Zinc in PDB 4xdp: Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris, PDB code: 4xdp 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)	31.42 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.870, 89.750, 98.280, 90.00, 96.31, 90.00
R / Rfree (%)	20.7 / 24.2

The structure of Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris also contains other interesting chemical elements:

Iron	(Fe)	2 atoms
Chlorine	(Cl)	6 atoms

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

Zinc binding site 1 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Bound to Tris within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:21.0 occ:1.00 NE2 A:HIS242 2.1 29.6 1.0 SG A:CYS236 2.3 28.7 1.0 SG A:CYS308 2.3 33.6 1.0 SG A:CYS310 2.3 37.0 1.0 CE1 A:HIS242 3.0 29.4 1.0 CD2 A:HIS242 3.1 27.5 1.0 CB A:CYS236 3.3 31.0 1.0 CB A:CYS308 3.4 33.6 1.0 CB A:CYS310 3.4 41.4 1.0 N A:CYS310 3.8 43.5 1.0 CA A:CYS308 3.9 33.6 1.0 N A:THR309 4.0 39.1 1.0 CA A:CYS310 4.1 43.3 1.0 ND1 A:HIS242 4.1 28.1 1.0 C A:CYS308 4.2 36.8 1.0 CG A:HIS242 4.2 26.6 1.0 NE A:ARG311 4.4 53.0 1.0 C A:CYS310 4.5 44.9 1.0 CA A:CYS236 4.6 32.0 1.0 NH2 A:ARG311 4.7 53.1 1.0 N A:ARG311 4.7 47.3 1.0 C A:THR309 4.7 44.0 1.0 CA A:PHE239 4.9 22.6 1.0 O A:ALA238 4.9 22.3 1.0 CZ A:ARG311 4.9 53.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Human KDM4C Catalytic Domain Bound to Tris


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 Bound to Tris within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:30.6 occ:1.00 NE2 B:HIS242 2.1 45.1 1.0 SG B:CYS236 2.3 41.7 1.0 SG B:CYS308 2.3 48.0 1.0 SG B:CYS310 2.3 56.9 1.0 CE1 B:HIS242 2.8 43.6 1.0 CB B:CYS236 3.3 44.1 1.0 CD2 B:HIS242 3.3 41.4 1.0 CB B:CYS310 3.4 58.9 1.0 CB B:CYS308 3.5 46.2 1.0 N B:CYS310 3.8 57.5 1.0 ND1 B:HIS242 4.0 42.0 1.0 CA B:CYS308 4.0 45.2 1.0 CA B:CYS310 4.1 59.6 1.0 N B:THR309 4.2 51.0 1.0 CG B:HIS242 4.2 40.5 1.0 C B:CYS308 4.4 48.6 1.0 C B:CYS310 4.6 61.2 1.0 CA B:CYS236 4.6 44.3 1.0 CG B:ARG311 4.6 63.8 1.0 N B:ARG311 4.7 62.5 1.0 O B:ALA238 4.7 32.1 1.0 CD B:ARG311 4.8 61.8 1.0 CA B:PHE239 4.8 32.5 1.0 C B:ALA238 4.9 33.1 1.0 NE B:ARG311 4.9 62.5 1.0 C B:THR309 4.9 56.9 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