Manganese in PDB 6o78: Crystal Structure of CSM1-CSM4 Cassette in Complex with Pppapapa

The structure of Crystal Structure of CSM1-CSM4 Cassette in Complex with Pppapapa, PDB code: 6o78 was solved by N.Jia, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.69 / 2.80
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	154.184, 154.184, 182.474, 90.00, 90.00, 120.00
R / Rfree (%)	25.7 / 30.4

The binding sites of Manganese atom in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Pppapapa (pdb code 6o78). 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 CSM1-CSM4 Cassette in Complex with Pppapapa, PDB code: 6o78:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Pppapapa


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 CSM1-CSM4 Cassette in Complex with Pppapapa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:0.8 occ:1.00 OD1 A:ASP588 2.7 81.2 1.0 OD1 A:ASP521 2.7 88.0 1.0 O2A E:ATP1 2.8 0.9 1.0 CG A:ASP521 3.4 83.8 1.0 OD2 A:ASP521 3.6 88.6 1.0 CG A:ASP588 3.6 81.1 1.0 O3' E:A3 3.7 86.1 1.0 C3' E:A3 3.8 87.3 1.0 OD2 A:ASP588 3.8 83.3 1.0 CB A:ALA589 3.9 76.8 1.0 O5' E:A3 3.9 0.7 1.0 PA E:ATP1 4.1 0.4 1.0 MN A:MN802 4.2 0.8 1.0 O5' E:ATP1 4.3 0.8 1.0 OP1 E:A3 4.4 0.7 1.0 O3A E:ATP1 4.6 0.1 1.0 CB A:ASP521 4.7 81.3 1.0 O A:ASP588 4.7 79.9 1.0 C2' E:A3 4.7 85.0 1.0 C A:ASP588 4.8 79.5 1.0 P E:A3 4.8 0.8 1.0 C8 E:ATP1 4.8 0.7 1.0 C5' E:A3 4.8 99.3 1.0 C4' E:A3 4.9 91.8 1.0 O3' E:A2 4.9 1.0 1.0 N A:ALA589 5.0 77.6 1.0 CA A:ALA589 5.0 76.7 1.0 CB A:ASP588 5.0 81.0 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Pppapapa


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 CSM1-CSM4 Cassette in Complex with Pppapapa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn802 b:0.8 occ:1.00 O A:VAL522 2.1 78.3 1.0 O3A E:ATP1 2.3 0.1 1.0 OD2 A:ASP588 2.5 83.3 1.0 O2G E:ATP1 2.8 99.6 1.0 OD2 A:ASP521 2.8 88.6 1.0 OD1 A:ASP521 2.9 88.0 1.0 CG A:ASP521 3.0 83.8 1.0 O1B E:ATP1 3.1 99.5 1.0 PB E:ATP1 3.2 97.3 1.0 C A:VAL522 3.3 78.0 1.0 O2A E:ATP1 3.4 0.9 1.0 PA E:ATP1 3.5 0.4 1.0 CG A:ASP588 3.6 81.1 1.0 PG E:ATP1 3.7 0.6 1.0 O3B E:ATP1 3.7 99.5 1.0 N A:VAL522 3.8 79.6 1.0 CA A:VAL522 4.0 79.2 1.0 OD1 A:ASP588 4.1 81.2 1.0 O5' E:ATP1 4.2 0.8 1.0 MN A:MN801 4.2 0.8 1.0 CB A:ASP521 4.3 81.3 1.0 NZ A:LYS648 4.3 86.8 1.0 C A:ASP521 4.3 79.5 1.0 CB A:LEU525 4.4 94.3 1.0 N A:ASP523 4.4 78.9 1.0 CB A:VAL522 4.5 78.0 1.0 O3G E:ATP1 4.5 0.8 1.0 O2B E:ATP1 4.6 98.5 1.0 O1A E:ATP1 4.6 0.4 1.0 CA A:ASP523 4.7 83.0 1.0 CA A:ASP521 4.7 79.4 1.0 CE A:LYS648 4.8 86.2 1.0 N A:LEU525 4.8 95.0 1.0 O A:ASP588 4.8 79.9 1.0 CB A:ASP588 4.8 81.0 1.0 O1G E:ATP1 4.9 97.7 1.0 N A:ARG524 4.9 92.2 1.0 C5' E:ATP1 4.9 0.5 1.0 C A:ASP523 5.0 87.4 1.0

N.Jia, R.Jones, G.Sukenick, D.J.Patel. Second Messenger CA4FORMATION Within the Composite CSM1 Palm Pocket of Type III-A Crispr-Cas Csm Complex and Its Release Path. Mol.Cell V. 75 933 2019.
ISSN: ISSN 1097-2765
PubMed: 31326272
DOI: 10.1016/J.MOLCEL.2019.06.013