Manganese in PDB 8ysk: Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn, PDB code: 8ysk 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)	23.25 / 1.98
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.274, 46.091, 59.889, 101.14, 106.9, 95.43
R / Rfree (%)	16.7 / 20.9

The binding sites of Manganese atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn (pdb code 8ysk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn, PDB code: 8ysk:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:27.5 occ:1.00 O A:HOH600 2.0 35.0 1.0 OD2 A:ASP129 2.0 29.4 1.0 OD2 A:ASP80 2.1 21.0 1.0 O A:HOH633 2.2 39.4 1.0 OD1 A:ASP78 2.2 35.6 1.0 OD2 A:ASP78 2.4 25.2 1.0 CG A:ASP78 2.6 29.9 1.0 CG A:ASP80 3.1 25.1 1.0 CG A:ASP129 3.1 30.9 1.0 O2A A:UTP401 3.3 27.4 0.8 OD1 A:ASP80 3.5 25.8 1.0 CB A:ASP129 3.6 28.6 1.0 MN A:MN403 3.7 24.8 1.0 CB A:ASP78 4.1 30.4 1.0 O A:HOH621 4.2 32.6 1.0 OD1 A:ASP129 4.2 35.6 1.0 CB A:ASP80 4.5 25.0 1.0 O3' A:UTP401 4.5 49.9 0.8 PA A:UTP401 4.6 29.6 0.8 C5' A:UTP401 4.7 36.6 0.8 CD2 A:HIS127 4.8 44.4 1.0 NE2 A:HIS127 4.8 43.4 1.0 CA A:ASP78 4.9 29.0 1.0 O5' A:UTP401 4.9 32.2 0.8 C A:ASP78 4.9 28.7 1.0 CA A:ASP80 4.9 25.8 1.0 CA A:ASP129 5.0 26.8 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Utp Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:24.8 occ:1.00 O1G A:UTP401 2.1 21.1 0.8 OD1 A:ASP80 2.1 25.8 1.0 O2B A:UTP401 2.1 21.6 0.8 O2A A:UTP401 2.2 27.4 0.8 O A:HOH548 2.2 20.6 1.0 OD2 A:ASP78 2.2 25.2 1.0 PB A:UTP401 3.2 21.7 0.8 CG A:ASP80 3.2 25.1 1.0 CG A:ASP78 3.3 29.9 1.0 PG A:UTP401 3.3 20.5 0.8 PA A:UTP401 3.4 29.6 0.8 O3B A:UTP401 3.5 23.7 0.8 O3A A:UTP401 3.6 24.7 0.8 OD2 A:ASP80 3.6 21.0 1.0 MN A:MN402 3.7 27.5 1.0 CB A:ASP78 3.9 30.4 1.0 O A:ASP78 4.0 27.4 1.0 O3G A:UTP401 4.0 19.8 0.8 OG A:SER62 4.0 21.4 1.0 OD1 A:ASP78 4.2 35.6 1.0 N A:SER62 4.2 20.2 1.0 C5' A:UTP401 4.3 36.6 0.8 O A:HOH578 4.3 20.9 1.0 O5' A:UTP401 4.4 32.2 0.8 CB A:ASP80 4.5 25.0 1.0 O1A A:UTP401 4.5 27.9 0.8 O A:HOH633 4.5 39.4 1.0 O2G A:UTP401 4.5 21.9 0.8 O A:HOH600 4.5 35.0 1.0 O1B A:UTP401 4.6 26.4 0.8 CA A:GLY61 4.6 20.1 1.0 CB A:SER62 4.7 19.8 1.0 C A:ASP78 4.7 28.7 1.0 C A:GLY61 5.0 19.3 1.0 CA A:ASP78 5.0 29.0 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