Manganese in PDB 4nyb: Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine, PDB code: 4nyb 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 / 3.10
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	65.243, 65.243, 103.269, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 24.9

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine (pdb code 4nyb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine, PDB code: 4nyb:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:0.2 occ:1.00 OP2 A:A80 3.5 0.8 1.0 OP2 A:G81 3.5 0.4 1.0 N7 A:G82 4.0 89.3 1.0 O6 A:G83 4.0 90.6 1.0 N7 A:G81 4.1 1.0 1.0 OP1 A:A80 4.2 0.1 1.0 P A:A80 4.4 0.6 1.0 OP2 A:U54 4.4 0.9 1.0 O6 A:G82 4.5 87.8 1.0 C8 A:G81 4.7 0.6 1.0 C6 A:G83 4.8 90.5 1.0 N7 A:A80 4.8 0.2 1.0 C8 A:G82 4.9 89.8 1.0 C5 A:G82 4.9 89.6 1.0 P A:G81 4.9 0.4 1.0 C8 A:A80 5.0 0.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn110 b:66.2 occ:1.00 OP2 A:U64 2.0 72.9 1.0 OP1 A:C63 2.3 75.6 1.0 O A:HOH203 2.5 37.2 1.0 OP2 A:C63 3.0 76.6 1.0 P A:C63 3.0 75.4 1.0 P A:U64 3.4 74.5 1.0 O5' A:C63 3.9 75.8 1.0 O3' A:C63 3.9 73.3 1.0 C3' A:C63 4.2 71.1 1.0 OP1 A:U64 4.2 73.0 1.0 O5' A:U64 4.5 74.0 1.0 O3' A:U62 4.5 76.3 1.0 O2' A:U62 4.6 83.9 1.0 C5' A:C63 4.9 72.5 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn112 b:0.3 occ:1.00 O6 A:G60 2.0 79.6 1.0 O6 A:G78 2.0 0.4 1.0 O6 A:G72 2.4 92.3 1.0 N1 A:G72 2.6 94.0 1.0 C6 A:G72 2.9 91.5 1.0 C6 A:G60 3.1 78.5 1.0 C6 A:G78 3.1 0.5 1.0 N1 A:G60 3.5 78.7 1.0 N1 A:G78 3.5 99.7 1.0 O4 A:U59 3.7 68.5 1.0 C2 A:G72 3.9 94.2 1.0 N1 A:A61 3.9 74.1 1.0 C2 A:A61 4.0 73.5 1.0 N3 A:C77 4.2 85.4 1.0 N2 A:G72 4.2 92.1 1.0 C5 A:G72 4.3 89.8 1.0 C5 A:G60 4.3 78.6 1.0 C5 A:G78 4.4 0.1 1.0 C4 A:U59 4.4 67.2 1.0 N4 A:C77 4.6 85.0 1.0 N6 A:A80 4.8 0.1 1.0 C2 A:G60 4.9 78.7 1.0 C4 A:C77 4.9 85.4 1.0 C2 A:G78 4.9 98.8 1.0 O2 A:C77 4.9 84.5 1.0 C5 A:U59 4.9 67.1 1.0 C2 A:C77 5.0 84.9 1.0 N3 A:G72 5.0 92.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine


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 (4- (1,2,3-Thiadiazol-4-Yl)Phenyl)Methanamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn114 b:84.6 occ:1.00 O A:HOH207 1.6 28.5 1.0 O A:HOH208 1.8 52.5 1.0 O A:HOH206 1.8 29.5 1.0 N7 A:G40 2.1 65.5 1.0 O A:HOH209 2.2 39.2 1.0 C8 A:G40 2.8 64.5 1.0 C5 A:G40 3.3 64.4 1.0 OP2 A:G40 3.8 59.8 1.0 O6 A:G40 4.0 62.7 1.0 C6 A:G40 4.0 62.9 1.0 N9 A:G40 4.1 63.5 1.0 C4 A:G40 4.4 64.6 1.0 OP2 A:U39 4.4 60.5 1.0 C5 A:U39 4.6 58.7 1.0 O5' A:G40 4.8 58.7 1.0 C6 A:U39 4.8 58.9 1.0 O A:HOH210 4.9 43.0 1.0 P A:G40 4.9 60.3 1.0 O5' A:U39 5.0 62.4 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