Sodium in PDB 3k2o: Structure of An Oxygenase

The structure of Structure of An Oxygenase, PDB code: 3k2o was solved by T.Krojer, M.A.Mcdonough, I.J.Clifton, M.Mantri, S.S.Ng, A.C.W.Pike, D.S.Butler, C.J.Webby, G.Kochan, C.Bhatia, J.E.Bray, A.Chaikuad, O.Gileadi, F.Von Delft, J.Weigelt, C.H.Arrowsmith, C.Bountra, A.M.Edwards, C.J.Schofield, K.L.Kavanagh, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.440, 102.030, 98.218, 90.00, 95.89, 90.00
R / Rfree (%)	19.2 / 22.5

The structure of Structure of An Oxygenase also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Structure of An Oxygenase (pdb code 3k2o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of An Oxygenase, PDB code: 3k2o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na337 b:43.4 occ:1.00 N A:LYS154 3.2 22.0 1.0 O A:HOH875 3.5 41.3 1.0 CL A:CL338 3.5 75.2 1.0 CG A:LYS154 3.7 26.4 1.0 O A:HOH449 3.7 42.8 1.0 O A:HOH460 3.8 68.0 1.0 CA A:PRO153 3.8 20.9 1.0 CB A:LYS154 3.9 26.2 1.0 C A:PRO153 4.0 21.6 1.0 CA A:LYS154 4.2 23.6 1.0 CB A:PRO153 4.3 24.4 1.0 CD A:LYS154 4.4 32.2 1.0 CE A:LYS154 4.8 36.1 1.0

Sodium binding site 2 out of 2 in the Structure of An Oxygenase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of An Oxygenase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na341 b:49.5 occ:1.00 O B:PHE155 3.1 27.9 1.0 O B:HOH398 3.2 41.5 1.0 N B:ASP158 3.2 28.2 1.0 CG B:ASP158 3.3 47.0 1.0 O B:HOH407 3.4 30.1 1.0 OD2 B:ASP158 3.4 38.9 1.0 CB B:ASP158 3.5 35.5 1.0 N B:THR157 3.6 22.2 1.0 C B:PHE156 3.7 26.9 1.0 CA B:PHE156 3.7 25.1 1.0 OD1 B:ASP158 3.7 45.0 1.0 C B:PHE155 3.9 27.3 1.0 CA B:ASP158 3.9 34.1 1.0 N B:PHE156 4.1 20.1 1.0 O B:HOH412 4.2 28.8 1.0 O B:HOH425 4.2 46.0 1.0 C B:THR157 4.3 26.5 1.0 O B:PHE156 4.3 25.0 1.0 CB B:SER290 4.4 22.8 1.0 CA B:THR157 4.4 24.4 1.0 O B:HOH437 4.8 26.8 1.0 OG1 B:THR157 5.0 31.9 1.0

M.Mantri, T.Krojer, E.A.Bagg, C.A.Webby, D.S.Butler, G.Kochan, K.L.Kavanagh, U.Oppermann, M.A.Mcdonough, C.J.Schofield. Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6. J.Mol.Biol. V. 401 211 2010.
ISSN: ISSN 0022-2836
PubMed: 20685276
DOI: 10.1016/J.JMB.2010.05.054