Calcium in PDB 6zdy: Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc

The structure of Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc, PDB code: 6zdy was solved by L.Yatime, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.49 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.84, 40.62, 53.09, 90, 125, 90
R / Rfree (%)	17.6 / 20

The structure of Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc (pdb code 6zdy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc, PDB code: 6zdy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:24.7 occ:0.95 O A:GLU27 2.2 33.5 1.0 O A:SER24 2.3 28.9 1.0 O A:THR32 2.3 25.8 1.0 O A:HIS29 2.4 31.6 1.0 OE1 A:GLU37 2.4 26.8 1.0 O A:HOH355 2.5 31.8 1.0 OE2 A:GLU37 2.6 28.7 1.0 CD A:GLU37 2.9 25.0 1.0 C A:SER24 3.4 28.6 1.0 C A:GLU27 3.5 34.2 1.0 C A:THR32 3.5 23.9 1.0 C A:HIS29 3.6 32.2 1.0 CA A:SER24 3.9 26.3 1.0 N A:HIS29 4.1 33.5 1.0 N A:GLU27 4.1 33.9 1.0 C A:GLY28 4.2 34.2 1.0 N A:SER34 4.3 25.5 1.0 OG1 A:THR32 4.3 29.4 1.0 N A:THR32 4.3 26.1 1.0 CG A:GLU37 4.4 25.7 1.0 CA A:GLU27 4.4 35.8 1.0 CA A:PRO30 4.4 31.7 1.0 N A:GLY28 4.4 36.6 1.0 N A:LEU33 4.4 24.2 1.0 CA A:HIS29 4.4 32.9 1.0 N A:PRO30 4.4 31.2 1.0 CA A:LEU33 4.5 23.8 1.0 CA A:GLY28 4.5 36.0 1.0 N A:ARG25 4.5 31.2 1.0 CA A:THR32 4.5 25.3 1.0 CB A:SER24 4.5 26.8 1.0 O A:GLY28 4.6 36.4 1.0 C A:PRO30 4.6 29.9 1.0 O A:TYR23 4.6 31.3 1.0 N A:LYS26 4.7 34.6 1.0 CG A:GLU27 4.7 36.7 1.0 O A:HOH383 4.8 44.5 1.0 C A:LEU33 4.8 24.9 1.0 CA A:ARG25 4.9 35.6 1.0 C A:ARG25 4.9 33.8 1.0 O A:PRO30 5.0 30.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Wt Murine S100A9 Bound to Calcium and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:24.0 occ:0.95 OD1 A:ASP72 2.3 27.9 1.0 OD1 A:ASP68 2.3 26.2 1.0 OD1 A:ASN70 2.4 31.4 1.0 O A:GLN74 2.4 26.0 1.0 OE1 A:GLU79 2.4 27.2 1.0 O A:HOH356 2.4 31.5 1.0 OE2 A:GLU79 2.6 30.1 1.0 CD A:GLU79 2.8 28.3 1.0 CG A:ASP72 3.3 29.4 1.0 CG A:ASN70 3.5 31.7 1.0 CG A:ASP68 3.5 26.0 1.0 C A:GLN74 3.6 25.3 1.0 OD2 A:ASP72 3.7 31.6 1.0 ND2 A:ASN70 4.1 34.6 1.0 CA A:ASP68 4.1 25.6 1.0 N A:ASP72 4.2 29.0 1.0 N A:GLN74 4.3 25.9 1.0 CB A:ASP68 4.3 24.1 1.0 CG A:GLU79 4.3 26.8 1.0 OD2 A:ASP68 4.4 25.6 1.0 CA A:LEU75 4.4 23.5 1.0 N A:LEU75 4.4 24.2 1.0 N A:ASN70 4.5 30.1 1.0 C A:ASP68 4.5 27.9 1.0 N A:SER76 4.5 24.3 1.0 CG A:GLN74 4.5 34.3 1.0 CB A:ASP72 4.5 31.1 1.0 CA A:GLN74 4.5 26.3 1.0 O A:HOH379 4.5 51.5 1.0 O A:HOH315 4.6 39.2 1.0 N A:GLN71 4.6 31.4 1.0 CB A:ASN70 4.7 32.0 1.0 N A:THR69 4.7 28.6 1.0 CA A:ASP72 4.7 28.9 1.0 N A:ASN73 4.8 26.8 1.0 CA A:ASN70 4.9 31.4 1.0 C A:ASN70 4.9 31.9 1.0 C A:ASP72 4.9 27.5 1.0 C A:LEU75 4.9 23.3 1.0 CD2 A:LEU75 5.0 24.2 1.0

L.Signor, T.Paris, C.Mas, A.Picard, G.Lutfalla, E.Boeri Erba, L.Yatime. Divalent Cations Influence the Dimerization Mode of Murine S100A9 Protein By Modulating Its Disulfide Bond Pattern. J.Struct.Biol. V. 213 07689 2020.
ISSN: ESSN 1095-8657
PubMed: 33359632
DOI: 10.1016/J.JSB.2020.107689