Zinc 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:

Nickel	(Ni)	4 atoms
Chlorine	(Cl)	5 atoms

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

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:38.0 occ:1.00 NE2 A:HIS240 2.2 40.9 1.0 SG A:CYS306 2.2 37.9 1.0 SG A:CYS308 2.3 42.8 1.0 SG A:CYS234 2.4 34.2 1.0 CE1 A:HIS240 3.1 38.3 1.0 CD2 A:HIS240 3.2 39.2 1.0 CB A:CYS234 3.2 42.0 1.0 CB A:CYS308 3.3 45.7 1.0 CB A:CYS306 3.4 38.8 1.0 N A:CYS308 3.5 45.1 1.0 CA A:CYS308 3.9 44.7 1.0 CA A:CYS306 3.9 42.0 1.0 O A:HOH662 4.0 42.6 1.0 N A:SER307 4.1 41.4 1.0 CZ2 E:TRP9 4.2 49.7 1.0 C A:CYS306 4.2 40.0 1.0 ND1 A:HIS240 4.2 37.1 1.0 CG A:HIS240 4.3 39.9 1.0 C A:CYS308 4.4 47.3 1.0 N A:ARG309 4.5 48.4 1.0 CA A:CYS234 4.6 43.6 1.0 CH2 E:TRP9 4.6 49.5 1.0 O A:ALA236 4.6 40.0 1.0 CG A:ARG309 4.7 49.2 1.0 C A:SER307 4.7 46.5 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:40.2 occ:1.00 SG B:CYS306 2.1 39.3 1.0 NE2 B:HIS240 2.2 37.3 1.0 SG B:CYS234 2.3 42.7 1.0 SG B:CYS308 2.4 42.7 1.0 CB B:CYS234 3.0 46.9 1.0 CD2 B:HIS240 3.2 38.2 1.0 CE1 B:HIS240 3.2 36.4 1.0 CB B:CYS306 3.4 45.5 1.0 CB B:CYS308 3.5 45.5 1.0 N B:CYS308 3.6 45.2 1.0 CA B:CYS306 3.9 45.6 1.0 N B:SER307 3.9 44.3 1.0 CA B:CYS308 4.1 46.9 1.0 CZ2 F:TRP9 4.1 47.2 1.0 C B:CYS306 4.3 44.8 1.0 ND1 B:HIS240 4.3 36.1 1.0 CG B:HIS240 4.3 36.7 1.0 CA B:CYS234 4.4 49.5 1.0 O1 B:GOL407 4.5 48.8 1.0 N B:ARG309 4.6 48.2 1.0 C B:CYS308 4.6 48.2 1.0 CH2 F:TRP9 4.7 47.2 1.0 C B:SER307 4.7 47.9 1.0 O B:ALA236 4.8 34.7 1.0 CA B:SER307 4.9 47.9 1.0 CA B:PHE237 5.0 36.4 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn502 b:36.3 occ:1.00 NE2 C:HIS240 2.2 37.0 1.0 SG C:CYS306 2.3 37.1 1.0 SG C:CYS234 2.4 37.4 1.0 SG C:CYS308 2.4 42.1 1.0 CD2 C:HIS240 3.2 34.4 1.0 CE1 C:HIS240 3.2 36.0 1.0 CB C:CYS234 3.3 44.9 1.0 CB C:CYS306 3.4 37.3 1.0 N C:CYS308 3.8 50.6 1.0 N C:SER307 3.9 45.9 1.0 CA C:CYS306 3.9 40.6 1.0 CB C:CYS308 4.0 47.1 1.0 CZ2 G:TRP9 4.1 43.1 1.0 C C:CYS306 4.3 43.9 1.0 ND1 C:HIS240 4.3 35.7 1.0 CG C:HIS240 4.3 33.9 1.0 CH2 G:TRP9 4.4 45.5 1.0 CA C:CYS308 4.5 50.8 1.0 CA C:CYS234 4.7 44.3 1.0 O C:ALA236 4.8 29.2 1.0 C C:SER307 4.8 51.1 1.0 CA C:PHE237 4.8 32.7 1.0 CA C:SER307 4.9 48.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:46.4 occ:1.00 NE2 D:HIS240 2.1 47.1 1.0 SG D:CYS234 2.3 45.2 1.0 SG D:CYS308 2.3 52.8 1.0 SG D:CYS306 2.4 48.4 1.0 CE1 D:HIS240 2.8 42.9 1.0 CB D:CYS234 2.9 47.8 1.0 CD2 D:HIS240 3.4 43.0 1.0 CB D:CYS306 3.4 47.6 1.0 CB D:CYS308 3.5 57.1 1.0 N D:CYS308 3.8 54.9 1.0 ND1 D:HIS240 4.0 44.5 1.0 CA D:CYS306 4.1 49.4 1.0 CA D:CYS308 4.1 57.2 1.0 N D:SER307 4.2 55.6 1.0 CG D:HIS240 4.3 42.9 1.0 CA D:CYS234 4.4 48.1 1.0 CZ2 H:TRP9 4.4 56.0 1.0 C D:CYS306 4.4 51.7 1.0 C D:CYS308 4.6 59.7 1.0 O D:ALA236 4.8 34.5 1.0 CA D:PHE237 4.8 37.6 1.0 C D:SER307 4.9 56.1 1.0 N D:ARG309 5.0 59.9 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