Cobalt in PDB 6vem: Structure of Rna Octamer

The structure of Structure of Rna Octamer, PDB code: 6vem was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.72 / 1.56
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	37.921, 37.921, 57.852, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 24.4

The binding sites of Cobalt atom in the Structure of Rna Octamer (pdb code 6vem). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Structure of Rna Octamer, PDB code: 6vem:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Structure of Rna Octamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Rna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:38.9 occ:0.60 CO A:NCO101 0.0 38.9 0.6 N1 A:NCO101 2.0 39.9 0.6 N4 A:NCO101 2.0 41.2 0.6 N2 A:NCO101 2.0 58.4 0.6 N5 A:NCO101 2.0 35.2 0.6 N3 A:NCO101 2.0 40.3 0.6 N6 A:NCO101 2.0 49.6 0.6 O A:HOH201 4.2 47.1 1.0 O A:HOH205 4.3 45.1 1.0 OP1 A:G8 4.9 38.5 1.0

Cobalt binding site 2 out of 5 in the Structure of Rna Octamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Rna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:33.6 occ:0.50 CO A:NCO102 0.0 33.6 0.5 N4 A:NCO102 2.0 43.4 0.5 N5 A:NCO102 2.0 34.3 0.5 N4 A:NCO103 2.0 35.6 0.1 N3 A:NCO102 2.0 40.4 0.5 N6 A:NCO102 2.0 31.4 0.5 N2 A:NCO102 2.0 37.0 0.5 N1 A:NCO102 2.0 39.1 0.5 N1 A:NCO103 2.6 43.7 0.1 CO A:NCO103 3.1 40.8 0.5 N5 A:NCO103 3.2 39.6 0.1 O6 A:G6 3.9 34.9 1.0 O6 A:G7 4.1 32.9 1.0 O A:HOH208 4.2 76.9 1.0 N7 A:G6 4.3 38.6 1.0 O B:HOH214 4.4 39.6 1.0 N3 A:NCO103 4.4 36.0 0.1 N2 A:NCO103 4.6 32.9 0.1 C6 A:G6 4.7 30.0 1.0 C5 A:G6 4.9 32.3 1.0 N4 B:C10 4.9 32.9 1.0

Cobalt binding site 3 out of 5 in the Structure of Rna Octamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Rna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:40.8 occ:0.50 CO A:NCO103 0.0 40.8 0.5 N1 A:NCO103 2.0 43.7 0.1 N2 A:NCO103 2.1 32.9 0.1 N4 A:NCO103 2.2 35.6 0.1 N6 A:NCO103 2.2 40.2 0.1 N5 A:NCO103 2.3 39.6 0.1 N3 A:NCO103 2.3 36.0 0.1 N1 A:NCO102 2.3 39.1 0.5 N6 A:NCO102 2.5 31.4 0.5 N3 A:NCO102 2.8 40.4 0.5 CO A:NCO102 3.1 33.6 0.5 O6 A:G7 4.3 32.9 1.0 N5 A:NCO102 4.3 34.3 0.5 O6 A:G8 4.3 38.0 1.0 N4 A:NCO102 4.5 43.4 0.5 N7 A:G7 4.5 28.8 1.0 O A:HOH208 4.7 76.9 1.0 N2 A:NCO102 4.7 37.0 0.5

Cobalt binding site 4 out of 5 in the Structure of Rna Octamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Rna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Co104 b:32.8 occ:0.80 CO A:NCO104 0.0 32.8 0.8 N6 A:NCO104 2.0 37.9 0.8 N3 A:NCO104 2.0 41.4 0.8 N4 A:NCO104 2.0 34.1 0.8 N2 A:NCO104 2.0 39.9 0.8 N1 A:NCO104 2.0 34.8 0.8 N5 A:NCO104 2.0 32.6 0.8 OP1 A:G6 4.5 35.8 1.0 OP2 A:G7 4.9 32.0 1.0

Cobalt binding site 5 out of 5 in the Structure of Rna Octamer


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of Rna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:27.4 occ:0.30 CO B:NCO101 0.0 27.4 0.3 N4 B:NCO101 2.0 25.6 0.3 N3 B:NCO101 2.0 31.9 0.3 N6 B:NCO101 2.0 26.6 0.3 N5 B:NCO101 2.0 31.0 0.3 N1 B:NCO101 2.0 20.5 0.3 N2 B:NCO101 2.0 27.2 0.3 O B:HOH201 3.4 49.8 1.0 OP2 B:GMX13 3.8 41.1 1.0 O B:HOH203 3.8 47.6 1.0 OP2 B:C12 4.0 37.0 1.0 O B:HOH205 4.4 46.5 1.0

A.Mikami, N.Erande, S.Matsuda, A.Kel'in, L.B.Woods, T.Chickering, P.S.Pallan, M.K.Schlegel, I.Zlatev, M.Egli, M.Manoharan. Synthesis, Chirality-Dependent Conformational and Biological Properties of Sirnas Containing 5'-(R)- and 5'-(S)-C-Methyl-Guanosine. Nucleic Acids Res. V. 48 10101 2020.
ISSN: ESSN 1362-4962
PubMed: 32990754
DOI: 10.1093/NAR/GKAA750