Manganese in PDB 4nyc: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine, PDB code: 4nyc was solved by K.D.Warner, P.Homan, K.M.Weeks, A.G.Smith, C.Abell, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.15
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	65.122, 65.122, 101.975, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 26.4

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine also contains other interesting chemical elements:

Magnesium

(Mg)

11 atoms

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine (pdb code 4nyc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine, PDB code: 4nyc:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine


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 the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:92.5 occ:1.00 OP1 A:C63 2.1 95.4 1.0 OP2 A:U64 2.2 96.8 1.0 P A:U64 3.6 95.8 1.0 P A:C63 3.6 97.3 1.0 OP1 A:U64 4.1 95.2 1.0 OP2 A:C63 4.3 96.0 1.0 O3' A:C63 4.4 97.0 1.0 O5' A:C63 4.4 96.9 1.0 O3' A:U62 4.5 98.5 1.0 O5' A:U64 4.7 95.0 1.0 C3' A:C63 4.9 96.9 1.0

Manganese binding site 2 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine


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 the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.8 occ:1.00 N7 A:A41 2.3 73.8 1.0 O A:HOH203 3.1 65.1 1.0 C8 A:A41 3.2 73.3 1.0 O A:HOH201 3.4 57.5 1.0 C5 A:A41 3.5 72.8 1.0 N6 A:A41 3.8 69.7 1.0 C6 A:A41 4.1 71.4 1.0 O6 A:G42 4.2 75.2 1.0 O2' A:G40 4.3 72.8 1.0 N9 A:A41 4.4 73.8 1.0 C4 A:A41 4.6 72.9 1.0 O3' A:G40 4.7 74.9 1.0 C6 A:G42 4.9 77.2 1.0 OP1 A:A41 4.9 72.4 1.0

Manganese binding site 3 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine


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 the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:72.0 occ:1.00 O A:HOH202 1.9 42.1 1.0 O A:HOH205 2.4 51.7 1.0 N7 A:G40 2.4 78.4 1.0 C8 A:G40 3.3 76.9 1.0 C5 A:G40 3.5 78.8 1.0 O6 A:G40 3.8 76.5 1.0 C6 A:G40 4.0 78.4 1.0 O A:HOH204 4.2 59.4 1.0 N9 A:G40 4.5 77.4 1.0 OP2 A:U39 4.6 76.7 1.0 OP2 A:G40 4.6 75.8 1.0 C4 A:G40 4.6 79.1 1.0 C5 A:U39 4.8 74.7 1.0

Manganese binding site 4 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine


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 the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn109 b:0.8 occ:1.00 OP1 A:A2391 2.6 93.9 1.0 P A:A2391 3.9 94.1 1.0 C2' A:A2391 4.2 0.8 1.0 O3' A:C90 4.4 88.8 1.0 O5' A:A2391 4.4 96.6 1.0 O2' A:A2391 4.6 0.8 1.0 C8 A:A2391 4.6 0.5 1.0 C3' A:A2391 4.9 0.3 1.0

Manganese binding site 5 out of 5 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine


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 the E. Coli Thim Riboswitch in Complex with Thieno[2,3-B]Pyrazin-7-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn110 b:95.2 occ:1.00 N1 A:G72 2.1 0.6 1.0 O6 A:G60 2.3 91.9 1.0 O6 A:G78 2.4 0.7 1.0 C6 A:G72 2.9 0.7 1.0 O6 A:G72 2.9 0.8 1.0 C2 A:G72 3.1 0.5 1.0 N2 A:G72 3.2 0.1 1.0 C6 A:G60 3.3 90.8 1.0 C6 A:G78 3.4 0.7 1.0 N1 A:G78 3.6 0.5 1.0 N1 A:G60 3.6 90.2 1.0 O4 A:U59 3.7 93.0 1.0 N1 A:A61 3.9 97.9 1.0 C2 A:A61 4.0 97.1 1.0 C5 A:G72 4.2 0.3 1.0 N3 A:C77 4.3 98.9 1.0 N3 A:G72 4.3 0.7 1.0 C5 A:G60 4.5 90.9 1.0 N4 A:C77 4.6 98.4 1.0 C4 A:U59 4.6 92.8 1.0 MG A:MG112 4.7 77.8 1.0 C4 A:G72 4.7 0.6 1.0 C5 A:G78 4.7 0.2 1.0 C2 A:G78 4.9 0.9 1.0 C4 A:C77 4.9 99.4 1.0 C2 A:G60 5.0 88.7 1.0

K.D.Warner, P.Homan, K.M.Weeks, A.G.Smith, C.Abell, A.R.Ferre-D'amare. Validating Fragment-Based Drug Discovery For Biological Rnas: Lead Fragments Bind and Remodel the Tpp Riboswitch Specifically. Chem.Biol. V. 21 591 2014.
ISSN: ISSN 1074-5521
PubMed: 24768306
DOI: 10.1016/J.CHEMBIOL.2014.03.007