Magnesium in PDB 1vg9: The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein

The structure of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein, PDB code: 1vg9 was solved by A.Rak, O.Pylypenko, A.Niculae, K.Pyatkov, R.S.Goody, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.42 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.392, 144.691, 200.086, 90.00, 90.13, 90.00
R / Rfree (%)	20.6 / 25

The structure of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein (pdb code 1vg9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein, PDB code: 1vg9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2307 b:28.9 occ:1.00 OG1 B:THR22 1.9 20.1 1.0 O3B B:GDP2302 1.9 24.4 1.0 O B:HOH8359 2.0 16.8 1.0 O B:HOH8358 2.1 11.2 1.0 O B:HOH8006 2.3 12.1 1.0 O B:HOH8152 2.4 24.9 1.0 CB B:THR22 3.0 21.6 1.0 PB B:GDP2302 3.1 22.2 1.0 O1B B:GDP2302 3.5 23.7 1.0 N B:THR22 3.7 22.1 1.0 OD1 B:ASP63 3.8 24.8 1.0 CA B:THR22 3.9 22.4 1.0 O2A B:GDP2302 3.9 27.5 1.0 OD2 B:ASP63 4.1 25.6 1.0 O2B B:GDP2302 4.1 23.2 1.0 O3A B:GDP2302 4.1 25.2 1.0 CG2 B:THR22 4.1 17.7 1.0 OG1 B:THR64 4.3 21.5 1.0 CG B:ASP63 4.4 24.0 1.0 PA B:GDP2302 4.4 26.7 1.0 OE1 B:GLU68 4.5 19.9 1.0 CB B:LYS21 4.7 14.9 1.0 O1A B:GDP2302 4.7 23.4 1.0 C B:LYS21 4.8 21.2 1.0 NZ B:LYS21 4.9 12.7 1.0

Magnesium binding site 2 out of 4 in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2301 b:21.6 occ:1.00 OG1 D:THR22 1.8 14.5 1.0 O D:HOH8187 2.0 10.7 1.0 O3B D:GDP2300 2.0 29.2 1.0 O D:HOH8423 2.1 20.3 1.0 O D:HOH8422 2.2 13.9 1.0 O D:HOH8088 2.2 17.1 1.0 CB D:THR22 2.9 17.6 1.0 PB D:GDP2300 3.3 25.8 1.0 OD1 D:ASP63 3.6 21.1 1.0 N D:THR22 3.7 21.2 1.0 O1B D:GDP2300 3.7 28.0 1.0 CA D:THR22 3.9 19.9 1.0 CG2 D:THR22 4.0 9.7 1.0 OD2 D:ASP63 4.1 24.3 1.0 O2A D:GDP2300 4.1 28.0 1.0 O3A D:GDP2300 4.2 27.6 1.0 O2B D:GDP2300 4.2 27.2 1.0 CG D:ASP63 4.3 21.5 1.0 OG1 D:THR64 4.3 21.4 1.0 OE1 D:GLU68 4.4 15.6 1.0 O D:HOH8554 4.4 22.0 1.0 PA D:GDP2300 4.5 24.2 1.0 CB D:LYS21 4.7 18.1 1.0 C D:LYS21 4.8 22.3 1.0 O1A D:GDP2300 4.8 24.1 1.0 O D:HOH8086 5.0 28.3 1.0

Magnesium binding site 3 out of 4 in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg2306 b:19.8 occ:1.00 OG1 F:THR22 1.9 23.3 1.0 O3B F:GDP2305 1.9 26.3 1.0 O F:HOH9359 2.1 12.4 1.0 O F:HOH9358 2.1 13.9 1.0 O F:HOH9152 2.2 16.2 1.0 O F:HOH9006 2.3 10.8 1.0 CB F:THR22 3.0 23.1 1.0 PB F:GDP2305 3.2 25.9 1.0 O1B F:GDP2305 3.5 28.5 1.0 N F:THR22 3.6 22.9 1.0 OD1 F:ASP63 3.7 24.0 1.0 CA F:THR22 3.8 23.4 1.0 O2A F:GDP2305 4.0 28.2 1.0 OD2 F:ASP63 4.0 25.0 1.0 CG2 F:THR22 4.1 18.6 1.0 O2B F:GDP2305 4.1 22.4 1.0 O3A F:GDP2305 4.2 26.4 1.0 OG1 F:THR64 4.3 19.1 1.0 CG F:ASP63 4.3 23.9 1.0 OE1 F:GLU68 4.4 20.2 1.0 PA F:GDP2305 4.5 25.5 1.0 CB F:LYS21 4.6 18.1 1.0 C F:LYS21 4.7 23.4 1.0 O1A F:GDP2305 4.8 24.4 1.0 NZ F:LYS21 4.8 9.7 1.0 O F:HOH9127 5.0 30.6 1.0

Magnesium binding site 4 out of 4 in the The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structures of the Rep-1 Protein in Complex with C- Terminally Truncated RAB7 Protein within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg2304 b:25.9 occ:1.00 OG1 H:THR22 1.9 14.9 1.0 O3B H:GDP2303 1.9 24.8 1.0 O H:HOH9422 2.0 14.6 1.0 O H:HOH9187 2.1 9.7 1.0 O H:HOH9423 2.1 9.7 1.0 O H:HOH9088 2.2 20.6 1.0 CB H:THR22 3.1 18.1 1.0 PB H:GDP2303 3.2 21.4 1.0 OD1 H:ASP63 3.6 23.4 1.0 O1B H:GDP2303 3.6 23.9 1.0 N H:THR22 3.7 20.1 1.0 CA H:THR22 3.9 18.4 1.0 O2A H:GDP2303 4.1 26.8 1.0 OD2 H:ASP63 4.1 25.5 1.0 O3A H:GDP2303 4.2 23.9 1.0 O2B H:GDP2303 4.2 20.5 1.0 CG2 H:THR22 4.2 9.7 1.0 CG H:ASP63 4.3 23.6 1.0 OE1 H:GLU68 4.3 20.5 1.0 OG1 H:THR64 4.4 26.8 1.0 O H:HOH9579 4.4 19.5 1.0 PA H:GDP2303 4.5 25.3 1.0 CB H:LYS21 4.6 16.4 1.0 C H:LYS21 4.7 21.6 1.0 O H:HOH9162 4.8 27.3 1.0 O1A H:GDP2303 4.8 22.8 1.0 NZ H:LYS21 4.9 9.7 1.0 N H:LYS21 5.0 21.1 1.0 CE H:LYS21 5.0 14.1 1.0

A.Rak, O.Pylypenko, A.Niculae, K.Pyatkov, R.S.Goody, K.Alexandrov. Structure of the RAB7:Rep-1 Complex: Insights Into the Mechanism of Rab Prenylation and Choroideremia Disease Cell(Cambridge,Mass.) V. 117 749 2004.
ISSN: ISSN 0092-8674
PubMed: 15186776
DOI: 10.1016/J.CELL.2004.05.017