Sodium in PDB 5x6v: Crystal Structure of Human Heteroheptameric Complex

The structure of Crystal Structure of Human Heteroheptameric Complex, PDB code: 5x6v was solved by R.Yonehara, S.Nada, T.Nakai, M.Nakai, A.Kitamura, A.Ogawa, H.Nakatsumi, K.I.Nakayama, S.Li, D.M.Standley, E.Yamashita, A.Nakagawa, M.Okada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.36 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.099, 93.476, 125.452, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.3

The binding sites of Sodium atom in the Crystal Structure of Human Heteroheptameric Complex (pdb code 5x6v). 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 Human Heteroheptameric Complex, PDB code: 5x6v:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Heteroheptameric Complex


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 Human Heteroheptameric Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:52.3 occ:1.00 O C:ILE18 2.2 45.7 1.0 O C:MET13 2.3 42.1 1.0 O C:ASN15 2.4 50.4 1.0 C C:MET13 3.3 41.5 1.0 C C:ILE18 3.4 45.7 1.0 C C:ASN15 3.4 52.0 1.0 CA C:PRO16 3.9 53.0 1.0 CA C:MET13 4.0 35.6 1.0 N C:ILE18 4.0 45.8 1.0 CA C:ILE18 4.1 42.3 1.0 N C:PRO16 4.1 51.4 1.0 C C:PRO16 4.1 58.8 1.0 N C:ASN15 4.2 46.8 1.0 O C:PRO16 4.2 60.9 1.0 C C:LYS14 4.3 49.6 1.0 CE C:MET13 4.4 40.6 1.0 N C:LYS14 4.4 39.5 1.0 CB C:ILE18 4.4 43.1 1.0 N C:VAL19 4.4 40.6 1.0 CA C:ASN15 4.5 47.6 1.0 CB C:MET13 4.5 37.2 1.0 O C:LYS14 4.6 51.5 1.0 CA C:VAL19 4.7 39.8 1.0 CA C:LYS14 4.7 42.7 1.0 N C:SER17 4.8 52.9 1.0 SD C:MET13 5.0 42.6 1.0 C C:SER17 5.0 52.0 1.0

R.Yonehara, S.Nada, T.Nakai, M.Nakai, A.Kitamura, A.Ogawa, H.Nakatsumi, K.I.Nakayama, S.Li, D.M.Standley, E.Yamashita, A.Nakagawa, M.Okada. Structural Basis For the Assembly of the Ragulator-Rag Gtpase Complex. Nat Commun V. 8 1625 2017.
ISSN: ESSN 2041-1723
PubMed: 29158492
DOI: 10.1038/S41467-017-01762-3