Zinc in PDB 6g5x: Crystal Structure of KDM4A with Compound Yp-02-145

The structure of Crystal Structure of KDM4A with Compound Yp-02-145, PDB code: 6g5x was solved by P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.84 / 1.78
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.137, 148.615, 56.910, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.3

The structure of Crystal Structure of KDM4A with Compound Yp-02-145 also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of KDM4A with Compound Yp-02-145 (pdb code 6g5x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of KDM4A with Compound Yp-02-145, PDB code: 6g5x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of KDM4A with Compound Yp-02-145


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 Yp-02-145 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:30.8 occ:1.00 NE2 A:HIS240 2.0 28.7 1.0 SG A:CYS306 2.2 30.2 1.0 SG A:CYS234 2.3 30.4 1.0 SG A:CYS308 2.3 36.1 1.0 CE1 A:HIS240 2.9 35.9 1.0 CD2 A:HIS240 3.1 27.8 1.0 CB A:CYS234 3.2 31.2 1.0 CB A:CYS306 3.4 33.2 1.0 CB A:CYS308 3.4 52.2 1.0 N A:CYS308 3.6 47.4 1.0 CA A:CYS306 3.9 34.7 1.0 CA A:CYS308 3.9 58.6 1.0 N A:SER307 4.0 39.3 1.0 ND1 A:HIS240 4.1 33.0 1.0 CB A:LYS310 4.1 46.0 1.0 CG A:HIS240 4.2 30.6 1.0 C A:CYS306 4.2 42.8 1.0 C A:CYS308 4.4 48.6 1.0 N A:LYS310 4.4 36.6 1.0 CA A:CYS234 4.5 38.9 1.0 N A:ARG309 4.6 53.0 1.0 C A:SER307 4.7 54.5 1.0 O A:HOH731 4.7 38.5 1.0 O A:ALA236 4.7 24.3 1.0 CA A:PHE237 4.8 29.8 1.0 CA A:LYS310 4.8 41.4 1.0 N A:ASP311 4.9 55.1 1.0 CA A:SER307 4.9 52.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of KDM4A with Compound Yp-02-145


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 Yp-02-145 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:36.6 occ:1.00 NE2 B:HIS240 2.1 35.9 1.0 SG B:CYS234 2.2 35.0 1.0 SG B:CYS308 2.3 40.5 1.0 SG B:CYS306 2.3 35.5 1.0 CE1 B:HIS240 3.0 36.1 1.0 CB B:CYS234 3.1 38.0 1.0 CD2 B:HIS240 3.2 31.6 1.0 CB B:CYS308 3.3 39.6 1.0 CB B:CYS306 3.4 35.4 1.0 N B:CYS308 3.6 64.9 1.0 CA B:CYS306 3.9 45.1 1.0 CA B:CYS308 3.9 50.0 1.0 N B:SER307 4.0 51.0 1.0 ND1 B:HIS240 4.2 34.8 1.0 C B:CYS306 4.2 53.4 1.0 CB B:LYS310 4.3 78.5 1.0 CG B:HIS240 4.3 34.8 1.0 C B:CYS308 4.4 58.2 1.0 O B:HOH749 4.4 46.5 1.0 CA B:CYS234 4.5 43.0 1.0 N B:LYS310 4.5 62.3 1.0 N B:ARG309 4.6 73.7 1.0 C B:SER307 4.6 74.7 1.0 O B:ALA236 4.7 27.0 1.0 CG B:LYS310 4.8 57.2 1.0 CA B:PHE237 4.8 30.6 1.0 N B:ASP311 4.9 0.8 1.0 CA B:SER307 4.9 64.8 1.0 CA B:LYS310 5.0 85.7 1.0 C B:ALA236 5.0 33.1 1.0

P.H.Malecki, D.M.Carter, U.Gohlke, E.Specker, M.Nazare, M.S.Weiss, U.Heinemann. Crystal Structure of KDM4A with Compound Yp-02-145 To Be Published.