Magnesium in PDB 5yj9: Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp

The structure of Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp, PDB code: 5yj9 was solved by K.Okatsu, Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.74 / 2.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.028, 59.790, 50.822, 90.00, 101.82, 90.00
R / Rfree (%)	22.9 / 24.3

The binding sites of Magnesium atom in the Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp (pdb code 5yj9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp, PDB code: 5yj9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:85.5 occ:1.00 O D:HOH703 2.0 69.4 1.0 O2B D:ANP601 2.1 69.3 1.0 OD2 D:ASP359 2.5 77.3 1.0 OD1 D:ASP359 2.6 78.0 1.0 CG D:ASP359 2.9 75.7 1.0 OE2 D:GLU217 2.9 78.5 1.0 N3B D:ANP601 3.1 75.3 1.0 PB D:ANP601 3.2 69.5 1.0 CD D:GLU217 4.0 77.2 1.0 O1B D:ANP601 4.1 82.6 1.0 MG D:MG603 4.2 49.4 1.0 NZ D:LYS196 4.2 73.4 1.0 O3A D:ANP601 4.3 0.6 1.0 O2A D:ANP601 4.4 73.4 1.0 CB D:ASP359 4.4 69.8 1.0 OE1 D:GLU217 4.4 74.6 1.0 O1A D:ANP601 4.5 71.5 1.0 PA D:ANP601 4.6 73.7 1.0 CA D:GLY361 4.8 67.8 1.0 PG D:ANP601 4.8 98.8 1.0 N D:GLY361 4.9 64.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tribolium Castaneum PINK1 Kinase Domain in Complex with Amp-Pnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:49.4 occ:1.00 O D:HOH702 2.1 87.3 1.0 O1A D:ANP601 2.1 71.5 1.0 O D:HOH701 2.2 67.2 1.0 OD2 D:ASP359 2.2 77.3 1.0 OD1 D:ASN342 2.3 56.3 1.0 O1G D:ANP601 2.6 0.2 1.0 N3B D:ANP601 2.9 75.3 1.0 PG D:ANP601 3.1 98.8 1.0 CG D:ASP359 3.3 75.7 1.0 PA D:ANP601 3.3 73.7 1.0 CG D:ASN342 3.4 54.6 1.0 O3A D:ANP601 3.5 0.6 1.0 O2G D:ANP601 3.6 0.6 1.0 CB D:ASP359 3.6 69.8 1.0 PB D:ANP601 3.7 69.5 1.0 ND2 D:ASN342 3.9 54.8 1.0 O2B D:ANP601 4.1 69.3 1.0 MG D:MG602 4.2 85.5 1.0 OD1 D:ASP341 4.3 75.0 1.0 O2A D:ANP601 4.4 73.4 1.0 O5' D:ANP601 4.4 61.2 1.0 OD1 D:ASP359 4.4 78.0 1.0 O D:HOH703 4.5 69.4 1.0 OD2 D:ASP337 4.5 64.0 1.0 O3G D:ANP601 4.6 0.5 1.0 CB D:ASN342 4.6 52.5 1.0 C5' D:ANP601 4.8 62.8 1.0 NZ D:LYS339 4.8 76.6 1.0 CA D:ASN342 5.0 53.0 1.0

K.Okatsu, Y.Sato, K.Yamano, N.Matsuda, L.Negishi, A.Takahashi, A.Yamagata, S.Goto-Ito, M.Mishima, Y.Ito, T.Oka, K.Tanaka, S.Fukai. Structural Insights Into Ubiquitin Phosphorylation By PINK1. Sci Rep V. 8 10382 2018.
ISSN: ESSN 2045-2322
PubMed: 29991771
DOI: 10.1038/S41598-018-28656-8