Magnesium in PDB 9ash: Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage

The binding sites of Magnesium atom in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage (pdb code 9ash). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage, PDB code: 9ash:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:0.5 occ:1.00 OD1 A:ASP577 2.0 19.7 1.0 OD2 A:ASP576 2.3 12.5 1.0 OD2 A:ASP520 2.6 20.2 1.0 O2A P:ATP1 2.8 18.4 1.0 CG A:ASP577 2.9 20.6 1.0 OD2 A:ASP577 3.2 17.9 1.0 O3' A:ATP801 3.4 24.6 1.0 O5' P:ATP1 3.4 17.4 1.0 CG A:ASP576 3.4 11.5 1.0 CG A:ASP520 3.5 16.5 1.0 PA P:ATP1 3.5 20.2 1.0 OD1 A:ASP520 3.7 19.1 1.0 O A:HOH901 3.7 12.6 1.0 O1A P:ATP1 3.9 21.6 1.0 CB A:ASP576 4.0 8.8 1.0 MG A:MG803 4.1 7.5 1.0 O A:ASP576 4.1 23.4 1.0 C5' P:ATP1 4.2 9.5 1.0 C A:ASP576 4.3 6.2 1.0 CB A:ASP577 4.3 19.4 1.0 OD1 A:ASP576 4.5 23.7 1.0 N A:ASP577 4.6 4.8 1.0 O A:GLY575 4.6 14.8 1.0 CA A:ASP577 4.7 6.8 1.0 O A:HOH902 4.7 1.0 1.0 CB A:ASP520 4.8 12.3 1.0 CA A:ASP576 4.8 7.0 1.0 O2' A:ATP801 4.8 18.7 1.0 C3' A:ATP801 4.8 9.0 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:7.5 occ:1.00 OD1 A:ASP520 2.0 19.1 1.0 O A:VAL521 2.0 15.9 1.0 O2G P:ATP1 2.0 18.0 1.0 O1B P:ATP1 2.0 17.6 1.0 O2A P:ATP1 2.4 18.4 1.0 OD2 A:ASP576 2.8 12.5 1.0 OD1 A:ASP576 3.0 23.7 1.0 CG A:ASP520 3.1 16.5 1.0 C A:VAL521 3.2 6.5 1.0 PB P:ATP1 3.2 16.0 1.0 CG A:ASP576 3.3 11.5 1.0 PG P:ATP1 3.3 15.8 1.0 PA P:ATP1 3.6 20.2 1.0 OD2 A:ASP520 3.7 20.2 1.0 O3B P:ATP1 3.7 9.6 1.0 N A:VAL521 3.8 1.2 1.0 O3A P:ATP1 3.8 12.4 1.0 CA A:VAL521 4.0 9.0 1.0 MG A:MG802 4.1 0.5 1.0 O1G P:ATP1 4.1 17.4 1.0 N A:ASP522 4.2 7.6 1.0 C A:ASP520 4.3 7.0 1.0 C5' P:ATP1 4.3 9.5 1.0 O5' P:ATP1 4.3 17.4 1.0 CB A:ASP520 4.3 12.3 1.0 N A:ASN523 4.4 9.2 1.0 CA A:ASP522 4.4 5.0 1.0 O2B P:ATP1 4.4 27.0 1.0 CB A:VAL521 4.4 7.8 1.0 O3G P:ATP1 4.4 15.4 1.0 CE A:LYS636 4.5 7.1 1.0 N A:LEU524 4.5 1.4 1.0 NZ A:LYS636 4.5 13.0 1.0 C A:ASP522 4.6 11.7 1.0 CB A:LEU524 4.6 8.2 1.0 O A:ASP576 4.7 23.4 1.0 O1A P:ATP1 4.7 21.6 1.0 CA A:ASP520 4.8 1.8 1.0 CB A:ASP576 4.8 8.8 1.0 O A:ASP520 4.9 20.1 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Post-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:14.1 occ:1.00 OD1 A:ASP253 2.5 26.3 1.0 O A:MET254 2.6 10.4 1.0 O3B A:ATP801 2.7 11.5 1.0 O1A A:ATP801 3.3 18.1 1.0 O1G A:ATP801 3.6 21.9 1.0 C A:MET254 3.6 10.1 1.0 CG A:ASP253 3.7 26.6 1.0 O2B A:ATP801 3.7 26.0 1.0 PB A:ATP801 3.8 20.2 1.0 PG A:ATP801 3.8 23.7 1.0 OD2 A:ASP253 4.1 28.9 1.0 NZ A:LYS379 4.3 17.5 1.0 N A:MET254 4.3 9.3 1.0 O A:GLY308 4.3 18.4 1.0 CA A:SER255 4.4 6.3 1.0 PA A:ATP801 4.4 20.0 1.0 N A:SER255 4.4 16.1 1.0 OG A:SER255 4.5 19.7 1.0 O3A A:ATP801 4.6 17.9 1.0 CA A:MET254 4.6 11.5 1.0 C A:ASP253 4.7 10.0 1.0 O2G A:ATP801 4.8 14.3 1.0 O3G A:ATP801 4.9 13.8 1.0 O5' A:ATP801 4.9 7.3 1.0 CB A:ASP253 4.9 14.8 1.0 CB A:SER255 5.0 10.3 1.0

H.N.Goswami, F.Ahmadizadeh, B.Wang, D.Addo-Yobo, Y.Zhao, A.C.Whittington, H.He, M.P.Terns, H.Li. Molecular Basis For CA6 Synthesis By A Type III-A Crispr-Cas Enzyme and Its Conversion to CA4 Production. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38989619
DOI: 10.1093/NAR/GKAE603