Sodium in PDB 4krg: Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine

The structure of Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine, PDB code: 4krg was solved by S.G.Lee, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.54 / 1.68
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	72.998, 72.998, 360.620, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 14

The binding sites of Sodium atom in the Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine (pdb code 4krg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine, PDB code: 4krg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:13.6 occ:1.00 O A:HOH614 2.7 20.3 1.0 OG A:SER183 3.1 17.7 1.0 OG A:SER157 3.2 21.1 1.0 N A:SER183 3.2 16.5 1.0 CB A:SER183 3.6 14.5 1.0 CB A:CYS156 3.6 16.9 1.0 NH1 A:ARG330 3.9 18.6 1.0 CB A:SER157 3.9 18.9 1.0 CG A:ARG330 4.0 13.7 1.0 CA A:SER183 4.0 16.0 1.0 CA A:PHE182 4.1 15.6 1.0 CG A:ARG224 4.1 15.2 1.0 NE A:ARG224 4.1 19.2 1.0 C A:PHE182 4.1 17.8 1.0 C A:CYS156 4.2 16.4 1.0 O A:CYS156 4.4 18.6 1.0 CD A:ARG224 4.4 17.9 1.0 N A:SER157 4.5 18.0 1.0 CD1 A:LEU333 4.5 12.6 1.0 CA A:CYS156 4.6 17.0 1.0 O A:ARG181 4.6 22.4 1.0 CB A:ARG224 4.7 16.1 1.0 CD A:ARG330 4.7 14.0 1.0 CB A:PHE182 4.7 16.5 1.0 CA A:SER157 4.8 19.4 1.0 CZ A:ARG224 4.9 20.7 1.0 CB A:LEU333 4.9 15.6 1.0 SG A:CYS156 4.9 16.6 1.0 CZ A:ARG330 4.9 18.5 1.0 CB A:ARG330 5.0 14.2 1.0

Sodium binding site 2 out of 2 in the Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Semet Haemonchus Contortus Phosphoethanolamine N-Methyltransferase 1 in Complex with Phosphoethanolamine and S-Adenosylhomocysteine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:12.7 occ:1.00 O B:HOH633 3.1 17.1 1.0 OG B:SER157 3.2 21.2 1.0 N B:SER183 3.2 16.3 1.0 OG B:SER183 3.3 19.6 1.0 CB B:CYS156 3.6 16.6 1.0 CB B:SER183 3.6 18.5 1.0 NH1 B:ARG330 3.8 20.7 1.0 CB B:SER157 4.0 20.6 1.0 CA B:SER183 4.0 18.4 1.0 CA B:PHE182 4.0 18.0 1.0 CG B:ARG330 4.1 18.0 1.0 C B:PHE182 4.1 18.8 1.0 NE B:ARG224 4.3 18.9 1.0 C B:CYS156 4.3 16.9 1.0 CG B:ARG224 4.4 18.5 1.0 O B:CYS156 4.5 18.3 1.0 N B:SER157 4.6 18.9 1.0 CA B:CYS156 4.6 16.0 1.0 CD1 B:LEU333 4.6 12.9 1.0 O B:ARG181 4.6 16.9 1.0 CD B:ARG224 4.7 17.5 1.0 SG B:CYS156 4.7 18.9 1.0 CB B:PHE182 4.8 16.4 1.0 CD B:ARG330 4.8 17.5 1.0 CZ B:ARG330 4.9 21.6 1.0 CA B:SER157 4.9 18.4 1.0 CB B:ARG330 4.9 14.7 1.0 CZ B:ARG224 5.0 19.5 1.0

S.G.Lee, J.M.Jez. Evolution of Structure and Mechanistic Divergence in Di-Domain Methyltransferases From Nematode Phosphocholine Biosynthesis. Structure V. 21 1778 2013.
ISSN: ISSN 0969-2126
PubMed: 24012478
DOI: 10.1016/J.STR.2013.07.023