Sodium in PDB 1l2x: Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot

The structure of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot, PDB code: 1l2x was solved by M.Egli, G.Minasov, L.Su, A.Rich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.25
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	30.160, 30.160, 140.278, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 20.7

The structure of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Potassium	(K)	1 atom

The binding sites of Sodium atom in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot (pdb code 1l2x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot, PDB code: 1l2x:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Na61 b:29.4 occ:1.00 O A:HOH92 2.7 24.4 1.0 OP2 A:A21 2.7 14.8 1.0 N3 A:G16 2.8 13.5 1.0 O2' A:G16 2.9 17.4 1.0 N7 A:A21 3.1 26.8 1.0 C8 A:A21 3.3 26.5 1.0 C2' A:G16 3.4 15.3 1.0 C1' A:G16 3.5 13.8 1.0 N2 A:G16 3.6 13.9 1.0 O A:HOH125 3.6 21.9 1.0 C2 A:G16 3.6 13.8 1.0 O4' A:C17 3.8 14.9 1.0 C4 A:G16 3.8 13.4 1.0 P A:A21 3.9 15.7 1.0 N4 A:C22 4.0 38.1 0.5 O5' A:A21 4.0 18.1 1.0 N9 A:G16 4.1 13.7 1.0 C1' A:C17 4.1 14.3 1.0 N2 A:G6 4.4 15.5 1.0 O3' A:A20 4.4 15.0 1.0 C5 A:A21 4.4 26.9 1.0 N9 A:A21 4.6 25.3 1.0 C5 A:C22 4.6 30.9 0.5 O2' A:C17 4.6 16.9 1.0 N3 A:G6 4.6 14.5 1.0 C4' A:C17 4.6 16.3 1.0 C4 A:C22 4.7 29.2 0.5 N4 A:C22 4.7 28.9 0.5 O4' A:G16 4.8 16.7 1.0 O A:HOH118 4.8 36.1 1.0 C2 A:G6 4.8 13.6 1.0 C3' A:G16 4.8 15.7 1.0 N1 A:G16 5.0 12.5 1.0

Sodium binding site 2 out of 3 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Na62 b:23.6 occ:1.00 O2' A:C3 2.7 15.4 1.0 O2 A:C3 2.7 13.5 1.0 O A:HOH101 2.8 30.1 1.0 C2' A:C3 3.2 13.1 1.0 O4' A:G4 3.4 14.9 1.0 C1' A:C3 3.5 13.4 1.0 C2 A:C3 3.8 12.9 1.0 O A:HOH77 4.1 19.6 1.0 N2 A:G18 4.2 11.9 1.0 N1 A:C3 4.2 12.8 1.0 C4' A:G4 4.2 16.3 1.0 C1' A:G4 4.2 13.7 1.0 O A:HOH216 4.4 36.6 0.5 C5' A:G4 4.6 17.9 1.0 O4' A:C3 4.7 14.4 1.0 C3' A:C3 4.7 13.6 1.0 O A:HOH94 5.0 29.8 0.5

Sodium binding site 3 out of 3 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Na63 b:26.0 occ:1.00 O2' A:C5 2.6 20.2 1.0 OP1 A:A21 2.7 16.9 1.0 O4' A:G6 3.0 17.5 1.0 C4' A:G6 3.3 16.3 1.0 C5' A:G6 3.6 16.9 1.0 C2' A:C5 3.6 16.4 1.0 C3' A:A20 3.7 14.1 1.0 O A:HOH108 3.8 36.7 1.0 C8 A:A20 3.8 15.5 1.0 O A:HOH165 3.8 41.0 1.0 C2' A:A20 3.9 13.5 1.0 P A:A21 4.0 15.7 1.0 C1' A:G6 4.2 14.8 1.0 O3' A:A20 4.3 15.0 1.0 N7 A:A20 4.4 15.5 1.0 N9 A:A20 4.4 14.4 1.0 O5' A:G6 4.6 18.3 1.0 C1' A:C5 4.6 15.1 1.0 O3' A:C5 4.6 19.1 1.0 C3' A:C5 4.7 18.0 1.0 C1' A:A20 4.7 13.4 1.0 O2 A:C5 4.7 13.7 1.0 O2' A:G6 4.7 18.2 1.0 C3' A:G6 4.8 17.6 1.0 OP2 A:A21 4.9 14.8 1.0 C2' A:G6 4.9 15.7 1.0 C4' A:A20 5.0 13.9 1.0

M.Egli, G.Minasov, L.Su, A.Rich. Metal Ions and Flexibility in A Viral Rna Pseudoknot at Atomic Resolution. Proc.Natl.Acad.Sci.Usa V. 99 4302 2002.
ISSN: ISSN 0027-8424
PubMed: 11904368
DOI: 10.1073/PNAS.062055599