Sodium in PDB 2wce: Calcium-Free (Apo) S100A12

The structure of Calcium-Free (Apo) S100A12, PDB code: 2wce was solved by O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.56 / 1.77
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	77.516, 77.516, 99.076, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.5

The binding sites of Sodium atom in the Calcium-Free (Apo) S100A12 (pdb code 2wce). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Calcium-Free (Apo) S100A12, PDB code: 2wce:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Calcium-Free (Apo) S100A12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Calcium-Free (Apo) S100A12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1091 b:23.6 occ:1.00 O A:SER18 2.2 10.8 1.0 O A:LYS21 2.3 15.8 1.0 O A:THR26 2.3 12.0 1.0 O A:HIS23 2.3 13.4 1.0 O A:HOH2085 2.4 19.4 1.0 O A:HOH2052 2.6 14.2 1.0 C A:SER18 3.3 12.7 1.0 C A:LYS21 3.5 16.7 1.0 C A:THR26 3.5 14.2 1.0 C A:HIS23 3.5 13.6 1.0 CA A:SER18 3.8 11.7 1.0 N A:HIS23 4.0 15.2 1.0 N A:LYS21 4.1 16.1 1.0 C A:GLY22 4.1 16.0 1.0 CA A:LEU27 4.2 13.5 1.0 N A:THR26 4.3 14.5 1.0 CA A:LYS21 4.3 17.5 1.0 CB A:SER18 4.3 11.3 1.0 N A:LEU27 4.3 13.2 1.0 CA A:HIS23 4.4 15.5 1.0 O A:GLY22 4.4 16.7 1.0 O A:HOH2050 4.4 25.0 1.0 N A:VAL19 4.4 13.4 1.0 N A:GLY22 4.4 16.4 1.0 N A:PHE24 4.4 13.5 1.0 CA A:THR26 4.5 14.0 1.0 CA A:GLY22 4.5 16.8 1.0 C A:PHE24 4.5 13.5 1.0 CA A:PHE24 4.5 13.7 1.0 OE1 A:GLN67 4.5 16.4 1.0 O A:PHE24 4.7 13.6 1.0 CB A:LEU27 4.7 15.0 1.0 O A:HOH2038 4.7 22.2 1.0 OG1 A:THR26 4.7 16.7 1.0 C A:VAL19 4.7 14.2 1.0 CA A:VAL19 4.7 15.1 1.0 CB A:LYS21 4.8 18.1 1.0 N A:ARG20 4.8 15.2 1.0 O A:TYR17 4.9 11.6 1.0 N A:ASP25 4.9 14.7 1.0

Sodium binding site 2 out of 2 in the Calcium-Free (Apo) S100A12


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Calcium-Free (Apo) S100A12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1091 b:21.4 occ:1.00 O B:THR26 2.2 13.2 1.0 O B:SER18 2.3 12.2 1.0 O B:LYS21 2.3 16.6 1.0 O B:HIS23 2.3 14.2 0.5 O B:HIS23 2.3 14.7 0.5 O B:HOH2086 2.4 21.7 1.0 O B:HOH2049 2.7 13.7 1.0 C B:SER18 3.4 13.2 1.0 C B:THR26 3.5 13.6 1.0 C B:HIS23 3.5 15.4 0.5 C B:LYS21 3.5 17.3 1.0 C B:HIS23 3.5 15.9 0.5 N B:HIS23 3.9 17.0 0.5 CA B:SER18 3.9 12.7 1.0 N B:HIS23 3.9 17.5 0.5 C B:GLY22 4.1 17.9 1.0 N B:LYS21 4.1 16.0 1.0 N B:THR26 4.2 13.4 1.0 CA B:LEU27 4.2 15.0 1.0 CA B:HIS23 4.2 16.6 0.5 N B:LEU27 4.3 14.0 1.0 CA B:HIS23 4.3 17.4 0.5 CA B:LYS21 4.4 17.2 1.0 N B:GLY22 4.4 17.5 1.0 CB B:SER18 4.4 13.1 1.0 CA B:THR26 4.4 13.0 1.0 N B:PHE24 4.5 14.4 1.0 CA B:GLY22 4.5 17.6 1.0 O B:HOH2050 4.5 22.4 1.0 O B:GLY22 4.5 17.3 1.0 OG1 B:THR26 4.5 13.8 1.0 N B:VAL19 4.5 13.9 1.0 C B:PHE24 4.6 13.3 1.0 CA B:PHE24 4.6 14.0 1.0 OE1 B:GLN67 4.6 16.3 1.0 CB B:LEU27 4.7 16.3 1.0 O B:HOH2035 4.8 35.4 1.0 O B:PHE24 4.8 13.9 1.0 CB B:HIS23 4.8 17.2 0.5 N B:ASP25 4.8 13.2 1.0 N B:ARG20 4.9 14.1 1.0 CB B:LYS21 4.9 18.0 1.0 C B:VAL19 4.9 14.9 1.0 O B:TYR17 4.9 13.0 1.0 CA B:VAL19 4.9 15.7 1.0 O B:HOH2034 5.0 28.1 1.0

O.V.Moroz, E.V.Blagova, A.J.Wilkinson, K.S.Wilson, I.B.Bronstein. The Crystal Structures of Human S100A12 in Apo Form and in Complex with Zinc: New Insights Into S100A12 Oligomerisation. J.Mol.Biol. V. 391 536 2009.
ISSN: ISSN 0022-2836
PubMed: 19501594
DOI: 10.1016/J.JMB.2009.06.004