Sodium in PDB 6qvg: Human SHMT2 in Complex with Lometrexol

All present enzymatic activity of Human SHMT2 in Complex with Lometrexol:
2.1.2.1;

The structure of Human SHMT2 in Complex with Lometrexol, PDB code: 6qvg was solved by E.Scaletti, A.S.Jemth, T.Helleday, P.Stenmark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	208.26 / 2.32
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	158.807, 158.807, 208.257, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.6

The binding sites of Sodium atom in the Human SHMT2 in Complex with Lometrexol (pdb code 6qvg). 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 SHMT2 in Complex with Lometrexol, PDB code: 6qvg:

Sodium binding site 1 out of 1 in the Human SHMT2 in Complex with Lometrexol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human SHMT2 in Complex with Lometrexol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:57.0 occ:1.00 O A:HOH789 2.9 34.5 1.0 OE1 A:GLU47 2.9 56.1 1.0 O A:HOH832 3.0 27.4 1.0 NE1 A:TRP43 3.4 57.7 1.0 NE2 B:GLN341 3.4 34.7 1.0 O B:HOH795 3.4 39.9 1.0 CD A:GLU47 3.8 52.5 1.0 CE2 A:TRP43 3.9 56.0 1.0 CB A:SER52 3.9 40.8 1.0 OG A:SER52 3.9 42.7 1.0 CZ2 A:TRP43 4.0 55.7 1.0 CB B:ALA83 4.1 30.4 1.0 CD B:GLN341 4.1 36.3 1.0 CB A:GLU47 4.2 43.8 1.0 CD1 A:TRP43 4.3 58.5 1.0 CB B:SER81 4.3 30.2 1.0 CA A:GLY45 4.4 41.7 1.0 OG B:SER81 4.5 29.0 1.0 CG A:GLU47 4.6 47.4 1.0 OE2 A:GLU47 4.6 56.1 1.0 CG B:GLN341 4.6 35.9 1.0 O A:GLU47 4.7 42.8 1.0 OE1 B:GLN341 4.8 37.4 1.0 N A:GLU47 4.8 38.7 1.0 N A:GLY45 4.9 42.5 1.0 CA A:GLU47 5.0 40.3 1.0 C A:GLY45 5.0 40.3 1.0 CD2 A:TRP43 5.0 57.3 1.0

E.Scaletti, A.S.Jemth, T.Helleday, P.Stenmark. Structural Basis of Inhibition of the Human Serine Hydroxymethyltransferase SHMT2 By Antifolate Drugs. Febs Lett. V. 593 1863 2019.
ISSN: ISSN 0014-5793
PubMed: 31127856
DOI: 10.1002/1873-3468.13455