Sodium in PDB 4d1b: Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin

The structure of Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin, PDB code: 4d1b was solved by F.Brueckner, T.Geng, S.Weyand, D.Drew, S.Iwata, P.J.F.Henderson, A.D.Cameron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.706 / 3.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95.614, 106.742, 107.852, 90.00, 90.00, 90.00
R / Rfree (%)	28.35 / 30.81

The binding sites of Sodium atom in the Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin (pdb code 4d1b). 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 MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin, PDB code: 4d1b:

Sodium binding site 1 out of 1 in the Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of MHP1, A Nucleobase-Cation-Symport-1 Family Transporter, in A Closed Conformation with Benzyl-Hydantoin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1471 b:0.5 occ:1.00 O A:ALA38 2.3 0.7 1.0 O A:ALA309 2.4 0.1 1.0 OG1 A:THR313 2.4 0.5 1.0 OG A:SER312 2.5 0.7 1.0 O A:ILE41 2.7 0.6 1.0 CB A:SER312 3.0 0.7 1.0 N A:THR313 3.1 0.1 1.0 C A:SER312 3.1 0.0 1.0 C A:ALA309 3.3 1.0 1.0 CB A:THR313 3.3 0.4 1.0 CA A:SER312 3.4 0.8 1.0 C A:ALA38 3.4 0.0 1.0 O A:SER312 3.7 0.9 1.0 N A:SER312 3.7 0.3 1.0 CA A:THR313 3.7 0.0 1.0 C A:ILE41 3.8 0.2 1.0 CA A:ALA309 3.9 0.8 1.0 CA A:MET39 4.0 0.9 1.0 N A:MET39 4.1 0.4 1.0 C A:MET39 4.2 0.9 1.0 O A:MET39 4.3 0.7 1.0 N A:THR310 4.4 0.1 1.0 CB A:GLN42 4.4 0.6 1.0 O A:LEU308 4.5 0.8 1.0 CA A:ALA38 4.5 0.8 1.0 CA A:ILE41 4.6 0.2 1.0 CD1 A:LEU175 4.6 0.1 1.0 N A:ILE41 4.6 0.2 1.0 N A:GLN42 4.7 0.2 1.0 C A:THR310 4.7 0.8 1.0 CB A:ILE41 4.7 0.6 1.0 CB A:ALA309 4.7 0.1 1.0 CG2 A:THR313 4.7 0.5 1.0 CA A:THR310 4.8 0.5 1.0 O A:THR310 4.8 0.0 1.0 CA A:GLN42 4.8 0.7 1.0 CB A:ALA38 4.8 0.9 1.0 C A:TRP311 4.9 0.7 1.0 N A:ALA40 5.0 0.5 1.0

K.J.Simmons, S.M.Jackson, F.Brueckner, S.G.Patching, O.Beckstein, E.Ivanova, T.Geng, S.Weyand, D.Drew, J.Lanigan, D.J.Sharples, M.S.Sansom, S.Iwata, C.W.Fishwick, A.P.Johnson, A.D.Cameron, P.J.Henderson. Molecular Mechanism of Ligand Recognition By Membrane Transport Protein, MHP1. Embo J. V. 33 1831 2014.
ISSN: ISSN 0261-4189
PubMed: 24952894
DOI: 10.15252/EMBJ.201387557