Sodium in PDB 4pyj: Human Apo-Comt, Single Domain Swap

All present enzymatic activity of Human Apo-Comt, Single Domain Swap:
2.1.1.6;

The structure of Human Apo-Comt, Single Domain Swap, PDB code: 4pyj was solved by A.Ehler, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.36 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.882, 67.165, 128.827, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 26.3

The structure of Human Apo-Comt, Single Domain Swap also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Human Apo-Comt, Single Domain Swap (pdb code 4pyj). 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 Human Apo-Comt, Single Domain Swap, PDB code: 4pyj:

Sodium binding site 1 out of 1 in the Human Apo-Comt, Single Domain Swap


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Apo-Comt, Single Domain Swap within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:45.0 occ:1.00 O A:PHE239 2.4 50.2 1.0 O A:SER236 2.5 49.5 1.0 O A:VAL233 2.5 37.5 1.0 O A:ARG234 2.5 54.5 1.0 O A:HOH443 2.5 42.5 1.0 O A:HOH449 2.6 46.3 1.0 C A:ARG234 3.1 50.9 1.0 CA A:ARG234 3.5 46.5 1.0 C A:PHE239 3.5 45.6 1.0 C A:VAL233 3.5 45.6 1.0 C A:SER236 3.6 51.2 1.0 N A:SER236 3.9 43.3 1.0 N A:ARG234 4.0 42.4 1.0 N A:GLY235 4.1 44.9 1.0 SG A:CYS241 4.1 44.3 1.0 CA A:PHE239 4.2 44.9 1.0 CB A:PHE239 4.2 36.5 1.0 C A:GLY235 4.3 48.1 1.0 CA A:SER236 4.3 48.5 1.0 N A:PHE239 4.3 46.7 1.0 O A:HOH445 4.5 61.8 1.0 N A:GLU240 4.5 48.4 1.0 CA A:GLY235 4.6 45.5 1.0 N A:SER237 4.6 57.6 1.0 CA A:GLU240 4.7 47.5 1.0 N A:CYS241 4.7 47.3 1.0 O A:GLY235 4.8 54.3 1.0 CB A:CYS241 4.8 39.0 1.0 CB A:SER236 4.8 47.9 1.0 CA A:VAL233 4.8 44.5 1.0 CB A:ARG234 4.8 53.6 1.0 CA A:SER237 4.9 57.7 1.0

A.Ehler, J.Benz, D.Schlatter, M.G.Rudolph. Mapping the Conformational Space Accessible to Catechol-O-Methyltransferase. Acta Crystallogr.,Sect.D V. 70 2163 2014.
ISSN: ISSN 0907-4449
PubMed: 25084335
DOI: 10.1107/S1399004714012917