Sodium in PDB 7bqj: The Structure of Pdxi

The structure of The Structure of Pdxi, PDB code: 7bqj was solved by Y.J.Cai, M.Ohashi, J.H.Zhou, Y.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.79 / 1.98
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.163, 87.163, 294.404, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 20.9

The binding sites of Sodium atom in the The Structure of Pdxi (pdb code 7bqj). 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 The Structure of Pdxi, PDB code: 7bqj:

Sodium binding site 1 out of 1 in the The Structure of Pdxi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Pdxi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:37.8 occ:1.00 O A:HOH693 2.9 33.2 1.0 O A:HIS315 3.2 28.9 1.0 O A:HOH766 3.3 27.4 1.0 O A:GLN287 3.3 24.9 1.0 C A:GLN287 3.6 25.2 1.0 N A:LYS317 3.6 25.1 1.0 N A:GLY265 3.7 23.8 1.0 CD2 A:HIS315 3.7 30.7 1.0 CB A:LYS317 3.8 25.4 1.0 C A:HIS315 3.9 28.9 1.0 CA A:LYS317 3.9 27.6 1.0 N A:GLU288 3.9 21.7 1.0 CA A:GLU288 3.9 22.8 1.0 CB A:GLN287 3.9 22.3 1.0 CG2 A:ILE264 4.0 23.1 1.0 CB A:HIS315 4.1 25.5 1.0 CG A:HIS315 4.2 29.6 1.0 CA A:GLY265 4.2 23.6 1.0 C A:ASP316 4.2 28.9 1.0 CA A:GLN287 4.4 21.7 1.0 C A:GLU288 4.5 24.8 1.0 CA A:HIS315 4.5 26.5 1.0 C A:ILE264 4.6 26.0 1.0 N A:ASP316 4.6 26.1 1.0 CA A:ASP316 4.7 26.9 1.0 CA A:ILE264 4.7 23.0 1.0 NE2 A:HIS315 4.8 28.8 1.0 N A:ARG289 4.8 23.0 1.0 CG A:LYS317 4.9 25.8 1.0 CB A:ILE264 5.0 25.1 1.0 OE1 A:GLN287 5.0 24.1 1.0

M.Ohashi, C.S.Jamieson, Y.Cai, D.Tan, D.Kanayama, M.C.Tang, S.M.Anthony, J.V.Chari, J.S.Barber, E.Picazo, T.B.Kakule, S.Cao, N.K.Garg, J.Zhou, K.N.Houk, Y.Tang. An Enzymatic Alder-Ene Reaction. Nature V. 586 64 2020.
ISSN: ESSN 1476-4687
PubMed: 32999480
DOI: 10.1038/S41586-020-2743-5