Magnesium in PDB 8ir4: Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442

The structure of Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442, PDB code: 8ir4 was solved by S.Xiang, W.Huang, F.Qiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.60 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.421, 76.098, 141.371, 90, 90, 90
R / Rfree (%)	18.1 / 21.3

The structure of Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442 (pdb code 8ir4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442, PDB code: 8ir4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442


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 the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1004 b:36.2 occ:1.00 O A:HOH1338 2.0 43.2 1.0 O A:HOH1118 2.0 29.6 1.0 O A:HOH1297 2.1 34.7 1.0 O A:HOH1318 2.2 27.5 1.0 O A:HOH1379 2.3 48.0 1.0 O A:HOH1248 4.0 27.5 1.0 O A:ALA120 4.1 17.1 1.0 O A:HOH1113 4.1 29.5 1.0 O A:LEU115 4.4 18.2 1.0 O A:HOH1105 4.6 30.1 1.0 O A:HOH1180 4.7 22.5 1.0 O A:GLY119 4.8 23.7 1.0 C A:LEU115 4.8 15.8 1.0 CA A:PRO121 4.9 16.3 1.0 C A:ALA120 4.9 16.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442


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 the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1005 b:38.1 occ:1.00 O A:HOH1364 2.0 40.8 1.0 O A:HOH1337 2.1 31.8 1.0 O A:HOH1146 2.1 23.7 1.0 O A:HOH1108 2.1 41.7 1.0 O A:HOH1124 2.1 36.9 1.0 O A:PHE182 3.9 25.0 1.0 O A:HOH1341 4.0 40.5 1.0 O A:ALA184 4.0 23.3 1.0 O A:LYS179 4.1 29.2 1.0 O A:LYS183 4.2 32.0 1.0 O A:HOH1352 4.3 47.0 1.0 C A:LYS179 4.6 23.9 1.0 O A:HOH1268 4.6 25.8 1.0 CB A:LYS179 4.6 28.1 1.0 C A:ALA184 4.7 21.4 1.0 O A:HOH1212 4.7 45.0 1.0 OD1 A:ASP180 4.7 44.6 1.0 C A:LYS183 4.8 25.8 1.0 CA A:PRO185 4.8 19.8 1.0 OE1 A:GLU176 5.0 64.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the SLF1 Brct Domain in Complex with A RAD18 Peptide Containing PS442 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg304 b:24.8 occ:1.00 O B:HOH521 1.8 28.5 1.0 O B:HOH445 2.0 24.1 1.0 OE2 B:GLU49 2.1 22.9 1.0 O A:HOH1153 2.1 26.9 1.0 O B:HOH462 2.3 26.6 1.0 O B:HOH443 2.3 24.2 1.0 CD B:GLU49 3.1 21.3 1.0 OE1 B:GLU49 3.4 19.4 1.0 O A:HOH1191 3.9 24.1 1.0 OE2 A:GLU49 3.9 28.1 1.0 O A:HOH1253 4.0 40.5 1.0 O B:HOH466 4.1 38.7 1.0 O B:GLU49 4.1 16.1 1.0 O B:HOH580 4.1 43.1 1.0 O B:HOH451 4.2 33.8 1.0 NZ A:LYS16 4.3 34.5 1.0 O A:HOH1293 4.4 29.0 1.0 O B:HOH622 4.4 32.4 1.0 CG B:GLU49 4.4 15.3 1.0 CD A:GLU49 4.4 21.6 1.0 OE1 A:GLU49 4.8 20.9 1.0 CB B:ARG50 5.0 23.0 1.0 C B:GLU49 5.0 16.5 1.0

W.Huang, F.Qiu, L.Zheng, M.Shi, M.Shen, X.Zhao, S.Xiang. Structural Insights Into RAD18 Targeting By the SLF1 Brct Domains. J.Biol.Chem. V. 299 05288 2023.
ISSN: ESSN 1083-351X
PubMed: 37748650
DOI: 10.1016/J.JBC.2023.105288