Calcium in PDB 5kty: Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State

The structure of Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State, PDB code: 5kty was solved by J.L.Klosowiak, P.J.Focia, S.E.Rice, D.M.Freymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.17 / 2.52
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.073, 74.073, 222.175, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.9

The structure of Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State (pdb code 5kty). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State, PDB code: 5kty:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:51.0 occ:1.00 O A:HOH829 2.1 61.6 1.0 OD1 A:ASP199 2.2 63.4 1.0 OD1 A:ASP197 2.2 51.0 1.0 OD1 A:ASP201 2.2 52.2 1.0 O A:THR203 2.2 48.1 1.0 OE1 A:GLU208 2.3 46.4 1.0 OE2 A:GLU208 2.6 50.5 1.0 CD A:GLU208 2.8 45.4 1.0 CG A:ASP201 3.2 53.0 1.0 CG A:ASP199 3.2 60.0 1.0 CG A:ASP197 3.3 47.9 1.0 C A:THR203 3.4 46.8 1.0 OD2 A:ASP201 3.5 56.4 1.0 OD2 A:ASP199 3.7 57.8 1.0 OD2 A:ASP197 4.1 47.7 1.0 ND2 A:ASN205 4.2 52.9 1.0 N A:ASN205 4.2 56.9 1.0 CA A:ASP197 4.2 45.1 1.0 CA A:LEU204 4.2 49.6 1.0 CB A:ASP197 4.2 40.3 1.0 N A:LEU204 4.3 43.1 1.0 CG A:GLU208 4.3 38.4 1.0 N A:THR203 4.3 48.3 1.0 N A:ASP201 4.3 50.8 1.0 N A:ASP199 4.4 42.5 1.0 CB A:ASP201 4.4 55.2 1.0 CA A:THR203 4.5 51.6 1.0 C A:ASP197 4.5 43.5 1.0 CB A:ASP199 4.5 56.0 1.0 N A:GLN198 4.6 44.4 1.0 N A:ASN200 4.6 46.1 1.0 OG1 A:THR203 4.6 47.0 1.0 CG A:ASN205 4.7 56.6 1.0 C A:LEU204 4.7 55.0 1.0 CA A:ASP199 4.8 43.4 1.0 CA A:ASP201 4.9 52.7 1.0 N A:GLY202 4.9 53.7 1.0 C A:ASP199 4.9 50.6 1.0 CB A:GLU208 5.0 44.7 1.0

Calcium binding site 2 out of 2 in the Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Hmiro Ef Hand and Cgtpase Domains, Gdp and CA2+ Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:56.9 occ:1.00 OD1 A:ASP319 2.2 65.0 1.0 OD1 A:ASP317 2.2 57.0 1.0 O A:ALA323 2.2 57.7 1.0 OD1 A:ASP321 2.2 55.5 1.0 OE1 A:GLU328 2.3 47.6 1.0 O A:HOH819 2.4 55.9 1.0 OE2 A:GLU328 2.7 54.9 1.0 CD A:GLU328 2.8 57.9 1.0 CG A:ASP319 3.0 61.0 1.0 OD2 A:ASP319 3.2 66.4 1.0 CG A:ASP321 3.3 47.3 1.0 CG A:ASP317 3.4 53.4 1.0 C A:ALA323 3.5 55.1 1.0 OD2 A:ASP321 3.7 52.5 1.0 CA A:ASP317 4.2 54.1 1.0 OD2 A:ASP317 4.2 52.1 1.0 N A:SER325 4.2 55.1 1.0 N A:ALA323 4.3 55.9 1.0 CA A:LEU324 4.3 53.0 1.0 CG A:GLU328 4.3 49.2 1.0 CB A:ASP317 4.3 48.9 1.0 N A:LEU324 4.3 56.4 1.0 N A:ASP321 4.4 52.7 1.0 CA A:ALA323 4.4 52.0 1.0 CB A:ASP319 4.5 47.1 1.0 N A:ASP319 4.5 52.3 1.0 C A:ASP317 4.6 50.5 1.0 CB A:ASP321 4.6 43.1 1.0 N A:ARG320 4.7 57.9 1.0 N A:LEU318 4.7 52.3 1.0 C A:LEU324 4.8 58.0 1.0 CA A:ASP319 4.9 55.8 1.0 OG A:SER325 4.9 49.6 1.0 CA A:ASP321 4.9 53.4 1.0 C A:ASP319 5.0 57.9 1.0 CB A:GLU328 5.0 41.8 1.0 CB A:ALA323 5.0 51.0 1.0

J.L.Klosowiak, S.Park, K.P.Smith, M.E.French, P.J.Focia, D.M.Freymann, S.E.Rice. Structural Insights Into Parkin Substrate Lysine Targeting From Minimal Miro Substrates. Sci Rep V. 6 33019 2016.
ISSN: ESSN 2045-2322
PubMed: 27605430
DOI: 10.1038/SREP33019