Manganese in PDB 7tzt: Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37)

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37), PDB code: 7tzt 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)	47.00 / 2.96
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	61.018, 61.018, 102.855, 90, 90, 120
R / Rfree (%)	24.3 / 25.7

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37) (pdb code 7tzt). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37), PDB code: 7tzt:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37)


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 N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:95.1 occ:1.00 N7 A:A41 2.0 70.3 1.0 C5 A:A41 2.9 64.1 1.0 C8 A:A41 3.1 74.1 1.0 N6 A:A41 3.1 71.8 1.0 C6 A:A41 3.4 66.0 1.0 C4 A:A41 4.1 66.2 1.0 N9 A:A41 4.2 70.9 1.0 N1 A:A41 4.7 60.5 1.0 O6 A:G42 4.8 60.8 1.0 OP1 A:C57 5.0 89.4 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37)


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 N1, N1-Dimethyl-N2-(Quinoxalin-6-Ylmethyl)Ethane-1,2-Diamine (Linked Compound 37) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:106.7 occ:1.00 N7 A:G40 2.0 98.0 1.0 O6 A:G40 2.8 107.9 1.0 C5 A:G40 2.8 97.0 1.0 C6 A:G40 3.1 102.2 1.0 C8 A:G40 3.2 100.3 1.0 C4 A:G40 4.1 93.2 1.0 OP2 A:U39 4.2 109.8 1.0 N9 A:G40 4.3 94.8 1.0 N1 A:G40 4.5 101.0 1.0 OP2 A:G40 4.8 94.8 1.0 C5 A:U39 4.9 98.1 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