Magnesium in PDB 5ksz: Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State

The structure of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State, PDB code: 5ksz 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)	24.68 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.180, 74.180, 218.859, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26.6

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

Chlorine

(Cl)

1 atom

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

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:52.6 occ:1.00 OD1 A:ASP199 2.0 77.7 1.0 O A:HOH804 2.0 67.5 1.0 OE1 A:GLU208 2.1 57.8 1.0 OD1 A:ASP201 2.1 56.4 1.0 O A:THR203 2.1 49.1 1.0 OD1 A:ASP197 2.1 69.2 1.0 CD A:GLU208 3.0 64.7 1.0 CG A:ASP199 3.0 78.0 1.0 CG A:ASP201 3.2 73.4 1.0 OE2 A:GLU208 3.2 78.9 1.0 CG A:ASP197 3.3 44.2 1.0 C A:THR203 3.4 67.7 1.0 OD2 A:ASP199 3.4 80.4 1.0 OD2 A:ASP201 3.6 79.8 1.0 OD2 A:ASP197 4.1 56.5 1.0 N A:ASN205 4.1 71.4 1.0 CA A:LEU204 4.2 62.6 1.0 N A:LEU204 4.2 67.6 1.0 CB A:ASP197 4.2 28.6 1.0 CA A:ASP197 4.2 43.6 1.0 N A:ASP201 4.3 68.4 1.0 N A:THR203 4.3 53.7 1.0 CB A:ASP199 4.3 80.0 1.0 N A:ASP199 4.4 58.9 1.0 CA A:THR203 4.4 64.5 1.0 CB A:ASP201 4.4 70.1 1.0 CG A:GLU208 4.4 61.3 1.0 OG1 A:THR203 4.4 76.5 1.0 ND2 A:ASN205 4.5 76.1 1.0 N A:ASN200 4.5 65.3 1.0 CG A:ASN205 4.5 67.9 1.0 C A:ASP197 4.5 64.7 1.0 OD1 A:ASN205 4.7 59.0 1.0 N A:GLN198 4.7 65.9 1.0 C A:LEU204 4.7 70.3 1.0 CA A:ASP199 4.7 66.7 1.0 CB A:GLU208 4.8 67.5 1.0 CA A:ASP201 4.8 68.2 1.0 C A:ASP199 4.8 69.7 1.0 N A:GLY202 4.9 49.9 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hmiro Ef Hand and Cgtpase Domains in the Gmppcp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:65.0 occ:1.00 OD1 A:ASP319 2.0 67.6 1.0 O A:ALA323 2.1 63.0 1.0 OE1 A:GLU328 2.1 61.7 1.0 OD1 A:ASP317 2.1 61.8 1.0 OD1 A:ASP321 2.1 58.4 1.0 O A:HOH801 2.1 55.1 1.0 CG A:ASP319 2.8 66.9 1.0 CD A:GLU328 2.9 64.1 1.0 OD2 A:ASP319 2.9 74.4 1.0 OE2 A:GLU328 3.0 63.7 1.0 CG A:ASP321 3.1 58.8 1.0 C A:ALA323 3.3 53.4 1.0 CG A:ASP317 3.3 56.5 1.0 OD2 A:ASP321 3.5 66.9 1.0 CA A:ASP317 4.0 56.9 1.0 N A:ALA323 4.1 69.7 1.0 N A:LEU324 4.1 54.2 1.0 CA A:LEU324 4.1 51.3 1.0 CB A:ASP317 4.2 50.6 1.0 CA A:ALA323 4.2 53.5 1.0 OD2 A:ASP317 4.2 63.0 1.0 CB A:ASP319 4.3 56.8 1.0 N A:SER325 4.3 53.8 1.0 CG A:GLU328 4.3 45.0 1.0 N A:ASP321 4.3 67.1 1.0 C A:ASP317 4.4 60.1 1.0 CB A:ASP321 4.4 58.1 1.0 N A:ASP319 4.5 57.3 1.0 N A:ARG320 4.7 60.6 1.0 C A:LEU324 4.7 57.9 1.0 CB A:ALA323 4.7 40.8 1.0 CA A:ASP319 4.8 55.3 1.0 N A:LEU318 4.8 65.0 1.0 CD2 A:LEU324 4.8 60.5 1.0 CA A:ASP321 4.8 67.3 1.0 O A:ASP317 4.9 60.2 1.0 C A:ASP319 4.9 58.9 1.0 CB A:GLU328 4.9 52.4 1.0 N A:CYS322 4.9 63.6 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