Sodium in PDB 7th5: Thermus Thermophilus Methylenetetrahydrofolate Reductase

All present enzymatic activity of Thermus Thermophilus Methylenetetrahydrofolate Reductase:
1.5.1.20;

The structure of Thermus Thermophilus Methylenetetrahydrofolate Reductase, PDB code: 7th5 was solved by K.Yamada, M.Koutmos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.496, 91.288, 130.261, 90, 90, 90
R / Rfree (%)	18.2 / 22.4

The binding sites of Sodium atom in the Thermus Thermophilus Methylenetetrahydrofolate Reductase (pdb code 7th5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thermus Thermophilus Methylenetetrahydrofolate Reductase, PDB code: 7th5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thermus Thermophilus Methylenetetrahydrofolate Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thermus Thermophilus Methylenetetrahydrofolate Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:37.8 occ:1.00 O A:LEU7 2.1 30.7 1.0 O A:ARG10 2.3 29.3 1.0 OE2 A:GLU267 2.3 45.4 1.0 O A:HOH680 2.4 38.5 1.0 O A:HOH644 2.4 35.4 1.0 O A:HOH615 3.1 42.7 1.0 C A:LEU7 3.2 30.6 1.0 HA A:LEU7 3.3 27.6 1.0 CD A:GLU267 3.6 44.1 1.0 C A:ARG10 3.6 33.8 1.0 CA A:LEU7 3.7 27.6 1.0 HA A:ARG11 3.8 35.7 1.0 HB3 A:GLU267 4.0 35.9 1.0 HB2 A:ARG10 4.0 35.0 1.0 HB3 A:LEU7 4.1 27.4 1.0 HD23 A:LEU7 4.2 27.8 1.0 H A:ARG10 4.2 31.7 1.0 O A:HOH606 4.2 49.0 1.0 OE1 A:GLU267 4.2 52.5 1.0 HA A:GLU267 4.2 32.2 1.0 HD21 A:LEU7 4.3 27.9 1.0 HA A:LYS8 4.3 32.3 1.0 N A:LYS8 4.4 30.7 1.0 O A:GLY12 4.4 31.2 1.0 O A:LEU6 4.5 24.9 1.0 N A:ARG11 4.5 32.4 1.0 CB A:LEU7 4.5 27.1 1.0 CA A:ARG11 4.5 35.7 1.0 CA A:ARG10 4.5 32.6 1.0 N A:ARG10 4.6 32.8 1.0 CB A:GLU267 4.6 35.8 1.0 CG A:GLU267 4.7 38.9 1.0 CD2 A:LEU7 4.7 27.7 1.0 CA A:LYS8 4.7 31.9 1.0 CB A:ARG10 4.7 35.2 1.0 C A:ARG11 4.8 36.8 1.0 C A:LYS8 4.9 33.2 1.0 O A:LYS8 4.9 35.6 1.0 O A:GLU267 4.9 27.7 1.0 CA A:GLU267 4.9 33.3 1.0 O A:ARG11 4.9 37.6 1.0 N A:LEU7 5.0 25.4 1.0 HG2 A:GLU267 5.0 39.2 1.0

Sodium binding site 2 out of 2 in the Thermus Thermophilus Methylenetetrahydrofolate Reductase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thermus Thermophilus Methylenetetrahydrofolate Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na501 b:35.0 occ:1.00 O B:HOH661 2.2 33.9 1.0 O B:LEU7 2.3 33.7 1.0 OE1 B:GLU267 2.3 42.9 1.0 O B:ARG10 2.4 30.7 1.0 O B:HOH620 2.5 41.3 1.0 C B:LEU7 3.4 27.8 1.0 HA B:LEU7 3.5 29.5 1.0 CD B:GLU267 3.6 45.8 1.0 C B:ARG10 3.6 31.7 1.0 HA B:ARG11 3.6 30.9 1.0 CA B:LEU7 4.0 31.1 1.0 HB3 B:GLU267 4.1 37.8 1.0 O B:HOH615 4.1 31.5 1.0 HA B:GLU267 4.2 33.9 1.0 HD23 B:LEU7 4.2 30.9 1.0 HB2 B:ARG10 4.2 34.0 1.0 OE2 B:GLU267 4.2 53.0 1.0 HB3 B:LEU7 4.3 29.4 1.0 HD13 B:LEU14 4.4 39.7 1.0 CA B:ARG11 4.4 31.4 1.0 HA B:LYS8 4.5 31.0 1.0 N B:ARG11 4.5 29.5 1.0 O B:GLY12 4.5 33.5 1.0 N B:LYS8 4.5 28.8 1.0 H B:ARG10 4.6 31.3 1.0 HD12 B:LEU14 4.6 39.8 1.0 CA B:ARG10 4.7 33.6 1.0 CB B:GLU267 4.7 38.0 1.0 CG B:GLU267 4.7 41.2 1.0 HD21 B:LEU7 4.7 30.9 1.0 CB B:LEU7 4.7 28.9 1.0 O B:LEU6 4.7 27.3 1.0 C B:ARG11 4.8 29.5 1.0 N B:ARG10 4.8 31.7 1.0 O B:GLU267 4.8 33.7 1.0 CA B:GLU267 4.9 34.4 1.0 CA B:LYS8 4.9 30.5 1.0 CD2 B:LEU7 4.9 31.7 1.0 CB B:ARG10 4.9 34.0 1.0 O B:ARG11 4.9 29.5 1.0 CD1 B:LEU14 5.0 40.7 1.0

K.Yamada, J.Mendoza, M.Koutmos. 5-Formyltetrahydrofolate Promotes Conformational Remodeling in A Methylenetetrahydrofolate Reductase Active Site and Inhibits Its Activity. J.Biol.Chem. 02855 2022.
ISSN: ESSN 1083-351X
PubMed: 36592927
DOI: 10.1016/J.JBC.2022.102855