Magnesium in PDB 3loa: Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna

The structure of Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna, PDB code: 3loa was solved by S.Dibrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.73 / 2.30
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	57.455, 57.455, 58.433, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 23.1

The structure of Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna (pdb code 3loa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna, PDB code: 3loa:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:64.7 occ:1.00 N4 A:C1404 3.4 59.9 1.0 C4 A:C1404 4.4 62.4 1.0 C5 A:C1404 4.5 54.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:70.4 occ:1.00 O2' B:A1500 2.9 50.2 1.0 O4' B:C1501 3.2 53.5 1.0 C2' B:A1500 3.4 47.4 1.0 C4' B:C1501 3.7 54.0 1.0 C5' B:C1501 3.8 55.3 1.0 N3 B:A1500 4.1 56.2 1.0 C1' B:C1501 4.3 53.7 1.0 C1' B:A1500 4.4 51.5 1.0 O5' B:C1501 4.5 60.6 1.0 C3' B:A1500 4.7 50.4 1.0 O3' B:A1500 4.8 48.5 1.0 C2 B:A1500 4.9 48.4 1.0 C4 B:A1500 4.9 48.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure Analysis of the Rna Construct with Two Adjacent Ligand Binding Sites of Helix H44 in 16S Ribosomal Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1507 b:57.2 occ:1.00 N7 B:G1488 3.0 57.9 1.0 O B:HOH9 3.1 55.6 1.0 O B:HOH20 3.2 53.8 1.0 BR B:5BU1487 3.8 74.2 1.0 C8 B:G1488 3.9 59.3 1.0 O B:HOH15 3.9 54.1 1.0 O4 B:5BU1487 4.1 51.2 1.0 C5 B:G1488 4.1 51.4 1.0 O6 B:G1488 4.1 50.6 1.0 C5 B:5BU1487 4.2 61.4 1.0 C4 B:5BU1487 4.3 54.8 1.0 C6 B:G1488 4.5 52.2 1.0 C6 B:5BU1487 5.0 61.5 1.0

S.M.Dibrov, J.Parsons, T.Hermann. A Model For the Study of Ligand Binding to the Ribosomal Rna Helix H44. Nucleic Acids Res. V. 38 4458 2010.
ISSN: ISSN 0305-1048
PubMed: 20215440
DOI: 10.1093/NAR/GKQ159