Zinc in PDB 6cg2: Crystal Structure of KDM4A with Compound 8

The structure of Crystal Structure of KDM4A with Compound 8, PDB code: 6cg2 was solved by D.J.Hosfield, Z.Nie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	140.30 / 2.34
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.457, 101.739, 142.287, 90.00, 99.51, 90.00
R / Rfree (%)	17.4 / 23.4

The structure of Crystal Structure of KDM4A with Compound 8 also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM4A with Compound 8 (pdb code 6cg2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of KDM4A with Compound 8, PDB code: 6cg2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of KDM4A with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of KDM4A with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:39.6 occ:1.00 NE2 A:HIS240 2.2 38.7 1.0 SG A:CYS306 2.2 35.0 1.0 SG A:CYS234 2.3 35.9 1.0 SG A:CYS308 2.5 50.2 1.0 CE1 A:HIS240 3.1 39.1 1.0 CB A:CYS234 3.2 37.9 1.0 CD2 A:HIS240 3.2 35.3 1.0 CB A:CYS308 3.4 52.5 1.0 CB A:CYS306 3.5 38.2 1.0 N A:CYS308 3.7 58.1 1.0 N A:SER307 3.9 50.1 1.0 CA A:CYS306 3.9 42.8 1.0 CA A:CYS308 4.0 53.3 1.0 C A:CYS306 4.2 45.1 1.0 NH1 A:ARG309 4.2 76.7 1.0 ND1 A:HIS240 4.3 35.2 1.0 CG A:HIS240 4.3 33.9 1.0 CD A:ARG309 4.5 59.9 1.0 CA A:CYS234 4.5 44.0 1.0 O A:ALA236 4.6 32.3 1.0 C A:CYS308 4.6 53.7 1.0 N A:ARG309 4.6 59.7 1.0 C A:SER307 4.6 60.6 1.0 CA A:SER307 4.8 56.0 1.0 CG A:ARG309 4.9 55.8 1.0 CA A:PHE237 4.9 33.3 1.0 O A:HOH713 5.0 39.3 1.0 C A:ALA236 5.0 35.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of KDM4A with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of KDM4A with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:42.9 occ:1.00 NE2 B:HIS240 2.1 37.9 1.0 SG B:CYS234 2.2 41.2 1.0 SG B:CYS306 2.2 39.3 1.0 SG B:CYS308 2.5 55.8 1.0 CD2 B:HIS240 3.0 33.6 1.0 CE1 B:HIS240 3.1 39.8 1.0 CB B:CYS234 3.3 48.1 1.0 CB B:CYS306 3.4 44.7 1.0 CB B:CYS308 3.5 51.0 1.0 CA B:CYS306 3.7 44.4 1.0 N B:CYS308 3.7 57.9 1.0 N B:SER307 3.9 49.4 1.0 CA B:CYS308 4.1 53.4 1.0 C B:CYS306 4.1 46.0 1.0 ND1 B:HIS240 4.2 36.0 1.0 CG B:HIS240 4.2 32.0 1.0 CA B:CYS234 4.6 52.0 1.0 O B:ALA236 4.6 36.7 1.0 C B:SER307 4.6 61.0 1.0 C B:CYS308 4.7 51.5 1.0 NE B:ARG309 4.8 71.0 1.0 CG B:ARG309 4.8 68.2 1.0 CA B:SER307 4.9 56.2 1.0 N B:ARG309 4.9 58.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of KDM4A with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of KDM4A with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn502 b:53.0 occ:1.00 SG C:CYS306 2.0 44.0 1.0 NE2 C:HIS240 2.1 48.3 1.0 SG C:CYS234 2.3 46.8 1.0 SG C:CYS308 2.4 55.0 1.0 CE1 C:HIS240 3.0 48.3 1.0 CB C:CYS234 3.2 50.5 1.0 CD2 C:HIS240 3.2 42.4 1.0 CB C:CYS306 3.3 52.0 1.0 CB C:CYS308 3.4 57.1 1.0 CA C:CYS306 3.9 55.1 1.0 N C:CYS308 3.9 66.4 1.0 N C:SER307 4.1 60.0 1.0 CA C:CYS308 4.1 57.3 1.0 ND1 C:HIS240 4.1 48.4 1.0 C C:CYS306 4.2 60.1 1.0 CG C:HIS240 4.3 43.1 1.0 O C:ALA236 4.5 43.0 1.0 CA C:CYS234 4.5 56.7 1.0 C C:CYS308 4.6 65.1 1.0 C C:SER307 4.8 70.3 1.0 NE C:ARG309 5.0 80.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of KDM4A with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of KDM4A with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn502 b:34.0 occ:1.00 SG D:CYS306 2.1 30.7 1.0 NE2 D:HIS240 2.2 28.4 1.0 SG D:CYS308 2.2 40.1 1.0 SG D:CYS234 2.4 34.8 1.0 CD2 D:HIS240 3.1 29.4 1.0 CE1 D:HIS240 3.2 28.8 1.0 CB D:CYS306 3.3 37.2 1.0 CB D:CYS234 3.3 38.2 1.0 CB D:CYS308 3.6 47.5 1.0 N D:CYS308 3.6 52.6 1.0 CA D:CYS306 3.8 39.7 1.0 N D:SER307 4.1 51.5 1.0 CA D:CYS308 4.1 48.3 1.0 C D:CYS306 4.2 44.5 1.0 CG D:HIS240 4.3 28.6 1.0 ND1 D:HIS240 4.3 29.1 1.0 C D:SER307 4.6 60.6 1.0 O D:ALA236 4.7 36.0 1.0 CA D:CYS234 4.7 43.3 1.0 N D:ARG309 4.8 56.9 1.0 C D:CYS308 4.8 51.1 1.0 CD D:ARG309 4.8 66.8 1.0 NE D:ARG309 4.8 70.9 1.0 CA D:SER307 4.9 56.5 1.0 CA D:PHE237 5.0 34.2 1.0

Z.Nie, L.Shi, C.Lai, S.M.O'connell, J.Xu, R.K.Stansfield, D.J.Hosfield, J.M.Veal, J.A.Stafford. Structure-Based Design and Discovery of Potent and Selective KDM5 Inhibitors. Bioorg. Med. Chem. Lett. V. 28 1490 2018.
ISSN: ESSN 1464-3405
PubMed: 29627262
DOI: 10.1016/J.BMCL.2018.03.083