Magnesium in PDB 8ysc: Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Atp (Form 1)

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Atp (Form 1), PDB code: 8ysc 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)	28.00 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.343, 46.559, 59.78, 99.69, 106.07, 99.37
R / Rfree (%)	16.9 / 21.2

The binding sites of Magnesium atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Atp (Form 1) (pdb code 8ysc). 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 Atp (Form 1), PDB code: 8ysc:
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 Atp (Form 1)


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 Atp (Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:24.5 occ:1.00 O A:HOH503 2.0 42.4 1.0 OD2 A:ASP80 2.2 30.0 1.0 OD2 A:ASP129 2.2 32.4 1.0 OD1 A:ASP78 2.3 45.1 1.0 OD2 A:ASP78 2.5 33.8 1.0 O2' A:ATP402 2.5 51.7 1.0 O3' A:ATP402 2.6 56.3 1.0 O2A A:ATP401 2.6 20.1 1.0 CG A:ASP78 2.7 36.8 1.0 CG A:ASP80 3.3 29.7 1.0 CG A:ASP129 3.3 35.2 1.0 C2' A:ATP402 3.5 59.2 1.0 C3' A:ATP402 3.6 58.6 1.0 OD1 A:ASP80 3.7 28.6 1.0 PA A:ATP401 3.7 21.7 1.0 MG A:MG404 3.7 25.5 1.0 CB A:ASP129 3.8 32.2 1.0 O1A A:ATP401 4.1 21.8 1.0 O5' A:ATP401 4.2 23.0 1.0 O A:HOH554 4.2 41.3 1.0 CB A:ASP78 4.2 37.0 1.0 OD1 A:ASP129 4.4 37.4 1.0 C5' A:ATP401 4.4 25.6 1.0 C4' A:ATP402 4.5 59.7 1.0 CB A:ASP80 4.6 28.6 1.0 O3G A:ATP401 4.7 24.1 1.0 C1' A:ATP402 4.8 53.0 1.0 NE2 A:HIS127 4.8 36.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Atp (Form 1)


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 Atp (Form 1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:25.5 occ:1.00 OD2 A:ASP78 1.9 33.8 1.0 O A:HOH521 2.0 24.0 1.0 OD1 A:ASP80 2.1 28.6 1.0 O1B A:ATP401 2.1 27.3 1.0 O3G A:ATP401 2.1 24.1 1.0 O2A A:ATP401 2.2 20.1 1.0 CG A:ASP78 3.1 36.8 1.0 PB A:ATP401 3.1 24.0 1.0 CG A:ASP80 3.1 29.7 1.0 PG A:ATP401 3.3 22.4 1.0 PA A:ATP401 3.4 21.7 1.0 OD2 A:ASP80 3.5 30.0 1.0 O3B A:ATP401 3.5 24.4 1.0 O3A A:ATP401 3.6 22.1 1.0 O A:ASP78 3.7 28.7 1.0 MG A:MG403 3.7 24.5 1.0 CB A:ASP78 3.8 37.0 1.0 O1G A:ATP401 4.0 26.5 1.0 OG A:SER62 4.0 22.6 1.0 O A:HOH554 4.0 41.3 1.0 OD1 A:ASP78 4.1 45.1 1.0 O A:HOH570 4.1 25.6 1.0 N A:SER62 4.2 22.6 1.0 C5' A:ATP401 4.2 25.6 1.0 O A:HOH503 4.2 42.4 1.0 O5' A:ATP401 4.3 23.0 1.0 O2B A:ATP401 4.4 25.6 1.0 CB A:ASP80 4.4 28.6 1.0 O2G A:ATP401 4.5 30.1 1.0 C A:ASP78 4.6 31.1 1.0 CA A:GLY61 4.6 23.3 1.0 O1A A:ATP401 4.6 21.8 1.0 CB A:SER62 4.6 22.5 1.0 CA A:ASP78 4.9 33.4 1.0 C A:GLY61 4.9 22.9 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