Magnesium in PDB 5clq: Ran Y39A in Complex with Gppnhp and RANBD1

The structure of Ran Y39A in Complex with Gppnhp and RANBD1, PDB code: 5clq 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)	19.98 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	102.530, 170.920, 135.650, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 25.4

The binding sites of Magnesium atom in the Ran Y39A in Complex with Gppnhp and RANBD1 (pdb code 5clq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ran Y39A in Complex with Gppnhp and RANBD1, PDB code: 5clq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ran Y39A in Complex with Gppnhp and RANBD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ran Y39A in Complex with Gppnhp and RANBD1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:81.0 occ:1.00 OG1 A:THR24 2.0 88.1 1.0 O1B A:GNP301 2.1 84.4 1.0 OG1 A:THR42 2.1 90.1 1.0 O2G A:GNP301 2.2 96.5 1.0 O A:HOH401 2.7 68.6 1.0 CB A:THR42 3.1 84.9 1.0 PG A:GNP301 3.1 92.3 1.0 PB A:GNP301 3.2 80.7 1.0 CB A:THR24 3.3 78.6 1.0 O3G A:GNP301 3.3 84.0 1.0 N3B A:GNP301 3.5 81.9 1.0 N A:THR24 3.7 81.0 1.0 O2B A:GNP301 3.8 72.3 1.0 OD1 A:ASP65 3.8 86.6 1.0 O A:THR66 3.9 81.3 1.0 N A:THR42 4.0 91.7 1.0 OD2 A:ASP65 4.0 84.4 1.0 CA A:THR24 4.1 81.0 1.0 CA A:THR42 4.1 89.7 1.0 CG2 A:THR42 4.1 83.7 1.0 CB A:LYS23 4.3 80.5 1.0 CG A:ASP65 4.3 87.5 1.0 NZ A:LYS23 4.3 74.9 1.0 CE A:LYS23 4.3 76.5 1.0 CA A:ALA67 4.4 91.4 1.0 CG2 A:THR24 4.4 70.9 1.0 O3A A:GNP301 4.5 80.4 1.0 O1G A:GNP301 4.5 91.1 1.0 O1A A:GNP301 4.5 86.6 1.0 O2A A:GNP301 4.7 82.1 1.0 C A:THR66 4.7 84.1 1.0 C A:LYS23 4.7 77.8 1.0 PA A:GNP301 4.8 84.0 1.0 N A:ALA67 4.9 88.0 1.0 N A:GLY68 4.9 95.0 1.0 CA A:LYS23 4.9 75.0 1.0

Magnesium binding site 2 out of 2 in the Ran Y39A in Complex with Gppnhp and RANBD1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ran Y39A in Complex with Gppnhp and RANBD1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:74.1 occ:1.00 OG1 C:THR24 1.9 75.3 1.0 O2G C:GNP302 2.0 74.3 1.0 OG1 C:THR42 2.0 70.4 1.0 O C:HOH404 2.0 71.1 1.0 O2B C:GNP302 2.1 70.3 1.0 O C:HOH402 2.3 79.8 1.0 PG C:GNP302 3.1 73.0 1.0 CB C:THR42 3.2 76.2 1.0 CB C:THR24 3.2 67.1 1.0 PB C:GNP302 3.3 66.4 1.0 N3B C:GNP302 3.4 75.7 1.0 O1G C:GNP302 3.7 73.6 1.0 N C:THR24 3.8 70.3 1.0 OD2 C:ASP65 3.9 63.6 1.0 N C:THR42 3.9 76.6 1.0 CA C:THR24 4.0 70.2 1.0 CA C:THR42 4.1 81.4 1.0 O1B C:GNP302 4.1 72.3 1.0 OD1 C:ASP65 4.2 75.6 1.0 CG2 C:THR42 4.2 83.2 1.0 CG2 C:THR24 4.2 65.2 1.0 CG C:ASP65 4.4 73.6 1.0 O2A C:GNP302 4.4 70.2 1.0 O3A C:GNP302 4.4 81.6 1.0 O3G C:GNP302 4.4 79.4 1.0 O1A C:GNP302 4.6 70.0 1.0 O C:VAL40 4.6 74.0 1.0 PA C:GNP302 4.7 79.1 1.0 O C:THR66 4.7 83.6 1.0 CB C:LYS23 4.8 71.7 1.0 C C:LYS23 4.9 68.2 1.0 C C:ALA41 5.0 75.2 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