Calcium in PDB 4u78: Octameric Rna Duplex Soaked in Copper(II)Chloride

The structure of Octameric Rna Duplex Soaked in Copper(II)Chloride, PDB code: 4u78 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)	32.28 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	46.810, 46.810, 53.380, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.6

The structure of Octameric Rna Duplex Soaked in Copper(II)Chloride also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Calcium atom in the Octameric Rna Duplex Soaked in Copper(II)Chloride (pdb code 4u78). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Octameric Rna Duplex Soaked in Copper(II)Chloride, PDB code: 4u78:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Octameric Rna Duplex Soaked in Copper(II)Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Octameric Rna Duplex Soaked in Copper(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:19.1 occ:0.23 CU A:CU101 0.1 19.1 0.4 O4 A:U4 2.3 18.1 1.0 O A:HOH222 2.3 20.9 1.0 O B:HOH229 2.4 16.3 1.0 O A:HOH221 2.4 19.5 1.0 O B:HOH223 2.4 22.9 1.0 O A:HOH227 2.4 19.1 1.0 O B:HOH222 2.4 21.0 1.0 C4 A:U4 3.4 16.2 1.0 H41 B:C2 3.5 18.5 1.0 H61 B:A5 3.7 21.7 1.0 H5 A:U4 3.7 24.4 1.0 H62 A:A5 3.8 21.9 1.0 C5 A:U4 4.0 20.3 1.0 N4 B:C2 4.2 15.4 1.0 H61 A:A5 4.3 21.9 1.0 N6 A:A5 4.3 18.2 1.0 O B:HOH235 4.3 20.9 0.6 O B:HOH224 4.3 20.4 1.0 O A:HOH231 4.4 31.0 1.0 N6 B:A5 4.4 18.1 1.0 O6 A:G3 4.5 14.8 1.0 N7 A:G3 4.5 16.6 1.0 O A:HOH228 4.5 27.9 1.0 H42 B:C2 4.5 18.5 1.0 O A:HOH220 4.6 26.4 1.0 O A:HOH226 4.6 23.5 1.0 O B:HOH217 4.6 34.9 1.0 N3 A:U4 4.6 15.2 1.0 H62 B:A5 4.6 21.7 1.0 H5 B:C2 4.6 19.9 1.0 O6 B:G3 4.7 13.6 1.0 H3 A:U4 4.7 18.3 1.0 O B:HOH225 4.7 21.5 1.0 O4 B:U4 4.7 15.8 1.0 O A:HOH237 4.9 26.4 0.7 O A:HOH232 4.9 28.7 1.0

Calcium binding site 2 out of 2 in the Octameric Rna Duplex Soaked in Copper(II)Chloride


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Octameric Rna Duplex Soaked in Copper(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca103 b:18.1 occ:0.33 OP1 A:G7 2.4 18.6 1.0 O A:HOH216 2.4 23.7 1.0 P A:G7 3.6 18.4 1.0 O5' A:G7 3.7 19.4 1.0 H5' A:G7 3.7 23.8 1.0 C5' A:G7 4.2 19.9 1.0 O3' A:C6 4.5 15.8 1.0 O A:HOH209 4.5 31.4 1.0 OP2 A:G7 4.7 20.0 1.0 H4' A:G7 4.7 18.7 1.0 HO2' A:C6 4.8 20.2 1.0 H5'' A:G7 4.9 23.8 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