Sodium in PDB 8s9w: Murine S100A7/S100A15 in Presence of Calcium

The structure of Murine S100A7/S100A15 in Presence of Calcium, PDB code: 8s9w was solved by S.A.Harrison, A.Naretto, S.Balakrishnan, W.J.Chazin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.19 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.54, 68.4, 85.61, 90, 90, 90
R / Rfree (%)	18.6 / 23.6

The structure of Murine S100A7/S100A15 in Presence of Calcium also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Murine S100A7/S100A15 in Presence of Calcium (pdb code 8s9w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Murine S100A7/S100A15 in Presence of Calcium, PDB code: 8s9w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:40.9 occ:1.00 NE2 B:HIS18 1.8 52.9 1.0 NE2 A:HIS90 2.2 42.8 1.0 CE1 B:HIS18 2.5 48.5 1.0 OE2 B:GLU28 2.7 76.5 1.0 NE2 A:HIS94 2.8 84.2 1.0 CD2 B:HIS18 2.9 51.2 1.0 CD2 A:HIS90 3.2 46.4 1.0 CE1 A:HIS90 3.2 47.0 1.0 CD2 A:HIS94 3.4 81.5 1.0 ND1 B:HIS18 3.6 52.0 1.0 CE1 A:HIS94 3.8 87.1 1.0 CG B:HIS18 3.9 48.1 1.0 CD B:GLU28 3.9 67.9 1.0 CG A:HIS90 4.3 42.0 1.0 ND1 A:HIS90 4.3 46.4 1.0 O A:HOH346 4.3 60.1 1.0 CG A:HIS94 4.5 72.7 1.0 CG B:GLU28 4.6 63.1 1.0 ND1 A:HIS94 4.7 81.8 1.0 OE1 B:GLU28 4.9 67.5 1.0 CE1 A:PHE93 4.9 53.1 1.0 CD1 A:PHE93 5.0 49.1 1.0

Sodium binding site 2 out of 2 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:40.2 occ:1.00 NE2 B:HIS90 2.1 38.0 1.0 NE2 B:HIS94 2.2 66.6 1.0 NE2 A:HIS18 2.3 45.9 1.0 CE1 A:HIS18 2.3 49.9 1.0 O A:HOH308 2.7 56.0 1.0 OE2 A:GLU28 2.8 76.5 1.0 CE1 B:HIS90 2.8 41.7 1.0 CE1 B:HIS94 3.2 72.5 1.0 CD2 B:HIS94 3.3 66.3 1.0 CD2 B:HIS90 3.3 42.3 1.0 CD2 A:HIS18 3.6 39.5 1.0 ND1 A:HIS18 3.6 44.8 1.0 CD A:GLU28 3.8 64.9 1.0 ND1 B:HIS90 4.0 43.1 1.0 CG A:HIS18 4.2 39.4 1.0 OE1 A:GLU28 4.2 81.0 1.0 CG B:HIS90 4.3 37.9 1.0 ND1 B:HIS94 4.3 73.0 1.0 CG B:HIS94 4.4 69.0 1.0 CE1 B:PHE93 4.9 73.3 1.0 CD1 B:PHE93 4.9 67.5 1.0

S.A.Harrison, A.Naretto, S.Balakrishnan, Y.R.Perera, W.J.Chazin. Comparative Analysis of the Physical Properties of Murine and Human S100A7: Insight Into Why Zinc Piracy Is Mediated By Human But Not Murine S100A7. J.Biol.Chem. V. 299 05292 2023.
ISSN: ESSN 1083-351X
PubMed: 37769710
DOI: 10.1016/J.JBC.2023.105292