Sodium in PDB 3me4: Crystal Structure of Mouse Rank

The structure of Crystal Structure of Mouse Rank, PDB code: 3me4 was solved by S.W.Walter, C.Liu, X.Zhu, Y.Wu, R.J.Owens, D.I.Stuart, B.Gao, J.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.01
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.819, 94.245, 102.418, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.3

The structure of Crystal Structure of Mouse Rank also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Mouse Rank (pdb code 3me4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Mouse Rank, PDB code: 3me4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mouse Rank


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 Mouse Rank within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:23.6 occ:1.00 OG A:SER161 2.5 21.0 1.0 O A:VAL163 2.5 23.7 1.0 O A:HOH320 2.6 21.6 1.0 O A:PHE138 2.7 18.8 1.0 O A:CYS134 2.7 16.0 1.0 O A:ALA135 2.9 17.1 1.0 C A:CYS134 3.5 17.0 1.0 CB A:SER161 3.5 17.6 1.0 C A:ALA135 3.5 17.2 1.0 C A:VAL163 3.7 25.4 1.0 C A:PHE138 3.8 17.4 1.0 CB A:CYS134 3.9 18.8 1.0 N A:PRO136 4.0 19.5 1.0 N A:ALA135 4.2 16.7 1.0 CA A:PRO136 4.2 18.6 1.0 N A:SER165 4.3 18.8 1.0 CA A:CYS134 4.3 17.3 1.0 CA A:ALA135 4.3 18.1 1.0 O A:HOH250 4.5 30.4 1.0 N A:PHE138 4.5 12.9 1.0 CA A:PHE164 4.6 22.4 1.0 N A:VAL163 4.6 23.7 1.0 O A:SER165 4.6 16.6 1.0 N A:PHE164 4.6 24.0 1.0 CA A:GLY139 4.7 17.3 1.0 N A:GLY139 4.7 18.0 1.0 CA A:PHE138 4.7 17.3 1.0 CA A:SER161 4.7 18.3 1.0 CA A:VAL163 4.7 24.8 1.0 CG2 A:VAL163 4.8 24.2 1.0 C A:PHE164 4.8 22.4 1.0 CB A:SER165 4.8 19.2 1.0 C A:SER161 4.8 18.3 1.0 O A:ASP168 4.8 18.0 1.0 C A:PRO136 4.9 18.4 1.0 N A:GLY137 4.9 16.7 1.0 N A:CYS134 4.9 18.6 1.0 O A:SER161 5.0 17.6 1.0 CB A:PHE138 5.0 18.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mouse Rank


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mouse Rank within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:19.2 occ:1.00 O B:HOH251 2.5 17.3 1.0 O B:PHE138 2.5 17.4 1.0 O B:VAL163 2.5 19.7 1.0 O B:CYS134 2.6 17.3 1.0 OG B:SER161 2.6 18.1 1.0 O B:ALA135 2.7 17.2 1.0 C B:ALA135 3.4 16.4 1.0 C B:CYS134 3.4 17.8 1.0 CB B:SER161 3.5 21.4 1.0 C B:PHE138 3.7 17.8 1.0 C B:VAL163 3.7 21.2 1.0 CB B:CYS134 4.0 16.3 1.0 N B:PRO136 4.0 16.6 1.0 N B:ALA135 4.1 14.7 1.0 CA B:PRO136 4.1 16.5 1.0 N B:SER165 4.1 20.6 1.0 CA B:ALA135 4.2 14.4 1.0 CA B:CYS134 4.3 17.3 1.0 N B:PHE138 4.4 14.7 1.0 CA B:PHE164 4.5 19.2 1.0 CA B:PHE138 4.5 16.9 1.0 N B:PHE164 4.6 20.8 1.0 O B:SER165 4.6 18.4 1.0 N B:GLY139 4.6 15.1 1.0 N B:VAL163 4.6 21.0 1.0 CA B:GLY139 4.7 15.7 1.0 C B:PHE164 4.7 22.7 1.0 CG2 B:VAL163 4.7 22.7 1.0 CA B:VAL163 4.7 22.1 1.0 C B:PRO136 4.8 15.9 1.0 O B:HOH257 4.8 28.6 1.0 CA B:SER161 4.8 21.1 1.0 CB B:PHE138 4.8 18.2 1.0 C B:SER161 4.9 21.6 1.0 N B:GLY137 4.9 15.8 1.0 O B:ASP168 4.9 21.0 1.0 N B:CYS134 4.9 18.4 1.0 O B:SER161 5.0 23.8 1.0

C.Liu, T.S.Walter, P.Huang, S.Zhang, X.Zhu, Y.Wu, L.R.Wedderburn, P.Tang, R.J.Owens, D.I.Stuart, J.Ren, B.Gao. Structural and Functional Insights of Rankl-Rank Interaction and Signaling. J.Immunol. 2010.
ISSN: ISSN 0022-1767
PubMed: 20483727
DOI: 10.4049/JIMMUNOL.0904033