Magnesium in PDB 6iyb: Structure of Human ORP1 Ank - RAB7 Complex

The structure of Structure of Human ORP1 Ank - RAB7 Complex, PDB code: 6iyb was solved by J.Tong, Y.J.Im, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.29 / 2.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.136, 117.222, 130.476, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.2

The binding sites of Magnesium atom in the Structure of Human ORP1 Ank - RAB7 Complex (pdb code 6iyb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human ORP1 Ank - RAB7 Complex, PDB code: 6iyb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human ORP1 Ank - RAB7 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human ORP1 Ank - RAB7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:18.0 occ:1.00 O2B A:GTP1302 2.0 18.0 1.0 OG1 A:THR40 2.1 17.5 1.0 O3G A:GTP1302 2.1 20.0 1.0 O A:HOH1425 2.1 16.2 1.0 OG1 A:THR22 2.2 16.2 1.0 O A:HOH1431 2.2 17.7 1.0 CB A:THR22 3.1 17.2 1.0 CB A:THR40 3.2 17.7 1.0 PB A:GTP1302 3.2 15.9 1.0 PG A:GTP1302 3.2 19.1 1.0 O3B A:GTP1302 3.4 17.6 1.0 N A:THR40 3.7 19.5 1.0 O1G A:GTP1302 3.9 19.2 1.0 N A:THR22 4.0 17.4 1.0 O2A A:GTP1302 4.0 15.0 1.0 CA A:THR40 4.0 22.2 1.0 OD2 A:ASP63 4.1 19.9 1.0 CG2 A:THR22 4.1 20.2 1.0 CA A:THR22 4.1 18.5 1.0 O A:HOH1437 4.2 21.6 1.0 O3A A:GTP1302 4.2 18.9 1.0 O1B A:GTP1302 4.3 16.9 1.0 OD1 A:ASP63 4.3 21.8 1.0 CG2 A:THR40 4.3 18.7 1.0 O2G A:GTP1302 4.3 18.7 1.0 O A:LYS38 4.5 21.0 1.0 PA A:GTP1302 4.5 16.7 1.0 O A:THR64 4.5 18.8 1.0 CG A:ASP63 4.6 21.5 1.0 O1A A:GTP1302 4.6 18.5 1.0 C A:ALA39 4.6 26.6 1.0 CA A:ALA39 5.0 24.6 1.0 O A:HOH1467 5.0 31.2 1.0 CB A:LYS21 5.0 16.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Human ORP1 Ank - RAB7 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human ORP1 Ank - RAB7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1301 b:37.3 occ:1.00 O1B C:GTP1302 1.9 28.6 1.0 OG1 C:THR22 2.0 36.5 1.0 O3G C:GTP1302 2.0 32.2 1.0 O C:HOH1407 2.1 33.3 1.0 OG1 C:THR40 2.1 37.0 1.0 O C:HOH1403 2.4 34.6 1.0 CB C:THR22 3.1 41.2 1.0 PG C:GTP1302 3.2 35.1 1.0 PB C:GTP1302 3.2 33.4 1.0 CB C:THR40 3.3 36.4 1.0 O3B C:GTP1302 3.5 40.4 1.0 N C:THR22 3.7 37.6 1.0 O2G C:GTP1302 3.8 38.3 1.0 N C:THR40 3.9 36.9 1.0 OD2 C:ASP63 3.9 42.0 1.0 CA C:THR22 4.0 37.7 1.0 OD1 C:ASP63 4.1 41.2 1.0 O1A C:GTP1302 4.1 38.7 1.0 O2B C:GTP1302 4.2 34.6 1.0 CG2 C:THR22 4.2 36.3 1.0 CA C:THR40 4.2 37.2 1.0 O3A C:GTP1302 4.3 41.5 1.0 CG2 C:THR40 4.4 33.0 1.0 O1G C:GTP1302 4.4 38.3 1.0 O C:THR64 4.4 36.6 1.0 CG C:ASP63 4.4 43.5 1.0 O C:HOH1415 4.4 43.3 1.0 PA C:GTP1302 4.6 40.1 1.0 O2A C:GTP1302 4.6 40.2 1.0 O C:LYS38 4.7 45.0 1.0 CB C:LYS21 4.8 34.2 1.0 CE C:LYS21 4.8 30.8 1.0 C C:LYS21 4.9 35.1 1.0 C C:ALA39 4.9 38.2 1.0 NZ C:LYS21 4.9 32.1 1.0

J.Tong, L.Tan, C.Chun, Y.J.Im. Structural Basis of Human ORP1-RAB7 Interaction For the Late-Endosome and Lysosome Targeting. Plos One V. 14 11724 2019.
ISSN: ESSN 1932-6203
PubMed: 30721249
DOI: 10.1371/JOURNAL.PONE.0211724