Manganese in PDB 3diy: Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak, PDB code: 3diy was solved by A.A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.193, 78.662, 140.522, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 23.7

The structure of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak also contains other interesting chemical elements:

Potassium	(K)	1 atom
Sodium	(Na)	8 atoms

The binding sites of Manganese atom in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak (pdb code 3diy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak, PDB code: 3diy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn250 b:46.5 occ:0.80 OP2 A:G46 2.7 29.5 1.0 P A:G46 3.9 29.7 1.0 O5' A:G46 4.2 28.8 1.0 N7 A:G46 4.4 27.0 1.0 C8 A:G46 4.5 26.5 1.0 OP2 A:G45 4.5 28.7 1.0 OP2 A:G43 4.6 25.6 1.0 N7 A:G43 4.6 23.4 1.0 C5 A:G43 4.6 23.5 1.0 O6 A:G43 4.7 23.5 1.0 C6 A:G43 4.7 23.6 1.0 OP1 A:G46 4.7 29.3 1.0

Manganese binding site 2 out of 2 in the Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystallization of the Thermotoga Maritima Lysine Riboswitch Bound to Lysine, MN2+ Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn251 b:51.8 occ:0.50 N7 A:GDP1 2.4 42.0 1.0 O1A A:GDP1 2.9 59.0 1.0 C8 A:GDP1 3.0 42.1 1.0 C5 A:GDP1 3.7 41.9 1.0 PA A:GDP1 4.1 61.1 1.0 O5' A:GDP1 4.1 55.7 1.0 O6 A:GDP1 4.3 41.9 1.0 N9 A:GDP1 4.4 42.6 1.0 C6 A:GDP1 4.4 41.8 1.0 C4 A:GDP1 4.7 42.1 1.0 O3A A:GDP1 4.8 73.2 1.0

A.Serganov, L.Huang, D.J.Patel. Structural Insights Into Amino Acid Binding and Gene Control By A Lysine Riboswitch. Nature V. 455 1263 2008.
ISSN: ISSN 0028-0836
PubMed: 18784651
DOI: 10.1038/NATURE07326