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

The binding sites of Magnesium atom in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Pre-Cleavage Stage (pdb code 9asi). 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 Pre-Cleavage Stage, PDB code: 9asi:
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 Pre-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 Pre-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:29.6 occ:1.00 OD1 A:ASP577 2.1 29.8 1.0 O2A A:ATP805 2.6 13.9 1.0 CG A:ASP577 3.0 26.6 1.0 OD2 A:ASP577 3.1 20.5 1.0 O3' A:ATP801 3.4 19.5 1.0 PA A:ATP805 3.7 14.0 1.0 OD2 A:ASP520 3.8 46.3 1.0 O1A A:ATP805 3.9 21.8 1.0 MG A:MG803 4.0 40.2 1.0 OD1 A:ASP520 4.0 49.1 1.0 O2' A:ATP801 4.1 36.8 1.0 O5' A:ATP805 4.1 10.3 1.0 C5' A:ATP805 4.2 18.1 1.0 CG A:ASP520 4.2 49.8 1.0 O A:ASP576 4.2 34.1 1.0 CB A:ASP577 4.4 31.2 1.0 CG A:ASP576 4.4 43.9 1.0 OD2 A:ASP576 4.4 47.3 1.0 CB A:ASP576 4.4 37.5 1.0 C3' A:ATP801 4.5 8.4 1.0 C4' A:ATP801 4.5 14.6 1.0 C A:ASP576 4.6 32.2 1.0 OD1 A:ASP576 4.9 44.6 1.0 C2' A:ATP801 4.9 22.1 1.0 O1B A:ATP805 5.0 11.5 1.0 N A:ASP577 5.0 30.1 1.0

Magnesium binding site 2 out of 3 in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Pre-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 Pre-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:40.2 occ:1.00 OD1 A:ASP520 2.0 49.1 1.0 OD1 A:ASP576 2.0 44.6 1.0 CG A:ASP576 2.3 43.9 1.0 OD2 A:ASP576 2.3 47.3 1.0 O2A A:ATP805 2.3 13.9 1.0 O1B A:ATP805 2.4 11.5 1.0 O A:VAL521 2.6 46.7 1.0 CG A:ASP520 3.0 49.8 1.0 PB A:ATP805 3.2 7.0 1.0 O2B A:ATP805 3.2 21.4 1.0 O A:ASP576 3.4 34.1 1.0 OD2 A:ASP520 3.5 46.3 1.0 PA A:ATP805 3.5 14.0 1.0 O3A A:ATP805 3.5 12.9 1.0 CB A:ASP576 3.6 37.5 1.0 C A:VAL521 3.7 45.3 1.0 N A:VAL521 3.7 41.8 1.0 MG A:MG802 4.0 29.6 1.0 CA A:VAL521 4.1 44.4 1.0 C A:ASP576 4.3 32.2 1.0 C A:ASP520 4.3 45.9 1.0 CB A:ASP520 4.4 44.1 1.0 CB A:VAL521 4.4 40.3 1.0 CA A:ASP576 4.4 30.9 1.0 O1A A:ATP805 4.5 21.8 1.0 C5' A:ATP805 4.5 18.1 1.0 CB A:LEU524 4.6 50.0 1.0 CA A:ASP520 4.6 39.7 1.0 O5' A:ATP805 4.6 10.3 1.0 OD1 A:ASP577 4.6 29.8 1.0 O3B A:ATP805 4.7 9.3 1.0 N A:ASP522 4.9 44.8 1.0

Magnesium binding site 3 out of 3 in the Cryo-Em Structure of the Active Lactococcus Lactis Csm Bound to Target in Pre-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 Pre-Cleavage Stage within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:17.4 occ:1.00 OD2 A:ASP253 2.8 7.8 1.0 O3B A:ATP801 2.9 15.8 1.0 O2B A:ATP801 3.1 27.6 1.0 O1A A:ATP801 3.3 30.3 1.0 O A:MET254 3.4 7.5 1.0 CG A:ASP253 3.5 13.4 1.0 PB A:ATP801 3.6 21.3 1.0 OD1 A:ASP253 3.7 11.9 1.0 PA A:ATP801 4.2 22.4 1.0 PG A:ATP801 4.3 29.1 1.0 C A:MET254 4.3 19.0 1.0 O5' A:ATP801 4.3 22.8 1.0 O1G A:ATP801 4.3 20.6 1.0 O3A A:ATP801 4.4 16.1 1.0 CA A:SER255 4.7 8.1 1.0 OG A:SER255 4.7 16.6 1.0 O1B A:ATP801 4.8 11.8 1.0 NZ A:LYS379 4.8 18.3 1.0 CB A:ASP253 4.9 14.7 1.0 N A:SER255 4.9 23.3 1.0 O A:GLY308 4.9 18.8 1.0 N A:MET254 4.9 0.0 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