Manganese in PDB 6o74: Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp

The structure of Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp, PDB code: 6o74 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)	49.41 / 2.71
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	156.432, 156.432, 185.473, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 25.9

The binding sites of Manganese atom in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp (pdb code 6o74). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp, PDB code: 6o74:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp


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 Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn803 b:70.5 occ:1.00 O2B A:ANP801 2.1 75.7 1.0 OD2 A:ASP521 2.1 66.7 1.0 O A:VAL522 2.2 57.5 1.0 O1G A:ANP801 2.3 65.4 1.0 OD2 A:ASP588 2.4 65.4 1.0 O1A A:ANP801 2.4 71.7 1.0 PB A:ANP801 3.0 67.8 1.0 O3A A:ANP801 3.0 64.3 1.0 CG A:ASP521 3.1 60.8 1.0 PA A:ANP801 3.2 68.0 1.0 C A:VAL522 3.4 58.4 1.0 PG A:ANP801 3.4 72.7 1.0 OD1 A:ASP521 3.5 62.4 1.0 CG A:ASP588 3.5 67.7 1.0 N3B A:ANP801 3.6 70.9 1.0 MN A:MN804 3.8 72.1 1.0 O5' A:ANP801 3.8 72.2 1.0 OD1 A:ASP588 3.9 70.8 1.0 N A:VAL522 3.9 60.1 1.0 NZ A:LYS648 4.1 70.3 1.0 O2G A:ANP801 4.1 67.8 1.0 CA A:VAL522 4.1 60.0 1.0 O1B A:ANP801 4.4 73.2 1.0 CB A:ASP521 4.4 59.6 1.0 N A:ASP523 4.5 59.4 1.0 C A:ASP521 4.5 63.8 1.0 CB A:LEU525 4.6 74.2 1.0 CB A:VAL522 4.6 61.9 1.0 O2A A:ANP801 4.6 70.6 1.0 O3G A:ANP801 4.7 75.8 1.0 N A:LEU525 4.7 74.1 1.0 N A:ARG524 4.7 79.5 1.0 CB A:ASP588 4.8 72.2 1.0 CE A:LYS648 4.8 67.5 1.0 CA A:ASP523 4.8 63.3 1.0 O A:ASP588 4.9 67.1 1.0 CA A:ASP521 4.9 60.9 1.0 C5' A:ANP801 4.9 70.6 1.0 C A:ASP523 5.0 70.0 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp


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 Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn804 b:72.1 occ:1.00 OD1 A:ASP521 2.1 62.4 1.0 O1A A:ANP801 2.2 71.7 1.0 OD2 A:ASP589 2.4 73.6 1.0 OD1 A:ASP588 2.6 70.8 1.0 CG A:ASP521 3.2 60.8 1.0 PA A:ANP801 3.5 68.0 1.0 CG A:ASP588 3.5 67.7 1.0 CG A:ASP589 3.5 74.0 1.0 OD2 A:ASP588 3.6 65.4 1.0 OD2 A:ASP521 3.7 66.7 1.0 MN A:MN803 3.8 70.5 1.0 CB A:ASP589 3.9 69.9 1.0 O2A A:ANP801 4.0 70.6 1.0 O5' A:ANP801 4.1 72.2 1.0 O3' A:ANP802 4.2 66.9 1.0 CB A:ASP521 4.5 59.6 1.0 O A:ASP588 4.5 67.1 1.0 C A:ASP588 4.6 65.8 1.0 OD1 A:ASP589 4.6 79.2 1.0 C3' A:ANP802 4.7 71.0 1.0 O3A A:ANP801 4.7 64.3 1.0 N A:ASP589 4.8 62.2 1.0 CB A:ASP588 4.8 72.2 1.0 O2' A:ANP802 4.9 76.1 1.0 CA A:ASP589 5.0 65.7 1.0 O1G A:ANP801 5.0 65.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of CSM1-CSM4 Cassette in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn805 b:0.6 occ:1.00 O1A A:ANP802 2.0 0.2 1.0 O1B A:ANP802 2.5 0.7 1.0 O A:PHE240 2.9 70.2 1.0 N3B A:ANP802 3.0 0.0 1.0 PB A:ANP802 3.0 0.4 1.0 PA A:ANP802 3.1 97.2 1.0 OD2 A:ASP239 3.2 1.0 1.0 O3A A:ANP802 3.3 0.5 1.0 O1G A:ANP802 3.3 0.7 1.0 C5' A:ANP802 3.6 78.4 1.0 PG A:ANP802 3.6 0.3 1.0 O5' A:ANP802 3.8 97.1 1.0 CG A:ASP239 4.0 92.3 1.0 NZ A:LYS367 4.0 81.4 1.0 OD1 A:ASP239 4.0 87.4 1.0 C A:PHE240 4.1 70.2 1.0 O3G A:ANP802 4.2 0.6 1.0 CD1 A:ILE243 4.2 70.1 1.0 O2A A:ANP802 4.4 93.3 1.0 O2B A:ANP802 4.5 0.0 1.0 CA A:SER241 4.5 73.0 1.0 N A:SER241 4.8 72.4 1.0 CG1 A:ILE243 4.8 68.3 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