Sodium in PDB 6gdy: Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG

The structure of Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG, PDB code: 6gdy was solved by M.S.Islam, C.J.Schofield, M.A.Mcdonough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 2.04
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.150, 96.990, 93.760, 90.00, 95.84, 90.00
R / Rfree (%)	18 / 21.6

The structure of Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG (pdb code 6gdy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG, PDB code: 6gdy:

Sodium binding site 1 out of 1 in the Crystal Structure of 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG


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 2OG Oxygenase JMJD6 (Aa 1-343) in Complex with Fe(II) and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:49.5 occ:1.00 N A:LEU87 3.2 34.6 1.0 O A:HOH668 3.5 38.6 1.0 CG A:LEU87 3.6 49.6 1.0 CA A:THR86 3.7 33.9 1.0 CB A:THR86 3.8 37.1 1.0 C A:THR86 4.0 34.0 1.0 CB A:LEU87 4.0 36.1 1.0 CA A:LEU87 4.2 36.5 1.0 CD2 A:LEU87 4.4 42.4 1.0 CG2 A:THR86 4.5 36.1 1.0 CD1 A:LEU87 4.5 53.5 1.0 O A:HOH741 4.7 51.3 1.0 CD1 A:ILE282 4.9 34.6 1.0 OG1 A:THR86 4.9 39.5 1.0 O A:TRP85 5.0 37.7 1.0

M.S.Islam, M.A.Mcdonough, R.Chowdhury, J.Gault, A.Khan, E.Pires, C.J.Schofield. Biochemical and Structural Investigations Clarify the Substrate Selectivity of the 2-Oxoglutarate Oxygenase JMJD6. J.Biol.Chem. V. 294 11637 2019.
ISSN: ESSN 1083-351X
PubMed: 31147442
DOI: 10.1074/JBC.RA119.008693