Manganese in PDB 6sh8: Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna

The structure of Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna (pdb code 6sh8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna, PDB code: 6sh8:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1104 b:77.1 occ:1.00 O1G K:ANP1103 2.0 39.0 1.0 O K:SER651 2.2 39.0 1.0 O2B K:ANP1103 2.4 39.0 1.0 O1A K:ANP1103 2.5 39.0 1.0 C K:SER651 3.4 39.0 1.0 PG K:ANP1103 3.4 39.0 1.0 PB K:ANP1103 3.6 39.0 1.0 OD2 K:ASP650 3.7 39.9 1.0 NZ K:LYS885 3.8 27.7 1.0 PA K:ANP1103 3.9 39.0 1.0 N3B K:ANP1103 4.0 39.0 1.0 CG K:ASP650 4.0 39.9 1.0 CB K:ASP650 4.0 39.9 1.0 O3A K:ANP1103 4.2 39.0 1.0 N K:SER651 4.2 39.0 1.0 O2G K:ANP1103 4.2 39.0 1.0 O3G K:ANP1103 4.3 39.0 1.0 N K:ASP652 4.3 40.9 1.0 CA K:ASP652 4.3 40.9 1.0 CA K:SER651 4.4 39.0 1.0 O2' K:ANP1103 4.5 39.0 1.0 C2' K:ANP1103 4.5 39.0 1.0 O5' K:ANP1103 4.5 39.0 1.0 C K:ASP650 4.6 39.9 1.0 N K:TYR653 4.6 37.3 1.0 OD1 K:ASP802 4.7 40.7 1.0 OD1 K:ASP650 4.8 39.9 1.0 CB K:LEU654 4.8 41.4 1.0 C K:ASP652 4.8 40.9 1.0 N K:LEU654 4.8 41.4 1.0 C3' K:ANP1103 4.8 39.0 1.0 O1B K:ANP1103 4.9 39.0 1.0 CA K:ASP650 4.9 39.9 1.0 OD1 K:ASP803 5.0 35.1 1.0

Manganese binding site 2 out of 3 in the Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1105 b:81.3 occ:1.00 OE2 K:GLU882 2.4 33.2 1.0 OE1 K:GLU882 2.5 33.2 1.0 CD K:GLU882 2.8 33.2 1.0 O2A K:ANP1103 2.8 39.0 1.0 O3G K:ANP1103 2.8 39.0 1.0 PA K:ANP1103 3.9 39.0 1.0 O1A K:ANP1103 4.1 39.0 1.0 PG K:ANP1103 4.1 39.0 1.0 CG K:GLU882 4.3 33.2 1.0 N3B K:ANP1103 4.6 39.0 1.0 O3A K:ANP1103 4.6 39.0 1.0 O1G K:ANP1103 4.7 39.0 1.0 OE2 K:GLU886 4.7 37.0 1.0

Manganese binding site 3 out of 3 in the Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of the Type III-B Cmr-Beta Bound to Cognate Target Rna and Amppnp, State 2, in the Presence of Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ K:Mn1106 b:58.4 occ:1.00 O1G K:ANP1102 2.0 28.4 1.0 O1A K:ANP1102 2.0 28.4 1.0 OD1 K:ASP206 2.1 38.2 1.0 O K:THR207 2.2 32.3 1.0 O2B K:ANP1102 2.3 28.4 1.0 PG K:ANP1102 3.2 28.4 1.0 CG K:ASP206 3.2 38.2 1.0 PA K:ANP1102 3.4 28.4 1.0 PB K:ANP1102 3.4 28.4 1.0 C K:THR207 3.5 32.3 1.0 O2G K:ANP1102 3.6 28.4 1.0 N3B K:ANP1102 3.7 28.4 1.0 OD2 K:ASP206 3.7 38.2 1.0 O3A K:ANP1102 3.8 28.4 1.0 C5' K:ANP1102 4.0 28.4 1.0 O5' K:ANP1102 4.1 28.4 1.0 N K:THR207 4.1 32.3 1.0 O K:GLY310 4.2 29.2 1.0 N K:GLY209 4.3 31.6 1.0 O3G K:ANP1102 4.3 28.4 1.0 CA K:THR207 4.3 32.3 1.0 N K:ILE208 4.4 25.7 1.0 C K:ASP206 4.4 38.2 1.0 CB K:ASP206 4.5 38.2 1.0 CA K:ILE208 4.5 25.7 1.0 O2A K:ANP1102 4.5 28.4 1.0 NZ K:LYS429 4.6 37.3 1.0 C K:ILE208 4.6 25.7 1.0 O1B K:ANP1102 4.8 28.4 1.0 CB K:THR207 4.8 32.3 1.0 CG2 K:VAL210 4.8 19.9 1.0 N K:VAL210 4.8 19.9 1.0 O K:ASP206 4.8 38.2 1.0 CE K:LYS429 4.8 37.3 1.0 NH1 K:ARG389 4.9 29.7 1.0 CA K:ASP206 4.9 38.2 1.0

N.Sofos, M.Feng, S.Stella, T.Pape, A.Fuglsang, J.Lin, Q.Huang, Y.Li, Q.She, G.Montoya. Structures of the Cmr-Beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B Crispr-Cas. Mol.Cell V. 79 741 2020.
ISSN: ISSN 1097-2765
PubMed: 32730741
DOI: 10.1016/J.MOLCEL.2020.07.008