Magnesium in PDB 6hxu: Crystal Structure of Human Rhob Q63L in Complex with Gtp

The structure of Crystal Structure of Human Rhob Q63L in Complex with Gtp, PDB code: 6hxu was solved by S.Soulie, R.Gence, S.Cabantous, I.Lajoie-Mazenc, G.Favre, J.D.Pedelacq, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.69 / 1.19
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.890, 61.460, 76.690, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Crystal Structure of Human Rhob Q63L in Complex with Gtp (pdb code 6hxu). 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 Human Rhob Q63L in Complex with Gtp, PDB code: 6hxu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Rhob Q63L in Complex with Gtp


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 Human Rhob Q63L in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:10.3 occ:1.00 O1B A:GTP201 2.0 9.5 1.0 O1G A:GTP201 2.0 11.3 1.0 OG1 A:THR37 2.1 12.4 1.0 OG1 A:THR19 2.1 10.1 1.0 O A:HOH375 2.1 11.6 1.0 O A:HOH323 2.1 11.3 1.0 HB A:THR37 3.1 13.7 1.0 H A:THR37 3.1 15.2 1.0 CB A:THR37 3.1 11.4 1.0 HB A:THR19 3.1 11.2 1.0 CB A:THR19 3.2 9.3 1.0 PG A:GTP201 3.2 10.9 1.0 PB A:GTP201 3.2 9.2 1.0 H A:THR19 3.3 10.6 1.0 O3B A:GTP201 3.4 9.1 1.0 N A:THR37 3.7 12.7 1.0 N A:THR19 3.9 8.8 1.0 HB2 A:LYS18 4.0 10.8 1.0 O2G A:GTP201 4.0 11.5 1.0 HG21 A:THR37 4.0 15.3 1.0 HG21 A:THR19 4.0 14.6 1.0 CA A:THR37 4.0 12.5 1.0 CA A:THR19 4.1 9.3 1.0 O2A A:GTP201 4.1 11.0 1.0 OD2 A:ASP59 4.1 11.1 1.0 CG2 A:THR37 4.2 12.8 1.0 OD1 A:ASP59 4.2 11.8 1.0 HE2 A:LYS18 4.2 11.8 1.0 CG2 A:THR19 4.2 12.2 1.0 O A:HOH329 4.3 25.0 1.0 O3A A:GTP201 4.3 9.6 1.0 O2B A:GTP201 4.3 9.7 1.0 HA A:PRO36 4.3 16.4 1.0 HE1 A:TYR34 4.4 17.0 1.0 HA A:THR19 4.4 11.2 1.0 O3G A:GTP201 4.4 12.9 1.0 O A:VAL35 4.5 14.6 1.0 HA A:THR37 4.5 15.0 1.0 O A:THR60 4.5 11.6 1.0 CG A:ASP59 4.5 11.6 1.0 PA A:GTP201 4.6 10.1 1.0 HG23 A:THR37 4.6 15.3 1.0 HG23 A:THR19 4.7 14.6 1.0 O A:HOH399 4.7 35.8 1.0 C A:PRO36 4.7 14.1 1.0 HZ1 A:LYS18 4.8 11.7 1.0 O1A A:GTP201 4.8 11.1 1.0 HZ3 A:LYS18 4.9 11.7 1.0 HG22 A:THR37 4.9 15.3 1.0 CB A:LYS18 4.9 9.0 1.0 HG22 A:THR19 4.9 14.6 1.0 C A:LYS18 5.0 9.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Rhob Q63L in Complex with Gtp


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 Human Rhob Q63L in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:10.7 occ:1.00 O A:HOH335 2.1 11.0 1.0 H A:GLY166 3.3 11.8 1.0 HA A:GLU165 3.8 12.2 1.0 HH12 A:ARG168 3.9 27.3 1.0 O A:HOH436 4.0 16.6 1.0 OE2 A:GLU169 4.2 12.6 1.0 N A:GLY166 4.2 9.9 1.0 O A:HOH378 4.3 12.0 1.0 OE1 A:GLU169 4.3 11.9 1.0 NH1 A:ARG168 4.6 22.8 1.0 HH22 A:ARG168 4.7 25.1 1.0 HA2 A:GLY166 4.7 12.3 1.0 CA A:GLU165 4.7 10.1 1.0 CD A:GLU169 4.7 11.7 1.0 HG3 A:GLU165 4.8 15.0 1.0 O A:LYS164 4.9 11.0 1.0 HH11 A:ARG168 5.0 27.3 1.0 C A:GLU165 5.0 9.0 1.0

N.Bery, L.Keller, M.Soulie, R.Gence, A.L.Iscache, J.Cherier, S.Cabantous, O.Sordet, I.Lajoie-Mazenc, J.D.Pedelacq, G.Favre, A.Olichon. A Targeted Protein Degradation Cell-Based Screening For Nanobodies Selective Toward the Cellular Rhob Gtp-Bound Conformation. Cell Chem Biol V. 26 1544 2019.
ISSN: ESSN 2451-9456
PubMed: 31522999
DOI: 10.1016/J.CHEMBIOL.2019.08.009