Sodium in PDB 5o2z: Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain

The structure of Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain, PDB code: 5o2z was solved by F.Boni, M.Milani, E.Mastrangelo, M.De Rosa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.39 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.290, 44.420, 58.010, 90.00, 110.13, 90.00
R / Rfree (%)	19.9 / 24.2

The structure of Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain (pdb code 5o2z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain, PDB code: 5o2z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:38.0 occ:1.00 O B:THR238 2.7 29.6 1.0 O B:HOH485 2.9 32.9 1.0 CB B:SER234 3.6 18.7 1.0 OG1 B:THR238 3.6 27.1 1.0 CB B:THR238 3.7 25.3 1.0 C B:THR238 3.8 27.5 1.0 O B:VAL233 3.9 23.2 1.0 O B:HOH472 4.0 42.6 1.0 CA B:SER234 4.1 18.4 1.0 O B:HOH489 4.3 60.2 1.0 CD B:PRO240 4.4 24.6 1.0 CA B:THR238 4.4 24.4 1.0 OE2 B:GLU235 4.4 31.4 1.0 N B:PRO240 4.7 23.3 1.0 C B:VAL233 4.7 21.9 1.0 OG B:SER234 4.8 23.7 1.0 N B:GLU239 4.8 22.6 1.0 N B:SER234 4.9 19.9 1.0 CG B:PRO240 4.9 26.4 1.0 CB B:PRO240 5.0 21.2 1.0 CG2 B:THR238 5.0 26.4 1.0

Sodium binding site 2 out of 2 in the Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Domain Swap Dimer of the G167R Variant of Gelsolin Second Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:51.8 occ:1.00 O B:HOH480 2.6 29.0 1.0 O A:HOH484 3.0 34.4 1.0 C B:GLY194 3.6 30.5 1.0 CA B:GLY194 3.7 25.6 1.0 N B:ASN195 3.8 27.2 1.0 O B:GLY194 3.9 25.9 1.0 CD B:ARG225 4.0 22.5 1.0 CG1 A:VAL158 4.2 28.1 1.0 OD1 B:ASN195 4.2 44.8 1.0 O B:HOH429 4.3 40.7 1.0 CG B:ASN195 4.4 36.6 1.0 ND2 B:ASN195 4.5 33.3 1.0 NE B:ARG225 4.5 27.2 1.0 CA B:ASN195 4.6 20.8 1.0 CZ B:ARG225 5.0 26.1 1.0 CB A:VAL158 5.0 39.8 1.0 NH1 B:ARG225 5.0 24.6 1.0

F.Boni, M.Milani, A.Barbiroli, L.Diomede, E.Mastrangelo, M.De Rosa. Gelsolin Pathogenic GLY167ARG Mutation Promotes Domain-Swap Dimerization of the Protein. Hum. Mol. Genet. V. 27 53 2018.
ISSN: ESSN 1460-2083
PubMed: 29069428
DOI: 10.1093/HMG/DDX383