Manganese in PDB 3oxe: Crystal Structure of Glycine Riboswitch, MN2+ Soaked

The structure of Crystal Structure of Glycine Riboswitch, MN2+ Soaked, PDB code: 3oxe was solved by L.Huang, A.Serganov, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.708, 83.708, 198.958, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 21.9

The structure of Crystal Structure of Glycine Riboswitch, MN2+ Soaked also contains other interesting chemical elements:

Magnesium

(Mg)

10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked (pdb code 3oxe). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 32 binding sites of Manganese where determined in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked, PDB code: 3oxe:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:0.3 occ:1.00 OP2 A:G35 2.3 70.6 1.0 OP1 A:A34 2.3 62.2 1.0 O A:HOH161 2.4 27.4 1.0 P A:G35 3.6 71.4 1.0 P A:A34 3.8 61.7 1.0 OP1 A:G35 4.1 71.8 1.0 C4' A:A33 4.3 57.4 1.0 O5' A:A34 4.4 63.3 1.0 CA A:GLY89 4.4 70.4 1.0 O5' A:G35 4.5 73.0 1.0 OP1 A:A65 4.5 62.1 1.0 O3' A:A33 4.6 59.9 1.0 O2' A:A81 4.6 63.1 1.0 C5' A:A34 4.7 64.8 1.0 C5' A:A33 4.7 55.9 1.0 O3' A:A34 4.7 70.2 1.0 OP2 A:A34 4.8 62.2 1.0 C3' A:A33 4.9 58.1 1.0

Manganese binding site 2 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:88.4 occ:1.00 O A:HOH159 1.8 30.3 1.0 O A:HOH160 1.8 29.9 1.0 OP2 A:A33 2.0 52.4 1.0 OP2 A:C66 2.2 56.7 1.0 O A:HOH158 2.3 36.4 1.0 O2' A:G32 2.3 55.2 1.0 C2' A:G32 3.1 54.2 1.0 OXT A:GLY89 3.2 69.3 1.0 P A:A33 3.3 52.5 1.0 C3' A:G32 3.5 53.1 1.0 P A:C66 3.6 56.4 1.0 O3' A:G32 3.7 52.6 1.0 O4 A:U69 4.2 64.9 1.0 OP1 A:C66 4.3 56.0 1.0 OP1 A:A33 4.3 52.1 1.0 O5' A:A33 4.3 54.0 1.0 C5' A:A33 4.3 55.9 1.0 C A:GLY89 4.3 69.8 1.0 O3' A:A65 4.4 58.4 1.0 O4 A:U67 4.5 59.1 1.0 C1' A:G32 4.5 54.6 1.0 C4' A:A65 4.5 59.7 1.0 O5' A:C66 4.6 56.0 1.0 C5 A:U67 4.6 58.0 1.0 O A:GLY89 4.7 69.9 1.0 C5' A:A65 4.8 60.2 1.0 C4 A:U67 4.9 58.7 1.0 C4' A:G32 5.0 53.4 1.0

Manganese binding site 3 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:0.9 occ:1.00 OP2 A:A75 2.4 57.6 1.0 OP1 A:A22 2.6 61.5 1.0 P A:A22 3.8 61.8 1.0 O3' A:A21 3.8 60.4 1.0 P A:A75 3.9 56.6 1.0 OP2 A:C74 4.3 61.9 1.0 N7 A:A75 4.4 57.5 1.0 O5' A:A75 4.5 56.6 1.0 OP1 A:C74 4.6 60.7 1.0 C8 A:A75 4.7 57.2 1.0 O3' A:C74 4.7 57.3 1.0 C5' A:A22 4.7 62.8 1.0 P A:C74 4.7 61.3 1.0 O5' A:A22 4.8 62.6 1.0 C3' A:C74 4.8 57.8 1.0 OP1 A:A75 4.8 56.4 1.0 O5' A:C74 4.8 60.5 1.0 OP2 A:A22 4.9 62.3 1.0

Manganese binding site 4 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.8 occ:1.00 OP1 A:A75 2.1 56.4 1.0 OP2 A:A76 2.5 58.2 1.0 OP1 A:C74 3.1 60.7 1.0 P A:A75 3.4 56.6 1.0 N6 A:A78 3.8 63.0 1.0 P A:A76 3.9 58.2 1.0 C5' A:C74 4.1 58.8 1.0 N7 A:A77 4.1 65.1 1.0 OP2 A:A75 4.1 57.6 1.0 N6 A:A77 4.1 66.5 1.0 O5' A:A75 4.2 56.6 1.0 N7 A:A76 4.3 62.8 1.0 P A:C74 4.4 61.3 1.0 O5' A:A76 4.5 59.3 1.0 O3' A:C74 4.6 57.3 1.0 O5' A:C74 4.6 60.5 1.0 C6 A:A78 4.6 63.4 1.0 C8 A:A76 4.7 62.2 1.0 OP1 A:A76 4.8 58.1 1.0 O3' A:A75 4.8 57.2 1.0 C5' A:A75 4.8 56.3 1.0 C5 A:A77 4.9 65.7 1.0 C3' A:A75 4.9 56.5 1.0 C4' A:C74 4.9 58.0 1.0 C6 A:A77 4.9 66.5 1.0

Manganese binding site 5 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.7 occ:1.00 OP2 A:A71 2.4 74.1 1.0 OP2 A:C70 2.5 73.2 1.0 P A:C70 3.5 73.7 1.0 O3' A:U69 3.6 71.6 1.0 P A:A71 3.8 75.1 1.0 O5' A:C70 3.9 74.6 1.0 O6 A:G72 3.9 61.9 1.0 N7 A:G72 4.2 64.0 1.0 O2' A:U69 4.2 68.7 1.0 N7 A:A71 4.4 67.7 1.0 OP1 A:A71 4.4 76.4 1.0 O5' A:A71 4.4 73.8 1.0 C8 A:A71 4.7 68.9 1.0 C6 A:G72 4.8 61.6 1.0 C3' A:U69 4.8 70.3 1.0 O3' A:C70 4.9 76.6 1.0 C5 A:G72 4.9 62.6 1.0 OP1 A:C70 4.9 73.8 1.0

Manganese binding site 6 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:0.5 occ:1.00 OP1 A:A33 2.9 52.1 1.0 OP1 A:C66 3.8 56.0 1.0 P A:A33 4.3 52.5 1.0 OP1 B:A33 4.6 50.9 1.0 OP2 A:A33 4.9 52.4 1.0

Manganese binding site 7 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:0.1 occ:1.00 OP2 A:U67 4.3 54.3 1.0 OP1 A:U67 4.3 54.1 1.0 OP2 A:G32 4.4 54.6 1.0 OP1 B:G10 4.4 53.4 1.0 OP2 A:C68 4.5 58.7 1.0 P A:U67 4.8 54.1 1.0

Manganese binding site 8 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn108 b:0.2 occ:1.00 N7 A:GDP1 2.6 0.8 1.0 C8 A:GDP1 3.2 0.9 1.0 O3A A:GDP1 3.4 0.4 1.0 C5 A:GDP1 3.8 0.7 1.0 O2A A:GDP1 4.0 0.8 1.0 O6 A:GDP1 4.1 0.9 1.0 PA A:GDP1 4.3 0.7 1.0 O1B A:GDP1 4.3 0.2 1.0 C6 A:GDP1 4.4 0.2 1.0 PB A:GDP1 4.5 0.0 1.0 N9 A:GDP1 4.5 0.1 1.0 C4 A:GDP1 4.8 0.2 1.0 O5' A:GDP1 4.9 0.8 1.0

Manganese binding site 9 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn109 b:0.5 occ:1.00 O6 A:G8 2.3 64.7 1.0 O6 A:G80 2.8 63.3 1.0 C6 A:G8 3.3 63.3 1.0 O A:HOH164 3.5 16.8 1.0 C6 A:G80 3.8 62.5 1.0 C5 A:G8 4.0 62.1 1.0 N7 A:G8 4.1 61.6 1.0 N7 A:G80 4.1 63.7 1.0 OP2 A:G79 4.3 65.0 1.0 N1 A:G8 4.3 63.3 1.0 C5 A:G80 4.3 62.8 1.0 MN A:MN110 4.8 0.2 1.0

Manganese binding site 10 out of 32 in the Crystal Structure of Glycine Riboswitch, MN2+ Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Glycine Riboswitch, MN2+ Soaked within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn110 b:0.2 occ:1.00 OP2 A:A78 2.2 65.0 1.0 P A:A78 3.5 65.3 1.0 O5' A:A78 3.9 65.0 1.0 N7 A:G79 4.1 62.7 1.0 O6 A:G80 4.1 63.3 1.0 N7 A:A78 4.2 63.1 1.0 O6 A:G79 4.2 60.6 1.0 C8 A:A78 4.3 63.6 1.0 OP1 A:A78 4.4 65.8 1.0 O5' A:A77 4.7 64.3 1.0 O3' A:A77 4.7 64.9 1.0 OP1 A:A77 4.7 64.2 1.0 OP2 A:A77 4.8 63.7 1.0 MN A:MN109 4.8 0.5 1.0 C6 A:G80 4.8 62.5 1.0 C3' A:A77 4.8 64.7 1.0 C5 A:G79 4.9 62.2 1.0 C6 A:G79 4.9 61.3 1.0 P A:A77 4.9 63.8 1.0

L.Huang, A.Serganov, D.J.Patel. Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026