Sodium in PDB 6zm9: Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine

The structure of Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine, PDB code: 6zm9 was solved by X.Guo, S.Kanchugal P, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.53 / 1.45
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	154.324, 154.324, 154.324, 90, 90, 90
R / Rfree (%)	13.3 / 15.5

The binding sites of Sodium atom in the Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine (pdb code 6zm9). 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 Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine, PDB code: 6zm9:

Sodium binding site 1 out of 1 in the Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phage Sam Lyase in Complex with S-Methyl-5'-Thioadenosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:46.8 occ:1.00 HD12 A:LEU79 2.2 50.2 1.0 OD2 A:ASP48 2.7 18.1 1.0 HD13 A:LEU79 2.8 50.2 1.0 CD1 A:LEU79 2.8 41.9 1.0 HD11 A:LEU79 2.9 50.2 1.0 HB3 A:ASP48 3.0 18.1 1.0 O A:HOH393 3.2 44.5 1.0 CB A:ASP48 3.5 15.1 1.0 CG A:ASP48 3.5 15.8 1.0 HB2 A:ASP48 3.5 18.1 1.0 CG A:LEU79 4.2 37.4 1.0 HG A:LEU79 4.3 44.9 1.0 OD1 A:ASP48 4.7 18.8 1.0 HB2 A:LEU79 4.8 41.7 1.0 HD21 A:LEU79 4.9 45.5 1.0 CA A:ASP48 5.0 14.0 1.0

X.Guo, A.Soderholm, S.Kanchugal P, G.V.Isaksen, O.Warsi, U.Eckhard, S.Triguis, A.Gogoll, J.Jerlstrom-Hultqvist, J.Aqvist, D.I.Andersson, M.Selmer. Structure and Mechanism of A Phage-Encoded Sam Lyase Revises Catalytic Function of Enzyme Family. Elife V. 10 2021.
ISSN: ESSN 2050-084X
PubMed: 33567250
DOI: 10.7554/ELIFE.61818