Calcium in PDB 4u3l: Octameric Rna Duplex Co-Crystallized in Calcium(II)Chloride

The structure of Octameric Rna Duplex Co-Crystallized in Calcium(II)Chloride, PDB code: 4u3l 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)	32.31 / 1.48
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	47.671, 47.671, 51.885, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 18.8

The binding sites of Calcium atom in the Octameric Rna Duplex Co-Crystallized in Calcium(II)Chloride (pdb code 4u3l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Octameric Rna Duplex Co-Crystallized in Calcium(II)Chloride, PDB code: 4u3l:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Octameric Rna Duplex Co-Crystallized in Calcium(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 Co-Crystallized in Calcium(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:19.4 occ:1.00 O B:HOH220 2.3 18.4 1.0 O B:HOH219 2.4 23.6 1.0 O4 A:U4 2.4 18.1 1.0 O A:HOH215 2.4 20.4 1.0 O A:HOH214 2.4 21.5 1.0 O A:HOH212 2.4 21.8 1.0 O B:HOH216 2.5 21.6 1.0 C4 A:U4 3.5 18.9 1.0 C5 A:U4 4.1 17.4 1.0 O A:HOH221 4.1 30.5 1.0 N4 B:C2 4.1 18.0 1.0 O A:HOH216 4.3 26.5 1.0 O B:HOH227 4.3 26.8 1.0 N6 A:A5 4.3 19.1 1.0 N6 B:A5 4.3 18.6 1.0 O A:HOH222 4.4 28.5 1.0 O B:HOH217 4.4 20.9 1.0 O6 A:G3 4.6 17.9 1.0 N7 A:G3 4.6 19.1 1.0 O6 B:G3 4.6 15.8 1.0 N3 A:U4 4.6 17.1 1.0 O B:HOH222 4.7 25.9 1.0 O A:HOH220 4.7 26.2 1.0 O A:HOH213 4.7 21.7 1.0 O4 B:U4 4.7 18.4 1.0 O B:HOH202 4.8 29.3 1.0 C4 B:C2 5.0 16.3 1.0

Calcium binding site 2 out of 3 in the Octameric Rna Duplex Co-Crystallized in Calcium(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 Co-Crystallized in Calcium(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca102 b:18.4 occ:0.33 OP1 A:G7 2.3 21.1 1.0 O A:HOH208 2.5 25.8 1.0 P A:G7 3.6 18.9 1.0 O5' A:G7 3.8 18.2 1.0 C5' A:G7 4.4 17.5 1.0 O3' A:C6 4.5 17.9 1.0 OP2 A:G7 4.7 19.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Octameric Rna Duplex Co-Crystallized in Calcium(II)Chloride within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:21.9 occ:0.15 O2' B:A5 2.9 22.5 1.0 O B:HOH208 3.2 24.0 0.3 O3' B:A5 3.3 22.1 1.0 C5' B:C6 3.8 21.6 1.0 C2' B:A5 4.0 20.9 1.0 C3' B:A5 4.0 20.1 1.0 OP1 B:C6 4.2 24.9 1.0 C4' B:A5 4.3 21.6 1.0 P B:C6 4.3 23.4 1.0 O5' B:C6 4.4 21.5 1.0 C4' B:C6 4.7 22.4 1.0 O4' B:C6 4.8 19.2 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