Magnesium in PDB 6qtb: Crystal Structure of REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum

The structure of Crystal Structure of REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum, PDB code: 6qtb was solved by Y.L.Ahmed, M.Thoms, E.Hurt, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.58 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.553, 83.176, 77.686, 90.00, 117.72, 90.00
R / Rfree (%)	19 / 21.3

The binding sites of Magnesium atom in the Crystal Structure of REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum (pdb code 6qtb). 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 REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum, PDB code: 6qtb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum


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 REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5101 b:23.5 occ:1.00 O A:HOH5218 2.0 18.0 1.0 OG A:SER4789 2.0 18.7 1.0 OG1 A:THR4863 2.1 19.9 1.0 OE1 B:GLU88 2.1 22.1 1.0 OG A:SER4791 2.2 22.7 1.0 O A:HOH5232 2.2 22.2 1.0 CB A:SER4789 3.0 21.4 1.0 CD B:GLU88 3.1 25.5 1.0 CB A:SER4791 3.2 20.9 1.0 OE2 B:GLU88 3.3 22.4 1.0 CB A:THR4863 3.3 19.0 1.0 CG2 A:THR4863 3.7 18.7 1.0 N A:SER4791 4.0 19.2 1.0 OD1 A:ASP4787 4.1 23.9 1.0 OD2 A:ASP4787 4.1 19.8 1.0 O A:LEU4904 4.1 25.8 1.0 CA A:SER4791 4.2 23.0 1.0 OD2 A:ASP4902 4.2 20.5 1.0 OD1 A:ASP4902 4.3 21.2 1.0 CA A:SER4789 4.3 22.6 1.0 CG B:GLU88 4.5 24.4 1.0 CA A:THR4863 4.5 19.7 1.0 CG A:ASP4787 4.5 22.2 1.0 C A:SER4789 4.5 23.9 1.0 C1 A:GOL5102 4.7 69.2 1.0 CG A:ASP4902 4.7 19.5 1.0 N A:SER4790 4.8 22.1 1.0 N A:THR4863 4.9 20.1 1.0 O A:SER4789 4.9 23.4 1.0 C A:SER4791 4.9 22.1 1.0 N A:MET4792 4.9 20.0 1.0 CB B:GLU88 4.9 22.8 1.0 C3 A:GOL5102 5.0 62.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum


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 REA1-Midas/YTM1-Ubl Complex From Chaetomium Thermophilum within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg5101 b:21.7 occ:1.00 O D:HOH5257 2.0 18.7 1.0 O D:HOH5227 2.0 18.1 1.0 OG D:SER4791 2.1 21.6 1.0 OE1 E:GLU88 2.1 20.8 1.0 OG D:SER4789 2.1 19.9 1.0 OG1 D:THR4863 2.1 20.0 1.0 CD E:GLU88 3.1 23.3 1.0 CB D:SER4789 3.1 16.9 1.0 CB D:SER4791 3.2 19.4 1.0 CB D:THR4863 3.4 19.9 1.0 OE2 E:GLU88 3.4 21.7 1.0 CG2 D:THR4863 3.7 19.4 1.0 N D:SER4791 4.1 19.8 1.0 OD1 D:ASP4787 4.1 21.1 1.0 OD2 D:ASP4787 4.2 19.6 1.0 CA D:SER4791 4.2 19.6 1.0 O D:LEU4904 4.2 23.8 1.0 OD2 D:ASP4902 4.2 20.5 1.0 OD1 D:ASP4902 4.3 20.4 1.0 CA D:SER4789 4.4 20.6 1.0 CG E:GLU88 4.5 20.6 1.0 O1 E:GOL101 4.5 54.3 1.0 CG D:ASP4787 4.5 21.9 1.0 CA D:THR4863 4.6 20.1 1.0 C D:SER4789 4.6 22.6 1.0 CG D:ASP4902 4.7 20.9 1.0 N D:THR4863 4.9 21.2 1.0 C D:SER4791 4.9 24.5 1.0 N D:SER4790 4.9 21.9 1.0 N D:MET4792 4.9 23.1 1.0 O D:SER4789 4.9 19.6 1.0 CB E:GLU88 4.9 21.3 1.0 C1 E:GOL101 5.0 64.4 1.0

Y.L.Ahmed, M.Thoms, V.Mitterer, I.Sinning, E.Hurt. Crystal Structures of REA1-Midas Bound to Its Ribosome Assembly Factor Ligands Resembling Integrin-Ligand-Type Complexes. Nat Commun V. 10 3050 2019.
ISSN: ESSN 2041-1723
PubMed: 31296859
DOI: 10.1038/S41467-019-10922-6