Magnesium in PDB 5xis: Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I

All present enzymatic activity of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I:
2.3.2.27;

The structure of Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I, PDB code: 5xis was solved by T.S.Takahashi, Y.Sato, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.29 / 1.78
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.273, 66.291, 74.173, 76.47, 79.29, 80.49
R / Rfree (%)	21.9 / 24.5

The binding sites of Magnesium atom in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I (pdb code 5xis). 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 RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I, PDB code: 5xis:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I


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 RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:32.8 occ:1.00 OD1 F:ASP32 2.0 30.5 1.0 O B:HOH208 2.1 38.0 1.0 OD1 B:ASP32 2.1 37.5 1.0 O F:HOH130 2.1 32.2 1.0 O F:HOH134 2.1 31.4 1.0 O B:HOH205 2.2 35.2 1.0 CG F:ASP32 3.0 30.2 1.0 CG B:ASP32 3.1 35.8 1.0 OD2 F:ASP32 3.4 32.5 1.0 OD2 B:ASP32 3.5 34.0 1.0 OE1 B:GLN31 4.2 40.8 1.0 O F:ALA28 4.2 24.9 1.0 O B:ALA28 4.3 32.1 1.0 OE1 F:GLN31 4.3 28.4 1.0 CB F:ASP32 4.3 33.7 1.0 CB B:ASP32 4.5 33.6 1.0 N F:ASP32 4.6 28.9 1.0 CA F:ASP32 4.6 34.8 1.0 CD B:GLN31 4.7 37.2 1.0 CA B:ASP32 4.7 29.2 1.0 N B:ASP32 4.7 34.7 1.0 CD F:GLN31 4.8 29.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I


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 RNF168 UDM1 in Complex with LYS63-Linked Diubiquitin, Form I within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:51.1 occ:1.00 OD1 E:ASP32 1.9 41.1 1.0 O E:HOH112 1.9 52.1 1.0 O C:HOH217 2.0 50.1 1.0 OD1 C:ASP32 2.1 49.9 1.0 O E:HOH107 2.3 42.1 1.0 O C:HOH221 2.4 42.6 1.0 CG E:ASP32 2.9 47.1 1.0 CG C:ASP32 3.1 50.5 1.0 OD2 E:ASP32 3.2 42.5 1.0 OD2 C:ASP32 3.4 52.4 1.0 O E:ALA28 4.1 42.1 1.0 CB E:ASP32 4.2 45.6 1.0 OE1 C:GLN31 4.3 47.9 1.0 OE1 E:GLN31 4.5 43.6 1.0 CB C:ASP32 4.5 34.7 1.0 CA E:ASP32 4.5 41.6 1.0 N E:ASP32 4.6 35.8 1.0 O C:ALA28 4.6 43.9 1.0 CA C:ASP32 4.8 44.3 1.0 N C:ASP32 4.8 33.4 1.0 CD E:GLN31 4.9 43.6 1.0 CD C:GLN31 4.9 44.6 1.0

T.S.Takahashi, Y.Hirade, A.Toma, Y.Sato, A.Yamagata, S.Goto-Ito, A.Tomita, S.Nakada, S.Fukai. Structural Insights Into Two Distinct Binding Modules For LYS63-Linked Polyubiquitin Chains in RNF168. Nat Commun V. 9 170 2018.
ISSN: ESSN 2041-1723
PubMed: 29330428
DOI: 10.1038/S41467-017-02345-Y