Magnesium in PDB 5kut: HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound

The structure of HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound, PDB code: 5kut 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)	37.58 / 1.69
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.610, 122.760, 103.890, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 23.9

The binding sites of Magnesium atom in the HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound (pdb code 5kut). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound, PDB code: 5kut:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:20.7 occ:1.00 O1B A:GDP601 1.9 20.1 1.0 OE2 A:GLU471 2.0 20.3 1.0 O A:HOH744 2.1 20.5 1.0 OG A:SER430 2.1 21.1 1.0 O A:HOH771 2.1 22.0 1.0 O A:HOH740 2.1 23.3 1.0 CD A:GLU471 3.0 24.2 1.0 CB A:SER430 3.1 22.7 1.0 PB A:GDP601 3.2 23.3 1.0 OE1 A:GLU471 3.3 23.6 1.0 O2B A:GDP601 3.5 22.4 1.0 N A:SER430 3.8 17.1 1.0 CA A:SER430 4.0 19.4 1.0 O A:HOH789 4.1 30.8 1.0 O B:HOH806 4.1 51.0 1.0 O1A A:GDP601 4.2 21.6 1.0 O3B A:GDP601 4.2 21.5 1.0 O A:HOH821 4.2 46.5 1.0 O3A A:GDP601 4.3 23.2 1.0 CG A:GLU471 4.4 21.5 1.0 O B:HOH780 4.6 35.7 1.0 PA A:GDP601 4.6 23.1 1.0 O A:HOH714 4.8 32.1 1.0 CB A:LYS429 4.8 16.6 1.0 O2A A:GDP601 4.8 25.2 1.0 C A:LYS429 4.9 19.2 1.0 O A:HOH766 4.9 32.6 1.0 CE A:LYS429 4.9 17.9 1.0 NZ A:LYS429 4.9 20.5 1.0

Magnesium binding site 2 out of 3 in the HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:22.2 occ:1.00 O B:HOH784 2.0 23.8 1.0 O B:HOH751 2.1 22.0 1.0 OE2 B:GLU471 2.1 21.3 1.0 O2B B:GDP601 2.1 19.3 1.0 OG B:SER430 2.2 21.9 1.0 O B:HOH724 2.2 23.2 1.0 CD B:GLU471 3.0 27.8 1.0 OE1 B:GLU471 3.3 30.7 1.0 CB B:SER430 3.3 24.5 1.0 PB B:GDP601 3.4 21.5 1.0 O3B B:GDP601 3.5 26.7 1.0 N B:SER430 3.9 19.2 1.0 CA B:SER430 4.1 26.0 1.0 O B:HOH748 4.2 32.9 1.0 O2A B:GDP601 4.2 23.4 1.0 O1B B:GDP601 4.3 21.5 1.0 O3A B:GDP601 4.4 20.5 1.0 CG B:GLU471 4.4 20.0 1.0 O A:HOH782 4.5 36.0 1.0 PA B:GDP601 4.7 24.6 1.0 O B:HOH728 4.9 33.5 1.0 CB B:LYS429 4.9 19.2 1.0 O1A B:GDP601 4.9 27.2 1.0 CE B:LYS429 5.0 20.1 1.0 C B:LYS429 5.0 22.6 1.0 NZ B:LYS429 5.0 23.0 1.0 O B:HOH771 5.0 28.4 1.0

Magnesium binding site 3 out of 3 in the HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of HMIRO2 C-Terminal Gtpase Domain, Gdp-Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:27.9 occ:1.00 O C:HOH739 2.0 27.6 1.0 O2B C:GDP601 2.0 23.1 1.0 O C:HOH742 2.0 28.1 1.0 OE2 C:GLU471 2.1 25.6 1.0 OG C:SER430 2.1 26.3 1.0 O C:HOH713 2.4 27.9 1.0 CD C:GLU471 3.0 29.8 1.0 CB C:SER430 3.2 26.6 1.0 PB C:GDP601 3.2 25.9 1.0 OE1 C:GLU471 3.3 28.5 1.0 O1B C:GDP601 3.4 25.9 1.0 N C:SER430 3.8 21.2 1.0 CA C:SER430 4.0 24.0 1.0 O1A C:GDP601 4.0 29.0 1.0 O C:HOH748 4.2 35.1 1.0 O3B C:GDP601 4.2 26.2 1.0 O3A C:GDP601 4.3 31.1 1.0 CG C:GLU471 4.4 25.0 1.0 PA C:GDP601 4.5 30.8 1.0 O2A C:GDP601 4.8 32.1 1.0 O C:HOH774 4.8 26.6 1.0 CB C:LYS429 4.8 22.7 1.0 C C:LYS429 4.8 22.4 1.0 O C:HOH752 4.9 34.1 1.0 O C:HOH740 5.0 38.6 1.0 NZ C:LYS429 5.0 29.6 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