Cobalt in PDB 7y8p: Crystal Structure of 4'-Selenorna Duplex

The structure of Crystal Structure of 4'-Selenorna Duplex, PDB code: 7y8p was solved by J.Kondo, N.Minakawa, M.Ohta, H.Takahashi, N.Tarashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.25 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	26.951, 38.107, 31.882, 90, 113.47, 90
R / Rfree (%)	16 / 19.9

The binding sites of Cobalt atom in the Crystal Structure of 4'-Selenorna Duplex (pdb code 7y8p). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of 4'-Selenorna Duplex, PDB code: 7y8p:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of 4'-Selenorna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of 4'-Selenorna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:16.7 occ:1.00 CO A:NCO101 0.0 16.7 1.0 N4 A:NCO101 2.0 18.4 1.0 N1 A:NCO101 2.0 19.9 1.0 N5 A:NCO101 2.0 23.1 1.0 N6 A:NCO101 2.0 17.9 1.0 N2 A:NCO101 2.0 15.7 1.0 N3 A:NCO101 2.0 14.5 1.0 O A:HOH215 4.0 21.2 1.0 O B:HOH217 4.0 22.0 1.0 O6 A:G9 4.1 9.0 1.0 O6 B:G2 4.2 11.2 1.0 N7 A:G9 4.3 9.3 1.0 O A:HOH237 4.3 16.7 1.0 O4 A:U10 4.4 8.5 1.0 C6 A:G9 4.8 8.0 1.0 O B:HOH245 4.9 21.9 1.0 C5 A:G9 4.9 7.8 1.0 O A:HOH241 4.9 26.1 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of 4'-Selenorna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of 4'-Selenorna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:20.8 occ:0.53 CO A:NCO102 0.0 20.8 0.5 CO A:NCO102 0.2 20.4 0.5 N2 A:NCO102 1.9 17.4 0.5 N5 A:NCO102 1.9 18.0 0.5 N4 A:NCO102 2.0 10.8 0.5 N5 A:NCO102 2.0 17.3 0.5 N6 A:NCO102 2.0 19.1 0.5 N6 A:NCO102 2.0 19.3 0.5 N1 A:NCO102 2.0 22.0 0.5 N2 A:NCO102 2.0 17.2 0.5 N3 A:NCO102 2.0 19.1 0.5 N4 A:NCO102 2.0 15.0 0.5 N3 A:NCO102 2.1 16.7 0.5 N1 A:NCO102 2.1 21.8 0.5 O A:HOH202 3.7 19.7 1.0 OP1 A:U10 4.2 10.2 1.0 O A:HOH262 4.5 8.3 1.0 OP2 A:C11 4.8 10.3 1.0 O A:HOH219 4.9 15.9 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of 4'-Selenorna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of 4'-Selenorna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:20.4 occ:0.47 CO A:NCO102 0.0 20.4 0.5 CO A:NCO102 0.2 20.8 0.5 N1 A:NCO102 1.8 22.0 0.5 N4 A:NCO102 1.9 10.8 0.5 N3 A:NCO102 1.9 19.1 0.5 N3 A:NCO102 2.0 16.7 0.5 N2 A:NCO102 2.0 17.4 0.5 N5 A:NCO102 2.0 18.0 0.5 N1 A:NCO102 2.0 21.8 0.5 N6 A:NCO102 2.0 19.3 0.5 N4 A:NCO102 2.0 15.0 0.5 N5 A:NCO102 2.1 17.3 0.5 N6 A:NCO102 2.1 19.1 0.5 N2 A:NCO102 2.1 17.2 0.5 O A:HOH202 3.9 19.7 1.0 OP1 A:U10 4.2 10.2 1.0 O A:HOH262 4.5 8.3 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of 4'-Selenorna Duplex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of 4'-Selenorna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:21.9 occ:0.48 CO B:NCO101 0.0 21.9 0.5 N5 B:NCO101 2.0 17.9 0.5 N3 B:NCO101 2.0 20.0 0.5 N1 B:NCO101 2.0 20.5 0.5 N2 B:NCO101 2.0 17.2 0.5 N6 B:NCO101 2.0 17.5 0.5 N4 B:NCO101 2.0 18.7 0.5 O B:HOH206 4.0 21.5 1.0 O B:HOH219 4.3 20.5 1.0 O B:HOH232 4.3 22.5 1.0 OP1 B:C11 4.6 13.4 1.0 OP2 B:C12 4.7 12.2 1.0 O B:HOH228 4.9 16.0 1.0

M.Ota, H.Takahashi, Y.Nogi, Y.Kagotani, N.Saito-Tarashima, J.Kondo, N.Minakawa. Synthesis and Properties of Fully-Modified 4'-Selenorna, An Endonuclease-Resistant Rna Analog. Bioorg.Med.Chem. V. 76 17093 2022.
ISSN: ESSN 1464-3391
PubMed: 36434923
DOI: 10.1016/J.BMC.2022.117093