Sodium in PDB 5lr4: Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6, PDB code: 5lr4 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.26 / 1.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	49.870, 49.870, 123.735, 90.00, 90.00, 90.00
R / Rfree (%)	26.9 / 28.9

The structure of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Sodium atom in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 (pdb code 5lr4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6, PDB code: 5lr4:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:56.9 occ:1.00 HN41 A:CBV2 2.7 46.5 1.0 N4 A:CBV2 3.5 38.8 1.0 HN42 A:CBV2 3.8 46.5 1.0 H41 A:C3 3.9 35.4 1.0 O B:HOH113 3.9 37.0 1.0 BR A:CBV2 4.0 43.7 1.0 N4 A:C3 4.5 29.4 1.0 H42 A:C3 4.6 35.4 1.0 C4 A:CBV2 4.6 38.7 1.0 H1 A:G4 4.7 41.1 1.0 C5 A:CBV2 4.9 41.3 1.0

Sodium binding site 2 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:77.3 occ:1.00 O C:HOH207 2.6 45.3 1.0 O2' C:CBV2 3.0 35.9 1.0 HO2' C:CBV2 3.1 43.1 1.0 O D:HOH213 3.2 40.8 1.0 O4' C:C3 3.5 33.6 1.0 H2' C:CBV2 3.6 43.0 1.0 O2 C:CBV2 3.6 35.0 1.0 C2' C:CBV2 3.7 35.8 1.0 H1' C:CBV2 3.7 42.3 1.0 H4' C:C3 3.9 43.3 1.0 H5' C:C3 3.9 44.9 1.0 H1' C:C3 4.0 41.3 1.0 H22 D:G9 4.1 38.5 1.0 H21 D:G9 4.1 38.5 1.0 C4' C:C3 4.2 36.0 1.0 C1' C:CBV2 4.3 35.2 1.0 C1' C:C3 4.3 34.4 1.0 H4' A:C3 4.4 38.2 1.0 O C:HOH212 4.4 59.9 1.0 O C:HOH211 4.4 28.4 1.0 N2 D:G9 4.5 32.0 1.0 C5' C:C3 4.6 37.3 1.0 C2 C:CBV2 4.7 36.2 1.0 O2' A:C3 4.8 31.7 1.0 H1' D:C10 5.0 43.0 1.0

Sodium binding site 3 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:56.9 occ:1.00 HN42 C:CBV2 2.7 49.4 1.0 O D:HOH212 3.5 44.0 1.0 N4 C:CBV2 3.6 41.1 1.0 H41 C:C3 3.6 47.3 1.0 BR C:CBV2 3.8 48.5 1.0 HN41 C:CBV2 3.9 49.4 1.0 N4 C:C3 4.4 39.4 1.0 H1 C:G4 4.5 54.4 1.0 H42 C:C3 4.5 47.3 1.0 C4 C:CBV2 4.6 40.3 1.0 O6 C:G4 4.6 46.6 1.0 C5 C:CBV2 4.7 43.1 1.0 N1 C:G4 4.9 45.6 1.0

Sodium binding site 4 out of 4 in the Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rna Duplex Has Central Consecutive Ga Pairs Flanked By G-U Basepairs with A Methyl Group on the Adenine N6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:49.8 occ:1.00 H22 D:G1 2.6 28.1 1.0 H1' D:CBV2 2.8 42.1 1.0 N2 D:G1 3.4 23.4 1.0 H21 D:G1 3.7 28.1 1.0 C1' D:CBV2 3.8 35.1 1.0 O4' D:CBV2 3.9 33.4 1.0 C2 D:G1 4.4 22.4 1.0 O2' D:CBV2 4.4 38.9 1.0 N3 D:G1 4.5 26.7 1.0 O2 D:CBV2 4.5 34.7 1.0 N1 D:CBV2 4.6 34.2 1.0 C2' D:CBV2 4.8 38.4 1.0 H4' D:CBV2 4.8 43.6 1.0 C2 D:CBV2 4.9 34.2 1.0

L.Huang, S.Ashraf, J.Wang, D.M.Lilley. Control of Box C/D Snornp Assembly By N(6)-Methylation of Adenine. Embo Rep. V. 18 1631 2017.
ISSN: ESSN 1469-3178
PubMed: 28623187
DOI: 10.15252/EMBR.201743967