Potassium 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:

Magnesium

(Mg)

4 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3; 4;

Potassium 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 Potassium with other atoms in the K 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:K3303 b:32.1 occ:1.00 OE1 B:GLN71 2.8 22.9 1.0 O B:HOH8210 2.9 37.4 1.0 O19 B:P333302 2.9 36.2 1.0 C12 B:P333302 3.1 39.5 1.0 O16 B:P333302 3.2 32.7 1.0 C11 B:P333302 3.2 38.7 1.0 C21 B:P333302 3.3 33.6 1.0 O10 B:P333302 3.3 40.9 1.0 O22 B:P333302 3.5 37.6 1.0 C20 B:P333302 3.6 34.8 1.0 C15 B:P333302 3.7 35.6 1.0 CD B:GLN71 3.7 21.2 1.0 C8 B:P333302 3.7 39.9 1.0 O13 B:P333302 3.7 38.6 1.0 O7 B:P333302 3.8 41.3 1.0 C14 B:P333302 3.9 37.3 1.0 C18 B:P333302 3.9 32.9 1.0 C17 B:P333302 4.0 34.5 1.0 C9 B:P333302 4.1 39.8 1.0 NE2 B:GLN71 4.2 24.1 1.0 C6 B:P333302 4.2 37.6 1.0 CG B:GLN71 4.9 19.9 1.0 CB B:GLN71 4.9 16.4 1.0

Potassium 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 Potassium with other atoms in the K 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:K3305 b:32.3 occ:1.00 OE1 D:GLN71 2.6 26.5 1.0 O16 D:P333304 3.1 30.2 1.0 O7 D:P333304 3.2 40.8 1.0 C12 D:P333304 3.2 31.9 1.0 O22 D:P333304 3.2 38.1 1.0 O19 D:P333304 3.3 31.3 1.0 C11 D:P333304 3.3 33.7 1.0 C18 D:P333304 3.3 28.9 1.0 O10 D:P333304 3.5 37.5 1.0 C8 D:P333304 3.5 39.0 1.0 C6 D:P333304 3.6 41.2 1.0 CD D:GLN71 3.6 25.2 1.0 C20 D:P333304 3.6 33.5 1.0 C17 D:P333304 3.7 29.6 1.0 O13 D:P333304 3.8 33.0 1.0 C15 D:P333304 3.8 31.8 1.0 C14 D:P333304 3.9 33.7 1.0 C9 D:P333304 3.9 37.6 1.0 C21 D:P333304 4.0 35.2 1.0 C5 D:P333304 4.1 42.1 1.0 NE2 D:GLN71 4.3 28.4 1.0 CG D:GLN71 4.6 20.3 1.0 CB D:GLN71 4.9 16.0 1.0

Potassium 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 Potassium with other atoms in the K 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:K3307 b:33.7 occ:1.00 OE1 F:GLN71 2.6 24.4 1.0 O19 F:P333306 2.8 39.2 1.0 O16 F:P333306 3.0 34.5 1.0 O F:HOH9210 3.0 35.6 1.0 C12 F:P333306 3.2 36.6 1.0 C11 F:P333306 3.2 37.8 1.0 O10 F:P333306 3.2 39.9 1.0 C8 F:P333306 3.3 39.6 1.0 O22 F:P333306 3.4 40.7 1.0 O7 F:P333306 3.4 41.3 1.0 C21 F:P333306 3.5 38.9 1.0 CD F:GLN71 3.5 22.0 1.0 C20 F:P333306 3.7 39.2 1.0 C9 F:P333306 3.7 40.2 1.0 C18 F:P333306 3.7 36.0 1.0 C17 F:P333306 3.8 36.1 1.0 C6 F:P333306 3.8 39.2 1.0 O13 F:P333306 3.9 37.5 1.0 NE2 F:GLN71 4.0 24.4 1.0 C15 F:P333306 4.1 36.5 1.0 C14 F:P333306 4.1 37.3 1.0 CG F:GLN71 4.7 18.9 1.0 C5 F:P333306 4.8 39.2 1.0 CB F:GLN71 4.8 16.7 1.0

Potassium 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 Potassium with other atoms in the K 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:K3309 b:35.3 occ:1.00 OE1 H:GLN71 2.6 19.9 1.0 O16 H:P333308 3.0 34.9 1.0 O19 H:P333308 3.1 37.2 1.0 C12 H:P333308 3.3 38.0 1.0 O7 H:P333308 3.3 48.6 1.0 C11 H:P333308 3.3 40.8 1.0 O22 H:P333308 3.3 40.8 1.0 C18 H:P333308 3.4 34.8 1.0 CD H:GLN71 3.5 19.9 1.0 C8 H:P333308 3.6 46.5 1.0 C20 H:P333308 3.6 37.7 1.0 O10 H:P333308 3.6 44.5 1.0 C15 H:P333308 3.7 35.0 1.0 C6 H:P333308 3.7 50.7 1.0 C17 H:P333308 3.7 32.5 1.0 O13 H:P333308 3.8 39.5 1.0 C14 H:P333308 3.8 38.1 1.0 C9 H:P333308 4.0 45.0 1.0 C21 H:P333308 4.0 40.1 1.0 C5 H:P333308 4.1 52.0 1.0 NE2 H:GLN71 4.1 20.7 1.0 CG H:GLN71 4.5 17.6 1.0 O H:HOH9581 4.6 41.1 1.0 CB H:GLN71 4.8 15.5 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