Sodium in PDB 4nhx: Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog)

The structure of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog), PDB code: 4nhx was solved by S.Horita, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.24 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.401, 64.401, 232.041, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 21.5

The structure of Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog) also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog) (pdb code 4nhx). 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 Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog), PDB code: 4nhx:

Sodium binding site 1 out of 1 in the Crystal Structure of Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog)


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 Human OGFOD1, 2-Oxoglutarate and Iron-Dependent Oxygenase Domain Containing 1, in Complex with N-Oxalylglycine (Nog) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:83.1 occ:1.00 OG1 A:THR509 2.4 56.0 1.0 O A:HOH944 2.4 66.5 1.0 CB A:THR509 2.8 54.2 1.0 OD2 A:ASP506 2.9 65.3 1.0 CG A:ASP506 3.0 61.0 1.0 N A:ASP506 3.0 46.0 1.0 OD1 A:ASP506 3.1 58.2 1.0 CG2 A:THR509 3.3 50.9 1.0 CA A:ARG505 3.8 47.5 1.0 O A:TYR504 3.8 46.6 1.0 CB A:ASP506 3.8 56.9 1.0 C A:ARG505 3.8 47.8 1.0 CA A:ASP506 4.0 49.3 1.0 CA A:THR509 4.3 55.0 1.0 O A:ASP506 4.6 45.1 1.0 C A:TYR504 4.6 45.8 1.0 C A:ASP506 4.7 49.2 1.0 N A:ARG505 4.7 45.6 1.0 N A:THR509 4.7 61.0 1.0 CB A:ARG505 4.7 46.6 1.0 O A:ARG505 5.0 51.8 1.0

S.Horita, S.Horita, M.A.Mcdonough, C.J.Schofield. N/A N/A.