Sodium in PDB 6kqt: Crystal Structure of GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein

The structure of Crystal Structure of GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein, PDB code: 6kqt was solved by C.Yamada, T.Arakawa, M.J.Pichler, M.Abou Hachem, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.04 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	132.295, 132.295, 82.200, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 18.1

The binding sites of Sodium atom in the Crystal Structure of GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein (pdb code 6kqt). 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 Crystal Structure of GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein, PDB code: 6kqt:

Sodium binding site 1 out of 1 in the Crystal Structure of GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein


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 GH136 Lacto-N-Biosidase From Eubacterium Ramulus - Native Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:31.1 occ:1.00 O A:HOH879 2.2 31.4 1.0 O A:THR396 2.3 20.2 1.0 O A:ARG394 2.3 21.3 1.0 O A:HOH1326 2.4 36.4 1.0 O A:HOH1195 2.7 23.5 1.0 N A:THR396 3.3 21.8 1.0 C A:THR396 3.3 18.3 1.0 C A:ARG394 3.5 21.3 1.0 CA A:THR396 3.7 19.7 1.0 C A:GLY395 3.8 21.5 1.0 O A:HOH996 4.0 28.3 1.0 CA A:GLY395 4.1 22.4 1.0 O A:HOH1388 4.1 41.7 1.0 CE1 A:HIS398 4.2 20.0 1.0 CB A:THR396 4.2 17.9 1.0 O A:HOH1356 4.2 34.4 1.0 N A:GLY395 4.2 20.9 1.0 OE1 A:GLU356 4.3 27.6 1.0 O A:HOH894 4.3 31.4 1.0 ND1 A:HIS398 4.5 22.2 1.0 N A:LEU397 4.5 17.8 1.0 OE2 A:GLU356 4.5 21.2 1.0 O A:GLY395 4.6 19.4 1.0 CA A:ARG394 4.6 20.9 1.0 CB A:ARG394 4.7 21.9 1.0 CD A:GLU356 4.7 23.0 1.0

M.J.Pichler, C.Yamada, B.Shuoker, C.Alvarez-Silva, A.Gotoh, M.Leth, E.Schoof, T.Katoh, M.Sakanaka, T.Katayama, C.Jin, N.G.Karlsson, M.Arumugam, S.Fushinobu, M.Abou Hachem. Butyrate Producing Clostridiales Utilize Distinct Human Milk Oligosaccharides Correlating to Early Colonization and Prevalence in the Human Gut Nat Commun 2020.
ISSN: ESSN 2041-1723
DOI: 10.1101/2020.04.15.038927