Atomistry » Sodium » PDB 6zl4-7a2n » 6zm9
Atomistry »
  Sodium »
    PDB 6zl4-7a2n »
      6zm9 »

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

Protein crystallography data

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

Sodium Binding Sites:

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 6zm9

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Oct 8 15:38:38 2024

Last articles

Br in 1PWX
Br in 1QUI
Br in 1QH5
Br in 1P2X
Br in 1P5E
Br in 1Q3O
Br in 1PTH
Br in 1PWL
Br in 1P54
Br in 1PGN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy