Manganese in PDB 7tzu: Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)

The structure of Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38), PDB code: 7tzu was solved by A.Nuthanakanti, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.55 / 2.87
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.702, 61.702, 102.789, 90, 90, 120
R / Rfree (%)	22.9 / 27

The structure of Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) (pdb code 7tzu). 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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38), PDB code: 7tzu:
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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:117.4 occ:1.00 O6 A:G78 1.9 124.5 1.0 N1 A:G72 2.1 112.1 1.0 O6 A:G60 2.3 102.4 1.0 O6 A:G72 2.3 104.7 1.0 O A:HOH201 2.4 111.6 1.0 C6 A:G72 2.5 105.6 1.0 C6 A:G78 2.9 124.5 1.0 N1 A:G78 3.1 121.8 1.0 C2 A:G72 3.3 109.6 1.0 C6 A:G60 3.3 102.0 1.0 N2 A:G72 3.7 115.8 1.0 N1 A:G60 3.7 101.8 1.0 C5 A:G72 3.9 99.7 1.0 O4 A:U59 3.9 86.4 1.0 C2 A:A61 4.0 116.3 1.0 N1 A:A61 4.0 117.7 1.0 C5 A:G78 4.2 124.8 1.0 N3 A:G72 4.4 99.5 1.0 H10 A:KWL101 4.5 112.9 1.0 C2 A:G78 4.5 122.2 1.0 N4 A:C77 4.5 126.4 1.0 C4 A:G72 4.5 99.5 1.0 C5 A:G60 4.6 99.3 1.0 C4 A:U59 4.7 82.8 1.0 N6 A:A80 5.0 101.0 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:75.8 occ:1.00 N7 A:A41 2.3 44.0 1.0 O A:HOH202 2.3 48.1 1.0 N6 A:A41 2.5 59.0 1.0 C5 A:A41 2.9 44.0 1.0 C6 A:A41 3.0 52.7 1.0 C8 A:A41 3.5 52.6 1.0 C4 A:A41 4.2 44.9 1.0 N1 A:A41 4.3 53.2 1.0 N9 A:A41 4.5 49.3 1.0 O6 A:G42 4.5 48.8 1.0 OP1 A:C57 4.8 77.9 1.0 O3' A:A56 4.8 70.7 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn106 b:69.9 occ:1.00 N7 A:G40 2.3 64.7 1.0 C8 A:G40 3.2 69.0 1.0 C5 A:G40 3.4 69.7 1.0 O6 A:G40 3.7 74.1 1.0 C6 A:G40 3.9 76.0 1.0 OP2 A:G40 4.3 70.9 1.0 N9 A:G40 4.4 62.4 1.0 C4 A:G40 4.5 62.2 1.0 C5 A:U39 4.7 72.6 1.0 OP2 A:U39 4.7 81.2 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38)


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 Bound to 1-(4- (Piperazin-1-Yl)Pyridin-3-Yl)-N-(Quinoxalin-6-Ylmethyl)Methanamine (Linked Compound 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn107 b:145.7 occ:1.00 OP1 A:A69 2.2 114.8 1.0 P A:A69 3.4 114.2 1.0 OP2 A:A69 3.9 112.3 1.0 C5' A:A69 4.3 109.4 1.0 O5' A:A69 4.4 108.5 1.0 O3' A:U68 4.5 111.8 1.0 O4' A:A69 4.7 112.0 1.0 C8 A:A69 4.8 106.1 1.0

M.J.Zeller, O.Favorov, K.Li, A.Nuthanakanti, D.Hussein, A.Michaud, D.A.Lafontaine, S.Busan, A.Serganov, J.Aube, K.M.Weeks. Shape-Enabled Fragment-Based Ligand Discovery For Rna. Proc.Natl.Acad.Sci.Usa V. 119 60119 2022.
ISSN: ESSN 1091-6490
PubMed: 35561226
DOI: 10.1073/PNAS.2122660119