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

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Gtp, PDB code: 8ysg 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)	22.73 / 2.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.033, 100.404, 46.398, 90, 101.62, 90
R / Rfree (%)	24.2 / 27.2

The binding sites of Magnesium atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Gtp (pdb code 8ysg). 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 Gtp, PDB code: 8ysg:
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 Gtp


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:32.4 occ:1.00 OD1 A:ASP80 2.0 30.6 1.0 O2G A:GTP401 2.1 31.6 1.0 O A:HOH516 2.1 20.5 1.0 O2B A:GTP401 2.2 44.1 1.0 O1A A:GTP401 2.3 50.3 1.0 OD2 A:ASP78 2.3 37.6 1.0 CG A:ASP80 3.1 34.4 1.0 PB A:GTP401 3.2 46.4 1.0 PG A:GTP401 3.3 44.9 1.0 O3A A:GTP401 3.3 51.5 1.0 PA A:GTP401 3.3 56.1 1.0 O3B A:GTP401 3.5 44.5 1.0 CG A:ASP78 3.5 37.3 1.0 OD2 A:ASP80 3.7 33.5 1.0 O A:ASP78 3.8 33.9 1.0 OG A:SER62 3.8 22.5 1.0 C5' A:GTP401 3.9 49.2 1.0 O A:HOH566 4.0 35.5 1.0 N A:SER62 4.0 22.6 1.0 O3G A:GTP401 4.0 44.6 1.0 MG A:MG404 4.0 37.4 1.0 O5' A:GTP401 4.2 51.5 1.0 CB A:ASP78 4.3 35.4 1.0 O A:HOH549 4.3 32.4 1.0 CB A:ASP80 4.4 34.5 1.0 CA A:GLY61 4.4 21.6 1.0 O1G A:GTP401 4.4 44.1 1.0 OD1 A:ASP78 4.5 38.0 1.0 CB A:SER62 4.6 21.4 1.0 O2A A:GTP401 4.6 58.8 1.0 O1B A:GTP401 4.6 48.4 1.0 O2' A:GTP402 4.7 71.9 1.0 C A:GLY61 4.7 21.8 1.0 C A:ASP78 4.7 37.5 1.0 CA A:SER62 4.9 23.0 1.0

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


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 Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:37.4 occ:1.00 OD2 A:ASP129 2.1 38.5 1.0 O3' A:GTP402 2.3 67.8 1.0 OD1 A:ASP78 2.3 38.0 1.0 O2' A:GTP402 2.4 71.9 1.0 OD2 A:ASP78 2.6 37.6 1.0 OD2 A:ASP80 2.6 33.5 1.0 CG A:ASP78 2.8 37.3 1.0 O1A A:GTP401 2.9 50.3 1.0 C3' A:GTP402 3.2 78.3 1.0 CG A:ASP129 3.3 37.7 1.0 C2' A:GTP402 3.3 77.2 1.0 CG A:ASP80 3.6 34.4 1.0 C4' A:GTP402 3.8 79.8 1.0 OD1 A:ASP80 3.8 30.6 1.0 CB A:ASP129 3.9 35.4 1.0 MG A:MG403 4.0 32.4 1.0 PA A:GTP401 4.1 56.1 1.0 CB A:ASP78 4.3 35.4 1.0 OD1 A:ASP129 4.3 36.9 1.0 C1' A:GTP402 4.4 79.2 1.0 O A:HOH549 4.5 32.4 1.0 NE2 A:HIS127 4.5 44.8 1.0 O2A A:GTP401 4.5 58.8 1.0 O5' A:GTP401 4.6 51.5 1.0 O4' A:GTP402 4.7 79.2 1.0 O2G A:GTP401 4.8 31.6 1.0 C5' A:GTP401 4.8 49.2 1.0 CB A:ASP80 4.9 34.5 1.0 C5' A:GTP402 5.0 83.1 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