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

The structure of Calcium-Free (Apo) S100A12, PDB code: 2wcf 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)	78.34 / 2.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.185, 93.197, 144.532, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 32.3

The binding sites of Sodium atom in the Calcium-Free (Apo) S100A12 (pdb code 2wcf). 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: 2wcf:
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 B:Na1091 b:46.2 occ:1.00 O B:SER18 2.1 31.8 1.0 O B:HIS23 2.3 32.6 0.5 O B:LYS21 2.7 36.4 1.0 O B:THR26 2.7 31.8 1.0 C B:SER18 3.1 32.7 1.0 C B:HIS23 3.4 32.3 0.5 C B:LYS21 3.6 36.3 1.0 CA B:SER18 3.8 32.7 1.0 N B:LYS21 3.8 37.2 1.0 C B:THR26 3.9 31.9 1.0 N B:HIS23 3.9 32.9 0.5 N B:VAL19 4.1 33.3 1.0 CA B:LYS21 4.2 37.2 1.0 C B:GLY22 4.2 33.7 1.0 CA B:HIS23 4.3 32.6 0.5 N B:ARG20 4.3 35.9 1.0 CA B:LEU27 4.3 32.1 1.0 N B:PHE24 4.4 32.4 1.0 OE2 B:GLU31 4.4 41.2 1.0 CB B:LYS21 4.5 37.4 1.0 CA B:PHE24 4.5 31.8 1.0 CB B:LEU27 4.5 31.8 1.0 N B:GLY22 4.5 36.0 1.0 N B:LEU27 4.6 32.8 1.0 CA B:VAL19 4.6 34.6 1.0 CB B:SER18 4.6 32.9 1.0 CA B:GLY22 4.6 34.7 1.0 N B:THR26 4.7 32.1 1.0 C B:VAL19 4.7 35.6 1.0 O B:TYR17 4.7 32.5 1.0 C B:PHE24 4.7 31.8 1.0 O B:GLY22 4.8 34.0 1.0 CA B:THR26 4.9 31.6 1.0 O B:PHE24 4.9 31.6 1.0 C B:ARG20 4.9 36.8 1.0 N B:SER18 5.0 32.3 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 E:Na1090 b:54.6 occ:1.00 O E:THR26 2.2 33.6 1.0 O E:HIS23 2.5 32.7 1.0 O E:LYS21 2.5 32.5 1.0 O E:SER18 2.9 29.7 1.0 N E:HIS23 3.0 33.4 1.0 C E:THR26 3.2 33.7 1.0 NE2 E:GLN67 3.3 37.2 1.0 C E:HIS23 3.4 33.2 1.0 C E:LYS21 3.5 33.0 1.0 C E:GLY22 3.5 33.9 1.0 CA E:HIS23 3.7 33.4 1.0 CA E:GLY22 3.7 33.8 1.0 CA E:LEU27 3.9 35.5 1.0 OG1 E:THR26 4.0 33.4 1.0 N E:LEU27 4.0 34.3 1.0 N E:GLY22 4.0 33.5 1.0 C E:SER18 4.0 29.8 1.0 N E:THR26 4.2 33.2 1.0 CA E:THR26 4.2 33.3 1.0 CD E:GLN67 4.3 36.7 1.0 CB E:HIS23 4.4 33.3 1.0 O E:GLY22 4.4 34.2 1.0 OE1 E:GLN67 4.5 37.2 1.0 CA E:SER18 4.5 29.1 1.0 N E:PHE24 4.7 33.1 1.0 CB E:LEU27 4.7 36.5 1.0 CB E:THR26 4.7 33.5 1.0 CA E:LYS21 4.7 33.1 1.0 N E:LYS21 4.8 33.5 1.0 CB E:SER18 4.9 29.2 1.0 C E:LEU27 5.0 36.0 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