Magnesium in PDB 5ku1: HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State

The structure of HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State, PDB code: 5ku1 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)	29.81 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.136, 73.136, 217.142, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 26.4

The structure of HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State (pdb code 5ku1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State, PDB code: 5ku1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:52.1 occ:1.00 O A:THR203 2.1 59.3 1.0 OD1 A:ASP199 2.1 69.2 1.0 OD1 A:ASP197 2.1 66.5 1.0 OD1 A:ASP201 2.1 63.0 1.0 OE1 A:GLU208 2.1 63.7 1.0 OE2 A:GLU208 2.8 63.3 1.0 CD A:GLU208 2.8 56.5 1.0 CG A:ASP199 3.0 65.9 1.0 CG A:ASP201 3.1 70.6 1.0 C A:THR203 3.3 59.1 1.0 CG A:ASP197 3.3 56.6 1.0 OD2 A:ASP199 3.4 72.3 1.0 OD2 A:ASP201 3.5 73.8 1.0 CA A:LEU204 4.0 59.5 1.0 OD2 A:ASP197 4.1 56.8 1.0 N A:ASN205 4.1 54.2 1.0 N A:LEU204 4.1 57.0 1.0 CA A:ASP197 4.2 50.1 1.0 N A:THR203 4.3 63.5 1.0 CB A:ASP197 4.3 48.8 1.0 CG A:GLU208 4.3 54.8 1.0 CB A:ASP199 4.3 61.9 1.0 CA A:THR203 4.3 55.4 1.0 N A:ASP201 4.4 60.7 1.0 N A:ASP199 4.4 62.1 1.0 CB A:ASP201 4.4 70.4 1.0 OG1 A:THR203 4.4 58.6 1.0 C A:ASP197 4.5 64.3 1.0 ND2 A:ASN205 4.6 63.0 1.0 C A:LEU204 4.6 58.6 1.0 CG A:ASN205 4.6 49.2 1.0 N A:ASN200 4.7 65.4 1.0 N A:GLN198 4.7 63.2 1.0 CA A:ASP199 4.8 65.4 1.0 OD1 A:ASN205 4.8 58.4 1.0 CA A:ASP201 4.9 62.3 1.0 CB A:GLU208 4.9 43.8 1.0 C A:ASP199 4.9 69.2 1.0 CD2 A:LEU204 4.9 47.6 1.0 N A:GLY202 5.0 62.7 1.0 CB A:THR203 5.0 54.7 1.0

Magnesium binding site 2 out of 2 in the HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of HMIRO1 Ef Hand and Cgtpase Domains in the Gdp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:54.4 occ:1.00 OD1 A:ASP319 2.1 69.0 1.0 O A:ALA323 2.1 60.9 1.0 OD1 A:ASP321 2.1 71.0 1.0 OD1 A:ASP317 2.1 61.8 1.0 OE1 A:GLU328 2.1 62.3 1.0 CG A:ASP319 2.8 74.9 1.0 CG A:ASP321 2.8 69.1 1.0 CD A:GLU328 2.9 63.4 1.0 OD2 A:ASP319 2.9 80.8 1.0 OE2 A:GLU328 3.0 60.6 1.0 OD2 A:ASP321 3.0 62.3 1.0 C A:ALA323 3.3 55.0 1.0 CG A:ASP317 3.3 55.7 1.0 CA A:ASP317 4.1 55.8 1.0 N A:SER325 4.1 61.5 1.0 CA A:LEU324 4.1 57.6 1.0 CB A:ASP317 4.1 49.8 1.0 N A:ALA323 4.2 63.7 1.0 N A:LEU324 4.2 54.7 1.0 OD2 A:ASP317 4.2 55.5 1.0 CB A:ASP321 4.2 60.9 1.0 CB A:ASP319 4.3 68.4 1.0 N A:ASP321 4.3 66.0 1.0 CA A:ALA323 4.3 54.5 1.0 CG A:GLU328 4.3 54.3 1.0 N A:ASP319 4.4 60.5 1.0 C A:ASP317 4.5 63.9 1.0 C A:LEU324 4.6 58.1 1.0 N A:LEU318 4.7 61.8 1.0 CA A:ASP321 4.7 65.5 1.0 N A:ARG320 4.7 67.4 1.0 CA A:ASP319 4.8 59.3 1.0 OG A:SER325 4.8 66.8 1.0 CD2 A:LEU324 4.8 56.6 1.0 CB A:GLU328 4.9 53.4 1.0 CB A:ALA323 4.9 53.5 1.0 C A:ASP319 4.9 60.2 1.0 CB A:SER325 4.9 60.0 1.0 N A:CYS322 5.0 61.8 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