Cobalt in PDB 4u3r: Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride

The structure of Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride, PDB code: 4u3r was solved by M.F.Schaffer, B.Spingler, J.Schnabl, G.Peng, V.Olieric, R.K.O.Sigel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.34 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	46.977, 46.977, 53.300, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 19.8

The binding sites of Cobalt atom in the Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride (pdb code 4u3r). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride, PDB code: 4u3r:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:12.0 occ:0.20 O A:HOH214 2.1 18.9 1.0 OP1 A:G7 2.1 15.3 1.0 P A:G7 3.4 15.3 1.0 O5' A:G7 3.6 15.9 1.0 H5' A:G7 3.7 17.4 1.0 C5' A:G7 4.2 14.5 1.0 O3' A:C6 4.3 13.4 1.0 O A:HOH211 4.5 29.8 1.0 OP2 A:G7 4.5 13.0 1.0 HO2' A:C6 4.8 16.6 1.0 O A:HOH210 4.8 32.0 1.0 H4' A:G7 4.8 15.1 1.0 H5'' A:G7 4.9 17.4 1.0

Cobalt binding site 2 out of 3 in the Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:8.7 occ:0.51 O B:HOH122 2.1 20.4 1.0 O A:HOH223 2.1 18.9 1.0 O A:HOH226 2.1 15.9 1.0 O A:HOH224 2.1 20.6 1.0 O B:HOH120 2.1 12.7 1.0 O B:HOH123 2.1 17.5 1.0 O4 A:U4 2.4 14.4 1.0 C4 A:U4 3.5 14.6 1.0 H41 B:C2 3.5 16.9 1.0 H61 B:A5 3.8 18.5 1.0 H5 A:U4 3.8 19.4 1.0 H62 A:A5 3.9 16.5 1.0 C5 A:U4 4.1 16.1 1.0 N4 B:C2 4.2 14.1 1.0 O A:HOH242 4.3 31.5 1.0 O B:HOH124 4.3 16.2 1.0 H61 A:A5 4.4 16.5 1.0 O B:HOH139 4.4 26.3 1.0 N6 B:A5 4.4 15.4 1.0 N6 A:A5 4.4 13.7 1.0 O A:HOH234 4.5 29.5 1.0 O6 A:G3 4.5 13.7 1.0 O B:HOH140 4.5 36.2 1.0 H42 B:C2 4.5 16.9 1.0 N7 A:G3 4.5 12.7 1.0 H62 B:A5 4.6 18.5 1.0 H5 B:C2 4.6 16.9 1.0 O A:HOH245 4.6 19.9 1.0 O A:HOH225 4.6 20.7 1.0 O6 B:G3 4.7 10.9 1.0 O A:HOH230 4.7 23.4 1.0 N3 A:U4 4.7 11.6 1.0 O B:HOH121 4.7 15.6 1.0 H3 A:U4 4.7 13.9 1.0 O A:HOH229 4.8 26.3 1.0 O4 B:U4 4.8 9.9 1.0

Cobalt binding site 3 out of 3 in the Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Octameric Rna Duplex Co-Crystallized with Cobalt(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Co103 b:12.1 occ:0.23 O A:HOH231 2.1 25.3 1.0 O A:HOH236 2.1 34.7 1.0 O A:HOH237 2.1 27.6 0.8 O A:HOH243 2.1 23.7 1.0 O A:HOH235 2.1 26.0 1.0 O A:HOH227 2.1 20.3 1.0 O A:HOH241 3.4 32.3 1.0 H5 A:C6 3.4 13.9 1.0 O A:HOH212 3.8 34.7 1.0 C5 A:C6 4.2 11.6 1.0 OP2 A:C6 4.2 14.3 1.0 O A:HOH232 4.2 19.1 1.0 H41 A:C6 4.4 15.3 1.0 O A:HOH228 4.4 22.7 1.0 O A:HOH215 4.6 22.9 1.0 OP2 A:A5 4.6 13.9 1.0 O A:HOH225 4.8 20.7 1.0 H6 A:C6 4.8 16.6 1.0 O A:HOH246 4.9 25.5 1.0 C6 A:C6 4.9 13.8 1.0 N4 A:C6 5.0 12.8 1.0 N7 A:G7 5.0 9.9 1.0

M.F.Schaffer, G.Peng, B.Spingler, J.Schnabl, M.Wang, V.Olieric, R.K.Sigel. The X-Ray Structures of Six Octameric Rna Duplexes in the Presence of Different Di- and Trivalent Cations. Int J Mol Sci V. 17 2016.
ISSN: ESSN 1422-0067
PubMed: 27355942
DOI: 10.3390/IJMS17070988