Magnesium in PDB 8ysl: Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp and Atp

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp and Atp, PDB code: 8ysl 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)	26.59 / 1.98
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.269, 46.118, 60.466, 74.95, 73.03, 84.42
R / Rfree (%)	16.2 / 20

The binding sites of Magnesium atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp and Atp (pdb code 8ysl). 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 Utp and Atp, PDB code: 8ysl:
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 Utp and 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 in Complex with Utp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:19.3 occ:1.00 O2G A:ATP401 1.9 20.5 1.0 O2B A:ATP401 1.9 19.9 1.0 OD2 A:ASP80 2.0 23.4 1.0 O2A A:ATP401 2.0 19.9 1.0 O A:HOH579 2.1 20.0 1.0 OD2 A:ASP78 2.1 28.9 1.0 CG A:ASP80 3.1 22.2 1.0 PB A:ATP401 3.1 19.9 1.0 PG A:ATP401 3.2 20.0 1.0 CG A:ASP78 3.3 35.8 1.0 PA A:ATP401 3.3 23.8 1.0 OD1 A:ASP80 3.4 25.7 1.0 O3A A:ATP401 3.5 22.9 1.0 O3B A:ATP401 3.6 21.7 1.0 MG A:MG404 3.7 26.3 1.0 O A:ASP78 3.9 28.0 1.0 O A:HOH638 3.9 31.8 1.0 O3G A:ATP401 4.0 18.1 1.0 CB A:ASP78 4.0 32.1 1.0 OG A:SER62 4.0 19.5 1.0 C5' A:ATP401 4.1 20.0 1.0 O A:HOH620 4.2 20.9 1.0 O5' A:ATP401 4.2 22.2 1.0 N A:SER62 4.3 15.7 1.0 OD1 A:ASP78 4.3 40.7 1.0 O A:HOH662 4.4 42.9 1.0 CB A:ASP80 4.4 22.0 1.0 O1G A:ATP401 4.4 22.4 1.0 O1B A:ATP401 4.4 20.7 1.0 O1A A:ATP401 4.5 25.7 1.0 CA A:GLY61 4.6 17.5 1.0 C A:ASP78 4.7 29.0 1.0 CB A:SER62 4.7 15.1 1.0 CA A:ASP78 5.0 29.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp and 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 in Complex with Utp and Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:26.3 occ:1.00 OD1 A:ASP80 2.3 25.7 1.0 OD2 A:ASP129 2.4 30.8 1.0 O3' A:UTP402 2.5 45.1 0.5 O3' A:UTP402 2.5 45.0 0.5 O A:HOH662 2.5 42.9 1.0 OD2 A:ASP78 2.6 28.9 1.0 OD1 A:ASP78 2.7 40.7 1.0 O2A A:ATP401 2.7 19.9 1.0 CG A:ASP78 3.0 35.8 1.0 O2' A:UTP402 3.0 42.6 0.5 O2' A:UTP402 3.0 42.8 0.5 CG A:ASP80 3.3 22.2 1.0 CG A:ASP129 3.4 30.9 1.0 OD2 A:ASP80 3.6 23.4 1.0 C3' A:UTP402 3.6 44.0 0.5 MG A:MG403 3.7 19.3 1.0 C3' A:UTP402 3.7 44.0 0.5 PA A:ATP401 3.8 23.8 1.0 CB A:ASP129 3.8 28.6 1.0 C2' A:UTP402 3.9 42.8 0.5 C2' A:UTP402 3.9 42.8 0.5 O A:HOH518 4.1 41.9 1.0 C4' A:UTP402 4.2 44.4 0.5 O5' A:ATP401 4.2 22.2 1.0 O1A A:ATP401 4.2 25.7 1.0 C4' A:UTP402 4.3 44.6 0.5 C5' A:ATP401 4.4 20.0 1.0 O A:HOH638 4.4 31.8 1.0 CB A:ASP78 4.5 32.1 1.0 OD1 A:ASP129 4.5 31.6 1.0 NE2 A:HIS127 4.6 38.9 1.0 CB A:ASP80 4.7 22.0 1.0 O2G A:ATP401 4.7 20.5 1.0 C1' A:UTP402 5.0 40.6 0.5 C1' A:UTP402 5.0 40.6 0.5

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