Magnesium in PDB 8h0l: Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna

The structure of Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna, PDB code: 8h0l was solved by G.Liu, X.He, W.Hu, B.Yang, Q.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.13 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.865, 57.53, 177.362, 90, 90, 90
R / Rfree (%)	19.8 / 22.4

The binding sites of Magnesium atom in the Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna (pdb code 8h0l). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna, PDB code: 8h0l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:30.6 occ:1.00 O2 D:DT8 2.4 36.9 1.0 O A:ARG17 2.7 36.8 1.0 O D:HOH118 2.8 37.6 1.0 O A:HOH363 2.9 34.4 1.0 OD1 A:ASN16 2.9 27.0 1.0 O4' D:DC9 3.1 41.9 1.0 O A:HOH346 3.5 34.8 1.0 C2 D:DT8 3.5 31.8 1.0 C1' D:DT8 3.6 34.1 1.0 N2 C:DG4 3.7 32.0 1.0 C4' D:DC9 3.7 46.4 1.0 C A:ARG17 3.9 31.5 1.0 C1' D:DC9 3.9 46.5 1.0 CG A:ASN16 4.0 31.9 1.0 N A:ARG17 4.1 30.2 1.0 N1 D:DT8 4.1 31.9 1.0 O4' D:DT8 4.3 40.0 1.0 C5' D:DC9 4.3 53.1 1.0 N1 D:DC9 4.4 37.8 1.0 C2 C:DG4 4.6 26.7 1.0 C2' D:DT8 4.6 40.3 1.0 CA A:ARG17 4.6 33.9 1.0 ND2 A:ASN16 4.6 26.8 1.0 N3 D:DT8 4.6 35.0 1.0 C2 C:DA3 4.7 31.5 1.0 N3 C:DG4 4.8 27.8 1.0 C4' D:DT8 4.8 44.0 1.0 C6 D:DC9 4.9 41.8 1.0 C2 D:DC9 4.9 43.1 1.0 N A:ARG18 4.9 35.2 1.0 O3' D:DT8 4.9 42.9 1.0 O2 D:DC9 4.9 35.4 1.0 CA A:ASN16 5.0 29.0 1.0 C A:ASN16 5.0 24.3 1.0 CB A:ASN16 5.0 23.1 1.0

Magnesium binding site 2 out of 2 in the Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sulfur Binding Domain of Hga Complexed with Phosphorothioated Dna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg101 b:33.7 occ:1.00 O2 F:DT8 2.2 37.6 1.0 O B:ARG17 2.6 37.3 1.0 O B:HOH255 2.6 36.2 1.0 O F:HOH213 2.9 42.0 1.0 OD1 B:ASN16 2.9 25.7 1.0 O4' F:DC9 3.1 49.5 1.0 O B:HOH227 3.3 39.2 1.0 C2 F:DT8 3.4 41.3 1.0 N2 E:DG4 3.7 29.4 1.0 C1' F:DT8 3.7 46.0 1.0 C B:ARG17 3.7 28.9 1.0 C4' F:DC9 3.9 43.5 1.0 CG B:ASN16 3.9 23.4 1.0 C5' F:DC9 4.0 51.0 1.0 N B:ARG17 4.0 27.8 1.0 N1 F:DT8 4.0 39.3 1.0 C1' F:DC9 4.3 45.8 1.0 O4' F:DT8 4.3 44.1 1.0 C2 E:DA3 4.4 33.0 1.0 N3 F:DT8 4.4 35.9 1.0 ND2 B:ASN16 4.5 22.6 1.0 CA B:ARG17 4.5 25.2 1.0 C2 E:DG4 4.6 31.4 1.0 N1 F:DC9 4.6 42.1 1.0 N B:ARG18 4.7 27.4 1.0 O2 F:DC9 4.7 43.3 1.0 O B:HOH264 4.8 42.5 1.0 CA B:ARG18 4.8 30.8 1.0 CB B:ARG18 4.8 33.5 1.0 C2' F:DT8 4.8 48.4 1.0 C2 F:DC9 4.8 46.5 1.0 N3 E:DG4 4.9 26.5 1.0 O2 F:DC7 4.9 34.2 1.0 C B:ASN16 4.9 27.3 1.0 C4' F:DT8 4.9 49.8 1.0 CB B:ASN16 5.0 23.9 1.0 CA B:ASN16 5.0 21.3 1.0

W.Hu, B.Yang, Q.Xiao, Y.Wang, Y.Shuai, G.Zhao, L.Zhang, Z.Deng, X.He, G.Liu. Characterization of A Promiscuous Dna Sulfur Binding Domain and Application in Site-Directed Rna Base Editing. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 37702119
DOI: 10.1093/NAR/GKAD743