Magnesium in PDB 8ysu: Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp, PDB code: 8ysu was solved by Y.-C.Wang, C.-S.Yang, M.-H.Hou, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.88 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.363, 111.506, 46.981, 90, 100.42, 90
R / Rfree (%)	20.2 / 23.9

The binding sites of Magnesium atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp (pdb code 8ysu). 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 the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp, PDB code: 8ysu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp


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 Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:29.6 occ:1.00 O2B A:CTP401 2.0 32.8 1.0 OD2 A:ASP78 2.1 27.8 1.0 O2G A:CTP401 2.2 36.2 1.0 OD1 A:ASP80 2.2 29.6 1.0 O A:HOH516 2.2 25.8 1.0 O2A A:CTP401 2.2 38.6 1.0 PB A:CTP401 3.0 33.8 1.0 O3A A:CTP401 3.2 45.8 1.0 PA A:CTP401 3.3 52.2 1.0 CG A:ASP80 3.3 26.7 1.0 PG A:CTP401 3.3 30.4 1.0 CG A:ASP78 3.3 27.8 1.0 O3B A:CTP401 3.4 34.0 1.0 MG A:MG404 3.7 17.4 1.0 OD2 A:ASP80 3.8 23.8 1.0 O1G A:CTP401 3.8 33.3 1.0 O A:ASP78 3.9 23.4 1.0 OG A:SER62 4.0 19.2 1.0 CB A:ASP78 4.1 27.8 1.0 OD1 A:ASP78 4.2 34.3 1.0 N A:SER62 4.2 15.6 1.0 O A:HOH561 4.2 30.6 1.0 O5' A:CTP401 4.3 47.1 1.0 C5' A:CTP401 4.3 47.3 1.0 O1A A:CTP401 4.4 46.0 1.0 O1B A:CTP401 4.4 39.2 1.0 CB A:ASP80 4.5 25.0 1.0 CA A:GLY61 4.5 16.1 1.0 O3G A:CTP401 4.6 29.8 1.0 CB A:SER62 4.7 18.8 1.0 C A:ASP78 4.8 25.5 1.0 C A:GLY61 4.9 15.0 1.0 O A:HOH518 5.0 38.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp


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 Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:17.4 occ:1.00 O3' A:CTP402 2.1 93.3 1.0 OD2 A:ASP80 2.2 23.8 1.0 OD1 A:ASP78 2.3 34.3 1.0 OD2 A:ASP129 2.4 27.8 1.0 O2A A:CTP401 2.5 38.6 1.0 OD2 A:ASP78 2.6 27.8 1.0 O2' A:CTP402 2.7 71.3 1.0 CG A:ASP78 2.8 27.8 1.0 CG A:ASP80 3.1 26.7 1.0 C3' A:CTP402 3.3 97.9 1.0 OD1 A:ASP80 3.4 29.6 1.0 C2' A:CTP402 3.5 90.6 1.0 CG A:ASP129 3.5 24.4 1.0 MG A:MG403 3.7 29.6 1.0 PA A:CTP401 3.8 52.2 1.0 CB A:ASP129 3.9 23.0 1.0 O1A A:CTP401 4.3 46.0 1.0 CB A:ASP78 4.3 27.8 1.0 C4' A:CTP402 4.4 113.2 1.0 O5' A:CTP401 4.5 47.1 1.0 CB A:ASP80 4.5 25.0 1.0 OD1 A:ASP129 4.5 28.6 1.0 NE2 A:HIS127 4.6 30.6 1.0 C5' A:CTP401 4.6 47.3 1.0 O2G A:CTP401 4.8 36.2 1.0 C1' A:CTP402 4.8 96.3 1.0 O A:ASP78 4.8 23.4 1.0 C A:ASP78 5.0 25.5 1.0

C.S.Yang, M.Y.Shie, S.W.Huang, Y.C.Wang, M.H.Hou, C.J.Chen, Y.Chen. Structural Insights Into Signaling Promiscuity of the Cbass Anti-Phage Defense System From A Radiation-Resistant Bacterium. Int.J.Biol.Macromol. V. 295 39534 2025.
ISSN: ISSN 0141-8130
PubMed: 39761885
DOI: 10.1016/J.IJBIOMAC.2025.139534