Zinc in PDB 4xdo: Crystal Structure of Human KDM4C Catalytic Domain with Oga

The structure of Crystal Structure of Human KDM4C Catalytic Domain with Oga, PDB code: 4xdo was solved by K.K.Swinger, P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.58 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.930, 89.770, 98.460, 90.00, 96.49, 90.00
R / Rfree (%)	20 / 25.4

The structure of Crystal Structure of Human KDM4C Catalytic Domain with Oga also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Human KDM4C Catalytic Domain with Oga (pdb code 4xdo). 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 Human KDM4C Catalytic Domain with Oga, PDB code: 4xdo:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain with Oga


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 Human KDM4C Catalytic Domain with Oga within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.8 occ:1.00 NE2 A:HIS242 2.1 24.2 1.0 SG A:CYS308 2.2 26.1 1.0 SG A:CYS236 2.2 20.0 1.0 SG A:CYS310 2.4 25.5 1.0 CD2 A:HIS242 3.1 23.6 1.0 CE1 A:HIS242 3.1 25.6 1.0 CB A:CYS236 3.1 23.2 1.0 CB A:CYS308 3.5 27.7 1.0 CB A:CYS310 3.6 33.8 1.0 N A:CYS310 3.7 45.8 1.0 CA A:CYS308 4.0 26.7 1.0 CA A:CYS310 4.1 39.0 1.0 N A:THR309 4.2 35.8 1.0 ND1 A:HIS242 4.2 25.1 1.0 CG A:HIS242 4.3 24.1 1.0 C A:CYS308 4.3 30.4 1.0 CA A:CYS236 4.4 24.2 1.0 C A:CYS310 4.5 39.2 1.0 CD A:ARG311 4.7 45.7 1.0 N A:ARG311 4.7 39.5 1.0 CE A:MET314 4.7 51.4 1.0 NE A:ARG311 4.8 46.4 1.0 O A:ALA238 4.8 13.8 1.0 C A:THR309 4.8 49.8 1.0 CA A:PHE239 4.9 14.5 1.0 C A:ALA238 5.0 17.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain with Oga


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 Human KDM4C Catalytic Domain with Oga within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:35.8 occ:1.00 NE2 B:HIS242 2.1 31.6 1.0 SG B:CYS308 2.2 31.8 1.0 SG B:CYS236 2.3 32.6 1.0 SG B:CYS310 2.4 45.2 1.0 CE1 B:HIS242 3.0 31.3 1.0 CB B:CYS236 3.1 32.5 1.0 CD2 B:HIS242 3.3 30.0 1.0 CB B:CYS308 3.5 33.9 1.0 CB B:CYS310 3.5 48.6 1.0 N B:CYS310 3.8 54.4 1.0 CA B:CYS308 4.0 34.9 1.0 CA B:CYS310 4.1 50.3 1.0 ND1 B:HIS242 4.2 29.8 1.0 CG B:HIS242 4.3 31.8 1.0 N B:THR309 4.3 41.8 1.0 CA B:CYS236 4.4 35.2 1.0 C B:CYS308 4.5 39.3 1.0 C B:CYS310 4.5 50.3 1.0 O B:ALA238 4.7 27.9 1.0 CA B:PHE239 4.8 27.2 1.0 CE B:MET314 4.9 67.3 1.0 C B:ALA238 4.9 26.9 1.0 NE B:ARG311 4.9 55.9 1.0 N B:ARG311 4.9 53.6 1.0 C B:THR309 5.0 52.8 1.0 N B:PHE239 5.0 29.1 1.0 O B:CYS310 5.0 53.0 1.0

T.J.Wigle, K.K.Swinger, J.E.Campbell, M.D.Scholle, J.Sherrill, E.A.Admirand, P.A.Boriack-Sjodin, K.W.Kuntz, R.Chesworth, M.P.Moyer, M.P.Scott, R.A.Copeland. A High-Throughput Mass Spectrometry Assay Coupled with Redox Activity Testing Reduces Artifacts and False Positives in Lysine Demethylase Screening. J Biomol Screen 2015.
ISSN: ESSN 1552-454X
PubMed: 25755264
DOI: 10.1177/1087057115575689