Calcium in PDB 5faf: N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form)

The structure of N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form), PDB code: 5faf was solved by F.Boni, M.Milani, S.Ricagno, M.Bolognesi, M.De Rosa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.50 / 1.05
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.390, 50.120, 80.180, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 16.8

The structure of N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form) (pdb code 5faf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form), PDB code: 5faf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:14.3 occ:1.00 OD1 A:ASP187 2.3 14.5 1.0 OE2 A:GLU209 2.4 14.1 1.0 O A:HOH520 2.4 17.8 1.0 O A:GLY186 2.4 14.4 1.0 OD2 A:ASP259 2.5 17.6 1.0 O A:HOH462 2.5 17.5 1.0 OE1 A:GLU209 2.5 14.4 1.0 OD1 A:ASP259 2.7 18.3 1.0 CD A:GLU209 2.8 13.8 1.0 CG A:ASP259 2.9 16.8 1.0 C A:GLY186 3.4 13.1 1.0 CG A:ASP187 3.5 13.3 1.0 ND2 A:ASN206 4.0 19.0 1.0 CA A:ASP187 4.0 11.8 1.0 NZ A:LYS166 4.1 15.0 1.0 N A:ASP187 4.1 12.3 1.0 CG A:GLU209 4.3 13.6 1.0 CB A:ASP187 4.3 11.7 1.0 CA A:GLY186 4.3 13.6 1.0 OD2 A:ASP187 4.4 15.8 1.0 CB A:ASP259 4.4 17.6 1.0 O A:HOH443 4.5 21.1 1.0 CG A:LYS166 4.6 12.9 1.0 CA A:SER205 4.6 15.9 1.0 N A:ASN206 4.7 16.1 1.0 O A:ASN204 4.7 19.6 1.0 N A:GLY167 4.8 14.0 1.0 CG A:ASN206 4.9 20.1 1.0 O A:GLY167 4.9 21.6 1.0

Calcium binding site 2 out of 2 in the N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of N184K Pathological Variant of Gelsolin Domain 2 (Orthorhombic Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:20.2 occ:0.50 OE2 A:GLU258 2.1 33.1 1.0 O A:HOH550 2.3 26.9 1.0 O A:HOH548 2.6 46.4 1.0 CD A:GLU258 2.8 21.4 1.0 OE1 A:GLU258 2.8 26.1 1.0 O A:HOH546 4.2 41.6 1.0 CG A:GLU258 4.2 19.0 1.0 O A:HOH462 4.3 17.5 1.0 O A:HOH590 4.3 42.3 1.0 OD2 A:ASP259 4.4 17.6 1.0 N A:ASP259 4.7 15.9 1.0 O A:HOH514 4.7 31.1 1.0

F.Boni, M.Milani, R.Porcari, A.Barbiroli, S.Ricagno, M.De Rosa. Molecular Basis of A Novel Renal Amyloidosis Due to N184K Gelsolin Variant. Sci Rep V. 6 33463 2016.
ISSN: ESSN 2045-2322
PubMed: 27633054
DOI: 10.1038/SREP33463