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Bromine in PDB 5d8t: Rna Octamer Containing (S)-5' Methyl, 2'-F U.

Protein crystallography data

The structure of Rna Octamer Containing (S)-5' Methyl, 2'-F U., PDB code: 5d8t was solved by J.M.Harp, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.24 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 31.172, 31.172, 84.325, 90.00, 90.00, 90.00
R / Rfree (%) 12 / 15.7

Other elements in 5d8t:

The structure of Rna Octamer Containing (S)-5' Methyl, 2'-F U. also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Cobalt (Co) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Rna Octamer Containing (S)-5' Methyl, 2'-F U. (pdb code 5d8t). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Rna Octamer Containing (S)-5' Methyl, 2'-F U., PDB code: 5d8t:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 5d8t

Go back to Bromine Binding Sites List in 5d8t
Bromine binding site 1 out of 2 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Rna Octamer Containing (S)-5' Methyl, 2'-F U. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1

b:9.7
occ:1.00
BR A:CBV1 0.0 9.7 1.0
C5 A:CBV1 1.9 7.2 1.0
HN41 A:CBV1 2.7 7.0 1.0
C6 A:CBV1 2.8 7.2 1.0
H6 A:CBV1 2.9 7.3 1.0
C4 A:CBV1 2.9 6.9 1.0
HN32 B:NCO102 3.0 17.8 1.0
N4 A:CBV1 3.1 7.4 1.0
HN13 B:NCO101 3.2 13.0 1.0
HN11 B:NCO101 3.3 12.9 1.0
HN12 B:NCO101 3.4 12.7 1.0
N1 B:NCO101 3.5 13.3 1.0
HN33 B:NCO102 3.7 16.1 1.0
N3 B:NCO102 3.8 18.1 1.0
O B:HOH215 3.8 31.9 1.0
O B:HOH247 3.9 20.3 1.0
O A:HOH215 4.0 15.2 1.0
HN42 A:CBV1 4.0 6.9 1.0
N1 A:CBV1 4.1 7.8 1.0
HN31 B:NCO102 4.1 18.8 1.0
N3 A:CBV1 4.2 7.2 1.0
O5' A:CBV1 4.2 10.6 1.0
HN13 B:NCO102 4.4 15.4 1.0
O A:HOH202 4.4 24.0 1.0
C2 A:CBV1 4.7 8.1 1.0
HN63 B:NCO102 4.9 24.0 1.0
H3' A:CBV1 5.0 8.2 1.0

Bromine binding site 2 out of 2 in 5d8t

Go back to Bromine Binding Sites List in 5d8t
Bromine binding site 2 out of 2 in the Rna Octamer Containing (S)-5' Methyl, 2'-F U.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Rna Octamer Containing (S)-5' Methyl, 2'-F U. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1

b:9.9
occ:1.00
BR B:CBV1 0.0 9.9 1.0
C5 B:CBV1 1.9 8.4 1.0
HN41 B:CBV1 2.7 7.6 1.0
C6 B:CBV1 2.8 8.2 1.0
C4 B:CBV1 2.9 7.7 1.0
H6 B:CBV1 2.9 8.7 1.0
HN22 A:NCO101 3.1 14.9 1.0
N4 B:CBV1 3.1 8.0 1.0
O B:HOH252 3.7 23.3 1.0
O B:HOH219 3.7 12.7 1.0
O B:HOH249 4.0 16.7 1.0
N2 A:NCO101 4.0 14.6 1.0
O B:HOH232 4.0 18.0 1.0
O B:HOH222 4.0 13.9 1.0
HN41 A:NCO101 4.0 15.3 1.0
HN21 A:NCO101 4.0 14.3 1.0
HN42 B:CBV1 4.0 7.8 1.0
N1 B:CBV1 4.1 8.6 1.0
N3 B:CBV1 4.1 8.0 1.0
O5' B:CBV1 4.3 14.3 1.0
HN42 A:NCO101 4.3 14.4 1.0
HN23 A:NCO101 4.4 15.9 1.0
N4 A:NCO101 4.6 14.8 1.0
C2 B:CBV1 4.7 8.8 1.0
H4' B:CBV1 4.8 10.7 1.0
O B:HOH245 4.9 22.1 1.0
H3' B:CBV1 5.0 10.8 1.0

Reference:

A.V.Kel In, I.Zlatev, J.Harp, M.Jayaraman, A.Bisbe, J.O Shea, N.Taneja, R.M.Manoharan, S.Khan, K.Charisse, M.A.Maier, M.Egli, K.G.Rajeev, M.Manoharan. Structural Basis of Duplex Thermodynamic Stability and Enhanced Nuclease Resistance of 5'-C-Methyl Pyrimidine-Modified Oligonucleotides. J.Org.Chem. V. 81 2261 2016.
ISSN: ISSN 0022-3263
PubMed: 26940174
DOI: 10.1021/ACS.JOC.5B02375
Page generated: Wed Jul 10 23:23:33 2024

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