Magnesium 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:

Potassium	(K)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot, PDB code: 1l2x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg29 b:31.5 occ:1.00 OP1 A:G2 2.0 22.5 1.0 O1B A:GTP1 2.0 30.8 1.0 O A:HOH30 2.1 32.9 1.0 O A:HOH33 2.1 34.7 1.0 O A:HOH32 2.1 30.0 1.0 O A:HOH31 2.1 33.4 1.0 PB A:GTP1 3.3 30.4 1.0 P A:G2 3.4 19.9 1.0 O3B A:GTP1 3.6 33.1 1.0 O2A A:GTP1 4.0 28.7 1.0 O5' A:G2 4.1 18.0 1.0 C5' A:G2 4.1 17.3 1.0 O3A A:GTP1 4.2 27.4 1.0 O3' A:GTP1 4.3 17.1 0.5 O3' A:GTP1 4.3 18.2 0.5 O2B A:GTP1 4.4 31.2 1.0 O5' A:GTP1 4.4 23.1 0.5 O5' A:GTP1 4.4 23.8 0.5 O A:HOH85 4.4 25.0 1.0 OP2 A:G2 4.4 22.9 1.0 C3' A:GTP1 4.5 16.5 0.5 PA A:GTP1 4.5 28.1 1.0 C3' A:GTP1 4.5 18.3 0.5 C5' A:GTP1 4.8 20.5 0.5 C5' A:GTP1 5.0 21.9 0.5

Magnesium binding site 2 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg34 b:24.3 occ:1.00 O A:HOH36 2.0 23.9 1.0 OP2 A:G19 2.1 15.1 1.0 O A:HOH37 2.1 15.9 0.5 O A:HOH35 2.1 12.1 0.5 O A:HOH37 2.1 15.8 0.5 P A:G19 3.4 14.1 1.0 C5' A:G19 3.9 13.6 1.0 O5' A:G19 3.9 14.7 1.0 OP1 A:G19 4.1 18.3 1.0 O3' A:G18 4.5 11.9 1.0 O A:HOH218 4.7 22.8 0.5 O A:HOH73 4.9 29.3 1.0

Magnesium binding site 3 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg38 b:36.9 occ:1.00 O A:HOH39 2.0 25.2 1.0 O A:HOH43 2.1 37.2 1.0 O A:HOH42 2.1 44.4 1.0 O A:HOH44 2.1 39.4 1.0 O A:HOH41 2.1 30.2 1.0 O A:HOH40 2.2 23.8 1.0 OP2 A:G27 3.8 29.9 1.0 N7 A:G27 3.9 19.1 1.0 O A:HOH112 3.9 25.8 1.0 O A:HOH75 4.1 22.1 1.0 C8 A:G27 4.4 20.6 1.0 N7 A:G28 4.4 16.4 1.0 O A:HOH196 4.5 25.9 0.5 O A:HOH134 4.5 40.1 0.5 OP2 A:C26 4.8 33.9 1.0 C5 A:G27 4.9 18.4 1.0

Magnesium binding site 4 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg45 b:41.4 occ:1.00 O A:HOH47 1.9 15.0 0.5 O A:HOH46 2.1 23.9 1.0 O A:HOH47 2.1 26.1 0.5 O A:HOH49 2.1 27.6 1.0 O A:HOH51 2.1 38.6 1.0 O A:HOH48 2.1 29.3 0.5 O A:HOH50 2.1 40.2 1.0 O A:HOH48 3.2 20.4 0.5 O A:HOH78 4.0 26.2 1.0 O6 A:G7 4.1 17.4 1.0 O6 A:G6 4.1 14.8 1.0 O A:HOH149 4.2 36.8 0.5 N7 A:G6 4.2 14.9 1.0 O A:HOH213 4.3 27.1 0.5 O A:HOH154 4.4 21.5 0.6 O A:HOH190 4.4 27.5 0.5 O A:HOH123 4.5 31.4 1.0 O A:HOH67 4.6 27.0 1.0 O A:HOH70 4.6 17.9 1.0 O A:HOH213 4.8 32.9 0.5 O A:HOH135 4.8 30.8 0.5 C6 A:G6 4.8 14.7 1.0 C5 A:G6 4.8 14.3 1.0 N4 A:C14 4.9 19.2 1.0

Magnesium binding site 5 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg52 b:53.3 occ:1.00 O A:HOH56 2.0 34.1 0.5 O A:HOH58 2.1 69.8 0.5 O A:HOH53 2.1 37.2 1.0 O A:HOH57 2.2 31.5 0.5 O A:HOH54 2.2 24.8 1.0 O A:HOH55 2.3 46.7 0.5 O A:HOH56 2.9 23.7 0.5 O A:HOH72 3.8 26.0 1.0 O A:HOH140 3.8 37.2 1.0 O6 A:G4 3.9 14.2 1.0 O A:HOH114 4.2 24.2 1.0 O A:HOH123 4.2 31.4 1.0 O A:HOH103 4.2 22.5 1.0 N7 A:G4 4.6 14.1 1.0 N4 A:C3 4.7 12.9 1.0 C6 A:G4 4.8 12.3 1.0 C5 A:C3 5.0 12.2 1.0 O A:HOH217 5.0 38.0 0.5

Magnesium binding site 6 out of 6 in the Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Atomic Resolution Crystal Structure of A Viral Rna Pseudoknot within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg59 b:32.4 occ:1.00 O2B A:GTP1 1.8 31.2 1.0 O A:HOH60 1.9 25.5 0.5 O A:HOH35 2.0 15.8 0.5 O3G A:GTP1 2.3 47.9 1.0 PB A:GTP1 2.9 30.4 1.0 O3B A:GTP1 3.3 33.1 1.0 PG A:GTP1 3.3 24.7 0.1 O3A A:GTP1 3.6 27.4 1.0 O A:HOH182 3.7 24.1 0.5 O1B A:GTP1 4.2 30.8 1.0 O2G A:GTP1 4.2 32.5 0.1 N7 A:GTP1 4.2 16.4 0.5 O1G A:GTP1 4.5 37.6 0.1 O6 A:GTP1 4.8 15.5 0.5 N7 A:GTP1 4.9 13.3 0.5 C5 A:GTP1 4.9 13.8 0.5 C8 A:GTP1 5.0 17.3 0.5

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