Strontium in PDB 4o41: Amide Linked Rna

The structure of Amide Linked Rna, PDB code: 4o41 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)	28.00 / 1.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	22.360, 34.330, 43.300, 110.03, 94.24, 95.83
R / Rfree (%)	14.7 / 21.2

The binding sites of Strontium atom in the Amide Linked Rna (pdb code 4o41). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 2 binding sites of Strontium where determined in the Amide Linked Rna, PDB code: 4o41:
Jump to Strontium binding site number: 1; 2;

Strontium binding site 1 out of 2 in the Amide Linked Rna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Amide Linked Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr701 b:13.1 occ:0.68 O A:HOH840 2.5 27.3 1.0 O3' A:C113 2.6 16.2 1.0 O A:HOH866 2.6 21.2 1.0 O A:HOH817 2.6 18.2 1.0 O2' A:C113 2.6 14.2 1.0 O A:HOH815 2.6 19.3 1.0 C3' A:C113 3.5 13.9 1.0 C2' A:C113 3.5 13.0 1.0 C4' A:C113 4.2 13.9 1.0 O A:HOH852 4.5 25.1 1.0 O A:HOH827 4.6 23.1 1.0 C1' A:C113 4.9 12.9 1.0

Strontium binding site 2 out of 2 in the Amide Linked Rna


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Amide Linked Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Sr702 b:13.6 occ:0.57 O A:HOH835 2.1 39.0 1.0 O A:HOH805 2.4 18.9 1.0 O A:HOH814 2.5 17.9 1.0 O A:HOH811 2.6 17.5 1.0 O A:HOH821 2.6 20.1 1.0 O6 A:G110 2.8 9.9 1.0 N7 A:G110 2.8 12.1 1.0 O A:HOH838 2.8 23.9 1.0 C6 A:G110 3.4 9.2 1.0 C5 A:G110 3.4 11.4 1.0 N7 A:G109 3.4 13.4 1.0 C8 A:G110 3.9 12.6 1.0 C5 A:G109 4.1 12.2 1.0 C8 A:G109 4.1 13.5 1.0 O6 A:G109 4.2 11.6 1.0 OP2 A:G109 4.4 14.9 1.0 C6 A:G109 4.4 11.3 1.0 N4 A:C111 4.6 15.1 1.0 O A:HOH848 4.7 22.1 1.0 C4 A:G110 4.7 11.7 1.0 O A:HOH854 4.7 26.6 1.0 O A:HOH849 4.7 20.3 0.5 N1 A:G110 4.7 10.7 1.0 O B:HOH354 4.8 18.9 1.0 OP2 A:C108 5.0 12.6 1.0 N9 A:G110 5.0 12.1 1.0

D.Mutisya, C.Selvam, B.D.Lunstad, P.S.Pallan, A.Haas, D.Leake, M.Egli, E.Rozners. Amides Are Excellent Mimics of Phosphate Internucleoside Linkages and Are Well Tolerated in Short Interfering Rnas. Nucleic Acids Res. V. 42 6542 2014.
ISSN: ISSN 0305-1048
PubMed: 24813446
DOI: 10.1093/NAR/GKU235