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Strontium in PDB 4o41: Amide Linked Rna

Protein crystallography data

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

Strontium Binding Sites:

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 4o41

Go back to Strontium Binding Sites List in 4o41
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 4o41

Go back to Strontium Binding Sites List in 4o41
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

Reference:

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
Page generated: Wed Dec 16 02:24:05 2020

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