, B.Bhushan, Y.Goto, A.Tumber, T.Katoh, O.N.King, T.Passioura, L.J.Walport, S.B.Hatch, S.Madden, S.Muller, P.E.Brennan, R.Chowdhury, R.J.Hopkinson, H.Suga, C.J.Schofield. Highly Selective Inhibition of Histone Demethylases By De Novo Macrocyclic Peptides. Nat Commun V. 8 14773 2017.
ISSN: ESSN 2041-1723
PubMed: 28382930
DOI: 10.1038/NCOMMS14773