Zinc in PDB 6g5w: Crystal Structure of KDM4A with Compound Yp-03-038

The structure of Crystal Structure of KDM4A with Compound Yp-03-038, PDB code: 6g5w 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)	46.57 / 1.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.362, 148.574, 56.390, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 21.8

The structure of Crystal Structure of KDM4A with Compound Yp-03-038 also contains other interesting chemical elements:

Nickel	(Ni)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of KDM4A with Compound Yp-03-038 (pdb code 6g5w). 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-03-038, PDB code: 6g5w:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of KDM4A with Compound Yp-03-038


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-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:36.4 occ:1.00 NE2 A:HIS240 2.1 34.9 1.0 SG A:CYS306 2.2 37.1 1.0 SG A:CYS234 2.3 35.7 1.0 SG A:CYS308 2.3 40.5 1.0 CE1 A:HIS240 3.0 38.6 1.0 CD2 A:HIS240 3.1 42.8 1.0 CB A:CYS234 3.2 37.3 1.0 CB A:CYS306 3.3 31.3 1.0 CB A:CYS308 3.5 63.1 1.0 N A:CYS308 3.5 63.4 1.0 CA A:CYS306 3.9 36.2 1.0 CA A:CYS308 4.0 71.7 1.0 N A:SER307 4.0 53.5 1.0 CB A:LYS310 4.1 51.0 1.0 ND1 A:HIS240 4.2 39.8 1.0 C A:CYS306 4.2 39.6 1.0 CG A:HIS240 4.3 42.4 1.0 C A:CYS308 4.4 56.9 1.0 N A:LYS310 4.4 42.8 1.0 O A:HOH700 4.5 45.7 1.0 N A:ARG309 4.6 59.6 1.0 CA A:CYS234 4.6 35.3 1.0 C A:SER307 4.6 62.2 1.0 O A:ALA236 4.7 29.3 1.0 CA A:PHE237 4.8 32.3 1.0 CA A:LYS310 4.8 48.1 1.0 N A:ASP311 4.9 75.5 1.0 CA A:SER307 4.9 62.1 1.0 O A:CYS308 5.0 45.0 1.0 C A:ALA236 5.0 32.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of KDM4A with Compound Yp-03-038


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-03-038 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:39.6 occ:1.00 NE2 B:HIS240 2.2 37.9 1.0 SG B:CYS234 2.2 40.0 1.0 SG B:CYS306 2.3 40.7 1.0 SG B:CYS308 2.4 44.9 1.0 CE1 B:HIS240 3.0 36.1 1.0 CB B:CYS234 3.1 54.9 1.0 CD2 B:HIS240 3.2 33.4 1.0 CB B:CYS306 3.4 48.4 1.0 CB B:CYS308 3.4 39.8 1.0 N B:CYS308 3.7 63.7 1.0 CA B:CYS306 3.9 46.0 1.0 CA B:CYS308 4.0 52.5 1.0 N B:SER307 4.0 43.4 1.0 CB B:LYS310 4.2 73.8 1.0 ND1 B:HIS240 4.2 33.5 1.0 C B:CYS306 4.2 51.6 1.0 CG B:HIS240 4.3 36.6 1.0 CA B:CYS234 4.5 59.2 1.0 O B:HOH686 4.5 44.5 1.0 C B:CYS308 4.5 70.4 1.0 N B:LYS310 4.6 60.5 1.0 C B:SER307 4.7 77.8 1.0 O B:ALA236 4.7 32.5 1.0 CA B:PHE237 4.8 40.0 1.0 N B:ARG309 4.8 85.8 1.0 C B:ALA236 4.9 40.4 1.0 CA B:SER307 4.9 61.7 1.0 CA B:LYS310 5.0 72.2 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-03-038 To Be Published.