Magnesium in PDB 5cll: Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1

The structure of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1, PDB code: 5cll was solved by I.R.Vetter, S.Brucker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.81 / 2.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.600, 55.780, 122.930, 90.00, 90.05, 90.00
R / Rfree (%)	23.5 / 27.2

The structure of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 (pdb code 5cll). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1, PDB code: 5cll:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:27.4 occ:1.00 F1 A:BEF201 1.6 24.4 1.0 OG1 A:THR24 1.9 27.6 1.0 OG1 A:THR42 2.0 29.0 1.0 O3B A:GDP200 2.1 24.0 1.0 O A:HOH301 2.2 17.5 1.0 O A:HOH302 2.4 19.5 1.0 CB A:THR24 3.0 27.3 1.0 CB A:THR42 3.2 30.1 1.0 BE A:BEF201 3.2 24.0 1.0 PB A:GDP200 3.3 24.6 1.0 O2B A:GDP200 3.5 24.4 1.0 N A:THR24 3.7 24.7 1.0 OD2 A:ASP65 3.7 31.3 1.0 O2A A:GDP200 3.8 24.6 1.0 CA A:THR24 3.9 25.3 1.0 N A:THR42 4.0 33.3 1.0 CG2 A:THR24 4.1 28.1 1.0 OD1 A:ASP65 4.1 30.0 1.0 CA A:THR42 4.1 32.7 1.0 CG2 A:THR42 4.2 29.8 1.0 O3A A:GDP200 4.3 25.5 1.0 CG A:ASP65 4.3 30.2 1.0 F2 A:BEF201 4.4 24.0 1.0 O1B A:GDP200 4.4 24.7 1.0 PA A:GDP200 4.5 24.2 1.0 F3 A:BEF201 4.5 25.2 1.0 O A:VAL40 4.7 33.0 1.0 CB A:LYS23 4.7 24.0 1.0 C A:LYS23 4.8 23.6 1.0 O1A A:GDP200 4.8 24.9 1.0 O A:THR66 4.8 31.9 1.0 NZ A:LYS23 5.0 26.9 1.0 C A:ALA41 5.0 35.4 1.0

Magnesium binding site 2 out of 2 in the Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Truncated Ran Wild Type in Complex with Gdp-Bef and RANBD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:33.2 occ:1.00 F2 C:BEF201 1.7 25.5 1.0 OG1 C:THR24 1.9 29.4 1.0 O1B C:GDP200 1.9 25.6 1.0 OG1 C:THR42 2.2 31.5 1.0 O C:HOH301 2.2 17.0 1.0 O C:HOH302 2.4 19.3 1.0 CB C:THR24 3.1 28.8 1.0 PB C:GDP200 3.2 25.4 1.0 CB C:THR42 3.3 32.6 1.0 BE C:BEF201 3.3 25.5 1.0 O3B C:GDP200 3.5 25.3 1.0 N C:THR24 3.6 25.6 1.0 OD2 C:ASP65 3.8 30.0 1.0 O1A C:GDP200 3.9 24.1 1.0 CA C:THR24 3.9 27.0 1.0 N C:THR42 4.0 34.6 1.0 OD1 C:ASP65 4.1 29.2 1.0 CA C:THR42 4.2 35.0 1.0 F1 C:BEF201 4.2 26.1 1.0 CG2 C:THR24 4.2 29.7 1.0 O3A C:GDP200 4.2 25.1 1.0 O2B C:GDP200 4.3 24.8 1.0 CG2 C:THR42 4.3 32.5 1.0 CG C:ASP65 4.3 29.3 1.0 F3 C:BEF201 4.4 25.5 1.0 PA C:GDP200 4.4 23.5 1.0 O C:HOH311 4.5 22.8 1.0 CB C:LYS23 4.6 23.6 1.0 O C:THR66 4.7 30.0 1.0 O2A C:GDP200 4.7 23.5 1.0 C C:LYS23 4.7 24.0 1.0 O C:VAL40 4.8 34.7 1.0 NZ C:LYS23 4.9 25.7 1.0 CE C:LYS23 4.9 25.4 1.0

T.Rudack, S.Jenrich, S.Brucker, I.R.Vetter, K.Gerwert, C.Kotting. Catalysis of Gtp Hydrolysis By Small Gtpases at Atomic Detail By Integration of X-Ray Crystallography, Experimental, and Theoretical Ir Spectroscopy. J.Biol.Chem. V. 290 24079 2015.
ISSN: ESSN 1083-351X
PubMed: 26272610
DOI: 10.1074/JBC.M115.648071