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

The structure of Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp Mn, PDB code: 8ysm 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)	23.51 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.401, 46.765, 64.182, 105.45, 103.35, 99.33
R / Rfree (%)	17.3 / 19.3

The binding sites of Manganese atom in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp Mn (pdb code 8ysm). 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 Ctp Mn, PDB code: 8ysm:
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 Ctp 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 Ctp Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:16.6 occ:1.00 OD2 A:ASP129 2.1 20.2 1.0 OD2 A:ASP80 2.1 14.6 1.0 O A:HOH613 2.2 30.6 1.0 O A:HOH716 2.2 26.4 1.0 OD1 A:ASP78 2.3 18.5 1.0 OD2 A:ASP78 2.5 15.9 1.0 CG A:ASP78 2.7 18.9 1.0 CG A:ASP129 3.1 24.5 1.0 CG A:ASP80 3.2 15.6 1.0 O2A A:CTP401 3.4 20.4 1.0 OD1 A:ASP80 3.6 16.7 1.0 CB A:ASP129 3.6 20.9 1.0 MN A:MN403 3.7 15.3 1.0 O A:HOH774 4.0 31.3 1.0 OD1 A:ASP129 4.1 23.4 1.0 CB A:ASP78 4.2 16.6 1.0 CB A:ASP80 4.5 13.4 1.0 NE2 A:HIS127 4.6 27.5 1.0 PA A:CTP401 4.8 21.6 1.0 CD2 A:HIS127 4.8 26.8 1.0 CA A:ASP78 4.9 14.7 1.0 C A:ASP78 4.9 14.2 1.0 O A:ASP78 5.0 14.4 1.0 CA A:ASP129 5.0 18.6 1.0 CA A:ASP80 5.0 13.5 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the Deinococcus Wulumuqiensis Cd-Ntase Dwcdnb in Complex with Ctp 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 Ctp Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:15.3 occ:1.00 OD2 A:ASP78 2.0 15.9 1.0 O2B A:CTP401 2.1 13.1 1.0 O1G A:CTP401 2.2 14.3 1.0 OD1 A:ASP80 2.2 16.7 1.0 O A:HOH530 2.2 15.9 1.0 O2A A:CTP401 2.3 20.4 1.0 CG A:ASP78 3.1 18.9 1.0 PB A:CTP401 3.2 14.8 1.0 CG A:ASP80 3.2 15.6 1.0 PG A:CTP401 3.4 13.2 1.0 PA A:CTP401 3.5 21.6 1.0 O3B A:CTP401 3.6 14.2 1.0 OD2 A:ASP80 3.6 14.6 1.0 O3A A:CTP401 3.7 18.4 1.0 MN A:MN402 3.7 16.6 1.0 CB A:ASP78 3.8 16.6 1.0 O A:ASP78 3.9 14.4 1.0 O3G A:CTP401 4.0 13.3 1.0 OG A:SER62 4.1 11.2 1.0 OD1 A:ASP78 4.1 18.5 1.0 O A:HOH551 4.1 29.6 1.0 C5' A:CTP401 4.3 26.0 1.0 N A:SER62 4.3 8.9 1.0 O A:HOH684 4.4 13.6 1.0 O5' A:CTP401 4.5 25.3 1.0 O A:HOH716 4.5 26.4 1.0 O A:HOH613 4.5 30.6 1.0 CB A:ASP80 4.6 13.4 1.0 O1B A:CTP401 4.6 16.5 1.0 O2G A:CTP401 4.6 14.7 1.0 O1A A:CTP401 4.6 19.2 1.0 CA A:GLY61 4.7 9.4 1.0 C A:ASP78 4.7 14.2 1.0 CB A:SER62 4.8 10.9 1.0 CA A:ASP78 4.9 14.7 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