Sodium in PDB 6ymd: Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate

All present enzymatic activity of Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate:
2.1.2.1;

The structure of Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate, PDB code: 6ymd was solved by M.Ruszkowski, B.Sekula, I.Nogues, A.Tramonti, S.Angelaccio, R.Contestabile, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.49 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.050, 94.202, 142.972, 90.00, 90.00, 90.00
R / Rfree (%)	12.9 / 15

The binding sites of Sodium atom in the Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate (pdb code 6ymd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate, PDB code: 6ymd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate


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 Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:14.1 occ:1.00 O A:HOH831 2.4 17.4 1.0 O A:VAL326 2.4 14.6 1.0 O A:HOH800 2.4 18.0 1.0 O A:LEU328 2.4 14.1 1.0 O A:LEU323 2.4 15.7 1.0 C A:LEU328 3.4 12.8 1.0 C A:LEU323 3.6 13.4 1.0 C A:VAL326 3.6 13.9 1.0 N A:LEU328 3.8 13.9 1.0 O A:HOH603 4.0 22.6 1.0 N A:THR329 4.2 13.8 1.0 O A:ARG324 4.2 17.9 1.0 CB A:LEU323 4.2 14.8 1.0 N A:VAL326 4.2 15.3 1.0 C A:ARG324 4.2 15.7 1.0 CA A:LEU328 4.3 13.1 1.0 CA A:THR329 4.3 12.3 1.0 CA A:ARG324 4.3 14.4 1.0 N A:ARG324 4.4 13.2 1.0 CA A:VAL326 4.4 14.3 1.0 CA A:LEU323 4.5 13.3 1.0 O A:HOH641 4.5 17.3 1.0 N A:ASN327 4.6 14.0 1.0 CA A:ASN327 4.6 13.6 1.0 C A:ASN327 4.6 13.5 1.0 O A:HOH1028 4.7 51.9 1.0 CB A:VAL326 4.7 14.7 1.0 N A:SER325 4.9 16.4 1.0 OG A:SER360 4.9 14.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Serine Hydroxymethyltransferase From Aphanothece Halophytica in the Covalent Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na506 b:41.1 occ:1.00 O B:HOH830 2.3 46.0 1.0 O B:PHE141 2.4 16.8 1.0 O B:HOH878 2.4 20.9 1.0 O B:GLY138 2.4 16.6 1.0 O B:HOH969 2.5 50.7 1.0 O B:HOH857 2.6 51.4 1.0 C B:PHE141 3.5 14.5 1.0 C B:GLY138 3.5 14.3 1.0 O B:HOH972 4.0 34.6 1.0 CA B:GLU142 4.0 16.6 1.0 O B:LYS139 4.1 18.1 1.0 N B:GLU142 4.1 15.2 1.0 C B:LYS139 4.3 15.9 1.0 N B:PHE141 4.3 15.0 1.0 O B:HOH823 4.3 60.0 1.0 CA B:GLY138 4.4 14.0 1.0 N B:ALA143 4.4 16.4 1.0 N B:LYS139 4.5 14.4 1.0 CA B:LYS139 4.5 16.3 1.0 CA B:PHE141 4.6 13.7 1.0 O B:HOH779 4.7 19.6 1.0 C B:GLU142 4.8 16.6 1.0 N B:TRP140 4.9 15.3 1.0

I.Nogues, A.Tramonti, S.Angelaccio, M.Ruszkowski, B.Sekula, R.Contestabile. Structural and Kinetic Properties of Serine Hydroxymethyltransferase From the Halophytic Cyanobacterium Aphanothece Halophytica Provide A Rationale For Salt Tolerance. Int.J.Biol.Macromol. 2020.
ISSN: ISSN 0141-8130
PubMed: 32417544
DOI: 10.1016/J.IJBIOMAC.2020.05.081