Sodium in PDB 6jm5: Crystal Structure of TBC1D23 C Terminal Domain

The structure of Crystal Structure of TBC1D23 C Terminal Domain, PDB code: 6jm5 was solved by Q.Sun, W.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.822, 48.950, 47.439, 90.00, 109.64, 90.00
R / Rfree (%)	15.7 / 20.7

The binding sites of Sodium atom in the Crystal Structure of TBC1D23 C Terminal Domain (pdb code 6jm5). 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 TBC1D23 C Terminal Domain, PDB code: 6jm5:

Sodium binding site 1 out of 1 in the Crystal Structure of TBC1D23 C Terminal Domain


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 TBC1D23 C Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:30.0 occ:1.00 O B:HOH381 2.0 31.7 1.0 O A:HOH307 2.4 28.2 1.0 O A:HOH266 2.4 15.8 1.0 O B:HOH366 2.6 15.5 1.0 O A:ASN80 2.7 10.3 1.0 O B:HOH309 2.9 26.4 1.0 OG B:SER102 3.1 10.6 1.0 CB B:SER102 3.4 7.5 1.0 C A:ASN80 3.8 9.0 1.0 O B:HOH390 3.9 32.4 1.0 O A:HOH218 3.9 12.5 1.0 O A:HOH254 4.0 9.0 1.0 CA A:ASN80 4.3 8.8 1.0 CB A:ASN80 4.5 11.7 1.0 O B:HOH351 4.6 34.2 1.0 O A:HOH306 4.6 54.1 1.0 CB A:SER102 4.6 8.5 1.0 O A:HOH277 4.7 25.6 1.0 O A:VAL82 4.8 9.8 1.0 O B:HOH346 4.8 9.2 1.0 O B:VAL82 4.9 8.0 1.0 O B:ASN80 4.9 12.5 1.0 CA B:SER102 4.9 6.4 1.0 ND2 A:ASN80 4.9 12.7 1.0 N A:SER81 4.9 9.0 1.0 OG A:SER102 5.0 11.4 1.0

W.Huang, Z.Liu, F.Yang, H.Zhou, X.Yong, X.Yang, Y.Zhou, L.Xue, Y.Zhang, D.Liu, W.Meng, W.Zhang, X.Zhang, X.Shen, Q.Sun, L.Li, C.Ma, Y.Wei, D.D.Billadeau, X.Mo, D.Jia. Structural and Functional Studies of TBC1D23 C-Terminal Domain Provide A Link Between Endosomal Trafficking and Pch. Proc.Natl.Acad.Sci.Usa V. 116 22598 2019.
ISSN: ESSN 1091-6490
PubMed: 31624125
DOI: 10.1073/PNAS.1909316116