Magnesium in PDB 7f6j: Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex

All present enzymatic activity of Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex:
3.6.5.2;

The structure of Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex, PDB code: 7f6j was solved by H.Khan, L.Chen, L.Tan, Y.J.Im, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.77 / 2.10
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	84.226, 84.226, 154.622, 90, 90, 120
R / Rfree (%)	20.7 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex (pdb code 7f6j). 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 the PDZD8 Coiled-Coil Domain - RAB7 Complex, PDB code: 7f6j:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex


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 the PDZD8 Coiled-Coil Domain - RAB7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:27.3 occ:1.00 O2B A:GTP502 2.0 28.4 1.0 OG1 A:THR22 2.0 23.0 1.0 O A:HOH608 2.1 26.8 1.0 O1G A:GTP502 2.1 29.1 1.0 OG1 A:THR40 2.1 29.2 1.0 O A:HOH609 2.2 29.5 1.0 CB A:THR22 3.1 27.0 1.0 CB A:THR40 3.1 27.9 1.0 PB A:GTP502 3.2 27.6 1.0 PG A:GTP502 3.2 27.2 1.0 O3B A:GTP502 3.5 26.4 1.0 N A:THR40 3.8 30.2 1.0 O2G A:GTP502 3.8 26.4 1.0 OD1 A:ASP63 3.8 31.0 1.0 N A:THR22 3.9 24.7 1.0 CA A:THR22 4.1 26.4 1.0 CA A:THR40 4.1 31.2 1.0 O2A A:GTP502 4.1 25.3 1.0 OD2 A:ASP63 4.1 27.3 1.0 CG2 A:THR22 4.2 30.5 1.0 CG2 A:THR40 4.2 29.1 1.0 O3A A:GTP502 4.3 32.3 1.0 O1B A:GTP502 4.3 28.3 1.0 O A:HOH610 4.4 34.7 1.0 CG A:ASP63 4.4 33.1 1.0 O A:LYS38 4.5 31.7 1.0 O3G A:GTP502 4.5 28.8 1.0 PA A:GTP502 4.5 29.2 1.0 O A:THR64 4.6 28.3 1.0 O1A A:GTP502 4.6 28.7 1.0 C A:ALA39 4.9 36.3 1.0 C A:LYS21 5.0 26.9 1.0 NZ A:LYS21 5.0 25.6 1.0 CB A:LYS21 5.0 26.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the PDZD8 Coiled-Coil Domain - RAB7 Complex


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 the PDZD8 Coiled-Coil Domain - RAB7 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:41.5 occ:1.00 O2B B:GTP502 1.8 36.8 1.0 OG1 B:THR40 1.9 43.6 1.0 O B:HOH608 2.1 45.6 1.0 OG1 B:THR22 2.2 30.3 1.0 O B:HOH615 2.3 36.1 1.0 O1G B:GTP502 2.4 52.4 1.0 PB B:GTP502 3.0 37.7 1.0 CB B:THR40 3.0 51.2 1.0 CB B:THR22 3.1 31.7 1.0 PG B:GTP502 3.3 60.9 1.0 O3B B:GTP502 3.3 38.9 1.0 O2A B:GTP502 3.5 37.1 1.0 N B:THR22 3.7 27.9 1.0 N B:THR40 3.7 64.1 1.0 O3G B:GTP502 3.7 63.3 1.0 CA B:THR40 3.9 58.8 1.0 CA B:THR22 4.0 33.4 1.0 O3A B:GTP502 4.0 35.0 1.0 OD2 B:ASP63 4.0 38.5 1.0 O1B B:GTP502 4.1 34.7 1.0 PA B:GTP502 4.2 35.5 1.0 CG2 B:THR40 4.2 47.4 1.0 OD1 B:ASP63 4.2 33.9 1.0 CG2 B:THR22 4.2 33.2 1.0 O B:HOH634 4.3 44.2 1.0 O1A B:GTP502 4.4 37.3 1.0 CG B:ASP63 4.6 35.5 1.0 O2G B:GTP502 4.7 61.7 1.0 O B:ALA65 4.7 51.9 1.0 C B:ALA39 4.7 65.2 1.0 CB B:LYS21 4.7 25.6 1.0 O B:LYS38 4.8 64.8 1.0 C B:LYS21 4.8 29.6 1.0 NZ B:LYS21 4.8 30.4 1.0

H.Khan, L.Chen, L.Tan, Y.J.Im. Structural Basis of Human PDZD8-RAB7 Interaction For the Er-Late Endosome Tethering. Sci Rep V. 11 18859 2021.
ISSN: ESSN 2045-2322
PubMed: 34552186
DOI: 10.1038/S41598-021-98419-5