Magnesium in PDB 8yso: Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb Ear-Cut Mutant in Complex with Atp

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb Ear-Cut Mutant in Complex with Atp, PDB code: 8yso 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)	23.97 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.331, 72.832, 100.998, 90, 90, 90
R / Rfree (%)	17.1 / 19.9

The binding sites of Magnesium atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb Ear-Cut Mutant in Complex with Atp (pdb code 8yso). 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 Ear-Cut Mutant in Complex with Atp, PDB code: 8yso:
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 Ear-Cut Mutant in Complex with Atp


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 Ear-Cut Mutant in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:6.0 occ:1.00 OD2 A:ASP80 2.2 12.4 1.0 OD2 A:ASP129 2.3 13.4 1.0 OD2 A:ASP78 2.5 16.0 1.0 O2' A:ATP402 2.5 21.8 1.0 O2A A:ATP401 2.5 12.3 1.0 OD1 A:ASP78 2.5 25.8 1.0 O A:HOH677 2.6 28.5 1.0 O3' A:ATP402 2.7 25.4 1.0 CG A:ASP78 2.8 20.4 1.0 CG A:ASP80 3.2 10.7 1.0 CG A:ASP129 3.4 12.7 1.0 MG A:MG404 3.5 2.0 1.0 C2' A:ATP402 3.6 22.6 1.0 OD1 A:ASP80 3.6 10.8 1.0 PA A:ATP401 3.7 10.9 1.0 C3' A:ATP402 3.7 26.9 1.0 CB A:ASP129 3.8 11.3 1.0 O A:HOH557 4.0 27.1 1.0 O A:HOH725 4.1 29.3 1.0 O5' A:ATP401 4.2 11.1 1.0 O1A A:ATP401 4.2 11.3 1.0 CB A:ASP78 4.3 19.6 1.0 OD1 A:ASP129 4.5 13.1 1.0 C4' A:ATP402 4.5 27.0 1.0 C5' A:ATP401 4.5 11.1 1.0 CB A:ASP80 4.6 9.8 1.0 NE2 A:HIS127 4.6 21.2 1.0 O3G A:ATP401 4.7 12.4 1.0 O A:HOH605 4.7 24.0 1.0 C1' A:ATP402 4.8 22.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb Ear-Cut Mutant in Complex with Atp


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 Ear-Cut Mutant in Complex with Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:2.0 occ:1.00 OD2 A:ASP78 2.0 16.0 1.0 OD1 A:ASP80 2.0 10.8 1.0 O3G A:ATP401 2.1 12.4 1.0 O1B A:ATP401 2.1 11.0 1.0 O A:HOH576 2.2 12.9 1.0 O2A A:ATP401 2.2 12.3 1.0 CG A:ASP80 3.0 10.7 1.0 CG A:ASP78 3.2 20.4 1.0 PB A:ATP401 3.2 10.8 1.0 PA A:ATP401 3.4 10.9 1.0 PG A:ATP401 3.4 12.4 1.0 OD2 A:ASP80 3.4 12.4 1.0 O3A A:ATP401 3.5 10.2 1.0 MG A:MG403 3.5 6.0 1.0 O3B A:ATP401 3.6 11.7 1.0 CB A:ASP78 3.9 19.6 1.0 O A:ASP78 3.9 13.2 1.0 O A:HOH725 4.0 29.3 1.0 OD1 A:ASP78 4.1 25.8 1.0 OG A:SER62 4.1 11.9 1.0 C5' A:ATP401 4.1 11.1 1.0 O2G A:ATP401 4.2 13.9 1.0 O5' A:ATP401 4.2 11.1 1.0 O A:HOH660 4.2 11.6 1.0 N A:SER62 4.3 8.9 1.0 CB A:ASP80 4.4 9.8 1.0 O1G A:ATP401 4.5 17.0 1.0 O A:HOH677 4.5 28.5 1.0 O1A A:ATP401 4.6 11.3 1.0 O2B A:ATP401 4.6 10.2 1.0 C A:ASP78 4.7 12.9 1.0 CA A:GLY61 4.7 8.5 1.0 CB A:SER62 4.7 10.5 1.0 CA A:ASP78 5.0 15.4 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