Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Murine S100A7/S100A15 in Presence of Calcium (pdb code 8s9w). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Murine S100A7/S100A15 in Presence of Calcium, PDB code: 8s9w:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:33.6 occ:1.00 O A:HOH325 2.3 40.3 1.0 OD1 A:ASN68 2.3 36.5 1.0 OD1 A:ASP66 2.3 40.2 1.0 O A:GLN72 2.3 35.7 1.0 OD1 A:ASP70 2.4 37.2 1.0 OE1 A:GLU77 2.5 36.5 1.0 OE2 A:GLU77 2.6 35.6 1.0 CD A:GLU77 2.9 38.8 1.0 CG A:ASP70 3.3 41.6 1.0 CG A:ASN68 3.4 42.5 1.0 CG A:ASP66 3.5 34.6 1.0 C A:GLN72 3.6 37.0 1.0 OD2 A:ASP70 3.7 40.9 1.0 ND2 A:ASN68 4.0 41.8 1.0 CA A:ASP66 4.2 35.8 1.0 CB A:ASP66 4.3 37.4 1.0 N A:GLN72 4.3 35.2 1.0 N A:ASP70 4.3 35.6 1.0 OD2 A:ASP66 4.3 36.4 1.0 CG A:GLU77 4.4 35.9 1.0 N A:ASN68 4.4 39.8 1.0 CG A:GLN72 4.4 38.9 1.0 N A:ILE73 4.4 33.5 1.0 C A:ASP66 4.5 42.0 1.0 CA A:ILE73 4.5 33.4 1.0 CA A:GLN72 4.5 34.1 1.0 CB A:ASP70 4.5 37.9 1.0 N A:CYS74 4.6 32.4 1.0 CB A:ASN68 4.6 38.1 1.0 N A:LYS69 4.7 39.1 1.0 N A:LYS67 4.7 40.9 1.0 CA A:ASP70 4.8 35.7 1.0 C A:ASN68 4.8 39.1 1.0 CA A:ASN68 4.8 38.6 1.0 N A:ASN71 4.9 32.7 1.0 C A:ASP70 5.0 34.4 1.0

Calcium binding site 2 out of 4 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:35.4 occ:1.00 OE1 A:GLU34 2.3 33.1 1.0 O A:ALA21 2.3 31.7 1.0 O A:GLU24 2.4 36.2 1.0 O A:THR29 2.4 36.2 1.0 O A:ASP26 2.4 42.5 1.0 O A:HOH336 2.4 33.9 1.0 OE2 A:GLU34 2.6 37.2 1.0 CD A:GLU34 2.8 31.7 1.0 C A:ALA21 3.4 31.7 1.0 C A:THR29 3.6 35.4 1.0 C A:GLU24 3.6 47.1 1.0 C A:ASP26 3.6 45.6 1.0 CA A:ALA21 3.8 31.1 1.0 N A:GLU24 4.1 41.4 1.0 C A:GLY25 4.3 45.6 1.0 CG A:GLU34 4.3 32.7 1.0 OG1 A:THR29 4.3 39.2 1.0 N A:ASP26 4.4 42.6 1.0 N A:SER31 4.4 31.4 1.0 CB A:ALA21 4.4 30.5 1.0 N A:LEU30 4.4 29.4 1.0 N A:THR29 4.4 36.9 1.0 CA A:LEU30 4.4 30.0 1.0 N A:LYS27 4.4 41.8 1.0 CA A:LYS27 4.4 45.3 1.0 CA A:GLU24 4.5 43.4 1.0 N A:ALA22 4.5 34.0 1.0 N A:GLY25 4.5 46.7 1.0 CA A:THR29 4.5 34.5 1.0 O A:GLY25 4.6 46.8 1.0 CA A:ASP26 4.6 45.9 1.0 N A:ARG23 4.6 35.2 1.0 CA A:GLY25 4.7 42.8 1.0 CG A:GLU24 4.7 48.9 1.0 O A:TYR20 4.7 34.3 1.0 C A:LYS27 4.8 42.1 1.0 C A:LEU30 4.8 31.6 1.0 O A:HOH347 4.8 43.4 1.0 C A:ALA22 5.0 39.8 1.0

Calcium binding site 3 out of 4 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:34.9 occ:1.00 O B:HOH313 2.1 40.9 1.0 OD1 B:ASP66 2.3 39.0 1.0 O B:GLN72 2.3 30.1 1.0 OD1 B:ASN68 2.3 36.0 1.0 OE1 B:GLU77 2.4 37.4 1.0 OD1 B:ASP70 2.4 38.7 1.0 OE2 B:GLU77 2.6 36.1 1.0 CD B:GLU77 2.8 38.0 1.0 CG B:ASP70 3.3 40.1 1.0 CG B:ASN68 3.4 43.9 1.0 CG B:ASP66 3.5 36.5 1.0 C B:GLN72 3.6 35.2 1.0 OD2 B:ASP70 3.6 38.3 1.0 ND2 B:ASN68 3.8 42.4 1.0 CA B:ASP66 4.2 34.4 1.0 N B:GLN72 4.2 34.5 1.0 OD2 B:ASP66 4.3 40.9 1.0 N B:ASP70 4.3 36.6 1.0 CG B:GLU77 4.3 35.3 1.0 CB B:ASP66 4.4 34.8 1.0 N B:ILE73 4.5 33.5 1.0 CB B:ASP70 4.5 36.9 1.0 CA B:ILE73 4.5 30.0 1.0 CG B:GLN72 4.5 43.9 1.0 CA B:GLN72 4.5 35.2 1.0 N B:ASN68 4.6 39.5 1.0 C B:ASP66 4.6 37.3 1.0 N B:CYS74 4.6 31.6 1.0 CB B:ASN68 4.6 39.5 1.0 N B:LYS69 4.7 42.5 1.0 CA B:ASP70 4.8 37.3 1.0 O B:HOH302 4.8 46.3 1.0 N B:LYS67 4.9 41.5 1.0 N B:ASN71 4.9 36.1 1.0 C B:ASN68 4.9 41.1 1.0 CA B:ASN68 4.9 41.1 1.0 C B:ASP70 5.0 36.4 1.0 C B:ILE73 5.0 30.3 1.0

Calcium binding site 4 out of 4 in the Murine S100A7/S100A15 in Presence of Calcium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Murine S100A7/S100A15 in Presence of Calcium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:35.2 occ:1.00 O B:ALA21 2.2 34.2 1.0 O B:HOH321 2.4 38.6 1.0 O B:GLU24 2.4 37.4 1.0 O B:ASP26 2.4 41.1 1.0 OE1 B:GLU34 2.4 33.2 1.0 O B:THR29 2.5 31.9 1.0 OE2 B:GLU34 2.6 35.6 1.0 CD B:GLU34 2.8 36.3 1.0 C B:ALA21 3.3 32.4 1.0 C B:GLU24 3.6 42.3 1.0 C B:ASP26 3.6 45.5 1.0 C B:THR29 3.6 33.1 1.0 CA B:ALA21 3.8 32.5 1.0 N B:GLU24 4.1 39.2 1.0 N B:ASP26 4.3 45.2 1.0 C B:GLY25 4.3 39.1 1.0 CG B:GLU34 4.3 34.7 1.0 OG1 B:THR29 4.4 39.8 1.0 CA B:GLU24 4.4 40.4 1.0 N B:LYS27 4.4 41.2 1.0 CA B:LYS27 4.4 45.2 1.0 N B:THR29 4.4 33.4 1.0 N B:ALA22 4.5 34.3 1.0 CA B:LEU30 4.5 30.7 1.0 N B:LEU30 4.5 33.6 1.0 N B:SER31 4.5 31.6 1.0 CA B:ASP26 4.5 41.9 1.0 O B:GLY25 4.5 46.8 1.0 CB B:ALA21 4.5 31.2 1.0 N B:GLY25 4.5 40.0 1.0 CA B:THR29 4.6 32.0 1.0 O B:HOH329 4.7 47.2 1.0 N B:ARG23 4.7 33.7 1.0 C B:LYS27 4.7 41.5 1.0 CA B:GLY25 4.7 42.5 1.0 O B:TYR20 4.8 32.5 1.0 C B:LEU30 4.8 31.4 1.0 C B:ALA22 4.9 41.6 1.0 CA B:ALA22 4.9 37.2 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