Sodium in PDB 6dtd: High-Resolution Crystal Structure of CAS13B From Prevotella Buccae

The structure of High-Resolution Crystal Structure of CAS13B From Prevotella Buccae, PDB code: 6dtd was solved by I.M.S.Slaymaker, F.Z.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.65 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.821, 124.646, 140.728, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.5

The structure of High-Resolution Crystal Structure of CAS13B From Prevotella Buccae also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the High-Resolution Crystal Structure of CAS13B From Prevotella Buccae (pdb code 6dtd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High-Resolution Crystal Structure of CAS13B From Prevotella Buccae, PDB code: 6dtd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High-Resolution Crystal Structure of CAS13B From Prevotella Buccae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Crystal Structure of CAS13B From Prevotella Buccae within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:60.7 occ:1.00 O C:HOH344 2.2 49.4 1.0 O2 C:U1 2.4 56.4 1.0 O C:HOH280 2.5 68.0 1.0 N7 C:G2 2.6 32.1 1.0 O C:HOH204 2.6 51.7 1.0 H8 C:G2 3.3 37.2 1.0 H3' C:U1 3.4 57.8 1.0 C8 C:G2 3.4 31.0 1.0 H3 C:U1 3.4 65.2 1.0 C2 C:U1 3.4 55.4 1.0 C5 C:G2 3.7 29.0 1.0 N3 C:U1 3.8 54.4 1.0 OP2 C:G2 3.9 38.5 1.0 O6 C:G2 4.0 32.1 1.0 H5'' C:U1 4.1 71.3 1.0 C6 C:G2 4.2 29.4 1.0 C3' C:U1 4.3 48.1 1.0 O A:HOH1832 4.3 51.6 1.0 O C:HOH319 4.4 43.0 1.0 H2' C:U1 4.4 63.2 1.0 O4 C:U3 4.5 27.4 1.0 HG A:SER658 4.5 34.6 0.4 O A:HOH1862 4.6 45.9 1.0 N9 C:G2 4.6 27.9 1.0 N1 C:U1 4.7 55.2 1.0 H5 C:U3 4.7 31.8 1.0 O C:HOH241 4.8 37.5 1.0 C4 C:G2 4.8 27.6 1.0 C2' C:U1 4.8 52.6 1.0 O5' C:G2 4.8 30.6 1.0 P C:G2 4.9 37.2 1.0 C5' C:U1 4.9 59.4 1.0 OG A:SER658 5.0 28.8 0.4

Sodium binding site 2 out of 2 in the High-Resolution Crystal Structure of CAS13B From Prevotella Buccae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Resolution Crystal Structure of CAS13B From Prevotella Buccae within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:53.5 occ:0.92 O C:HOH330 2.0 52.3 1.0 O C:HOH341 2.3 60.4 1.0 HO2' C:A31 2.3 47.8 1.0 O C:HOH212 2.3 41.4 1.0 O C:HOH335 2.6 46.7 1.0 O2' C:A31 2.8 39.8 1.0 H2' C:A31 3.4 42.4 1.0 C2' C:A31 3.7 35.4 1.0 H8 C:A31 3.8 34.7 1.0 O C:HOH261 3.9 61.2 1.0 OP1 C:G2 4.0 42.5 1.0 O A:HOH1438 4.2 41.1 1.0 O C:HOH243 4.3 34.8 1.0 OP2 C:A30 4.3 31.5 1.0 C8 C:A31 4.4 28.9 1.0 O C:HOH241 4.7 37.5 1.0 OP2 C:G2 4.7 38.5 1.0 H3' C:A31 4.7 42.0 1.0 C3' C:A31 4.8 35.0 1.0 C1' C:A31 4.8 32.7 1.0 P C:G2 4.8 37.2 1.0 N9 C:A31 4.8 30.7 1.0

I.M.Slaymaker, P.Mesa, M.J.Kellner, S.Kannan, E.Brignole, J.Koob, P.R.Feliciano, S.Stella, O.O.Abudayyeh, J.S.Gootenberg, J.Strecker, G.Montoya, F.Zhang. High-Resolution Structure of CAS13B and Biochemical Characterization of Rna Targeting and Cleavage. Cell Rep V. 26 3741 2019.
ISSN: ESSN 2211-1247
PubMed: 30917325
DOI: 10.1016/J.CELREP.2019.02.094