Sodium in PDB 6q2f: Structure of Rhamnosidase From Novosphingobium Sp. PP1Y

The structure of Structure of Rhamnosidase From Novosphingobium Sp. PP1Y, PDB code: 6q2f was solved by B.Terry, J.Ha, V.Izzo, M.H.Sazinsky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 2.20
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.809, 114.570, 158.797, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 17.7

The binding sites of Sodium atom in the Structure of Rhamnosidase From Novosphingobium Sp. PP1Y (pdb code 6q2f). 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 Structure of Rhamnosidase From Novosphingobium Sp. PP1Y, PDB code: 6q2f:

Sodium binding site 1 out of 1 in the Structure of Rhamnosidase From Novosphingobium Sp. PP1Y


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rhamnosidase From Novosphingobium Sp. PP1Y within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1201 b:37.7 occ:1.00 OE2 A:GLU585 2.4 35.6 1.0 OE1 A:GLU582 2.4 29.9 1.0 OE1 A:GLU643 2.6 31.2 1.0 OG A:SER503 2.6 31.7 1.0 OD1 A:ASP502 3.0 25.9 1.0 CD A:GLU582 3.4 33.2 1.0 CB A:SER503 3.4 26.4 1.0 CD A:GLU585 3.5 35.5 1.0 CD A:GLU643 3.5 32.4 1.0 OE2 A:GLU582 3.6 30.4 1.0 OE2 A:GLU643 3.7 45.4 1.0 O A:HOH1356 3.8 34.4 1.0 OE1 A:GLU585 3.9 37.3 1.0 N A:SER503 3.9 25.1 1.0 CG A:ASP502 4.1 29.5 1.0 O A:HOH1560 4.2 50.3 1.0 O A:HOH1421 4.2 34.7 1.0 CA A:SER503 4.3 26.6 1.0 O A:HOH1427 4.3 31.4 1.0 CH2 A:TRP57 4.5 23.9 1.0 OD2 A:ASP502 4.7 34.6 1.0 CG A:GLU585 4.7 28.9 1.0 O A:HOH1424 4.8 36.9 1.0 CG A:GLU582 4.8 28.2 1.0 CG A:GLU643 4.9 27.1 1.0 CB A:ALA607 4.9 20.3 1.0 CB A:GLU585 5.0 26.3 1.0

B.Terry, J.Ha, F.De Lise, F.Mensitieri, V.Izzo, M.H.Sazinsky. The Crystal Structure and Insight Into the Substrate Specificity of the Alpha-L Rhamnosidase Rha-P From Novosphingobium Sp. PP1Y. Arch.Biochem.Biophys. 08189 2019.
ISSN: ESSN 1096-0384
PubMed: 31726038
DOI: 10.1016/J.ABB.2019.108189