Sodium in PDB 2ypd: Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein

The structure of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein, PDB code: 2ypd was solved by M.Vollmar, C.Johansson, T.Krojer, G.Berridge, N.Burgess-Brown, C.Strain-Damerell, S.Froese, E.Williams, S.Goubin, D.Coutandin, F.Von Delft, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.82 / 2.10
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.718, 112.206, 165.173, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24

The structure of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein also contains other interesting chemical elements:

Mercury

(Hg)

11 atoms

The binding sites of Sodium atom in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein (pdb code 2ypd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein, PDB code: 2ypd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3504 b:17.9 occ:1.00 NH1 A:ARG2277 3.4 35.2 1.0 C A:MET2274 3.5 24.4 1.0 CA A:MET2274 3.5 24.3 1.0 N A:ALA2276 3.5 24.9 1.0 N A:ARG2277 3.6 25.6 1.0 CB A:ALA2276 3.8 25.8 1.0 CG A:ARG2277 3.8 26.9 1.0 N A:PRO2275 3.8 25.0 1.0 O A:MET2274 3.9 23.5 1.0 CB A:MET2274 4.0 24.2 1.0 CA A:ALA2276 4.0 25.8 1.0 CD A:PRO2275 4.1 25.4 1.0 CZ A:ARG2277 4.1 31.9 1.0 CB A:ARG2277 4.2 26.1 1.0 CD A:ARG2277 4.2 27.9 1.0 C A:ALA2276 4.3 25.8 1.0 C A:PRO2275 4.5 25.4 1.0 NE A:ARG2277 4.5 29.6 1.0 CA A:ARG2277 4.5 25.2 1.0 CG A:MET2274 4.6 24.2 1.0 CA A:PRO2275 4.7 24.9 1.0 O A:MET2273 4.7 25.5 1.0 CG A:PRO2275 4.8 25.2 1.0 OD2 A:ASP2214 4.8 59.0 1.0 N A:MET2274 4.8 25.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na3503 b:25.8 occ:1.00 C B:MET2274 3.2 40.9 1.0 CA B:MET2274 3.2 41.3 1.0 N B:ALA2276 3.4 35.7 1.0 NH1 B:ARG2277 3.5 30.3 1.0 N B:PRO2275 3.5 39.9 1.0 O B:MET2274 3.7 37.4 1.0 N B:ARG2277 3.7 30.0 1.0 CB B:MET2274 3.7 40.6 1.0 CD B:PRO2275 3.8 40.8 1.0 CB B:ALA2276 3.9 34.7 1.0 CG B:ARG2277 3.9 27.9 1.0 CA B:ALA2276 4.0 35.0 1.0 CB B:ARG2277 4.2 28.0 1.0 CD B:ARG2277 4.3 27.4 1.0 C B:PRO2275 4.3 37.6 1.0 CZ B:ARG2277 4.3 27.8 1.0 C B:ALA2276 4.3 31.8 1.0 CG B:MET2274 4.4 42.2 1.0 CA B:PRO2275 4.4 39.4 1.0 O B:MET2273 4.5 45.8 1.0 N B:MET2274 4.5 43.3 1.0 CG B:PRO2275 4.5 41.3 1.0 CA B:ARG2277 4.6 28.2 1.0 NE B:ARG2277 4.6 26.8 1.0 C B:MET2273 5.0 45.4 1.0 OD2 B:ASP2214 5.0 29.7 1.0

M.Vollmar, C.Johansson, T.Krojer, C.Strain-Damerell, S.Froese, E.Williams, D.Coutandin, F.Von Delft, J.Weigelt, C.H.Arrowsmith, C.Bountra, A.Edwards, U.Oppermann. Crystal Structure of the Jumonji Domain of Human Jumonji Domain Containing 1C Protein To Be Published.