Manganese in PDB 4nyd: Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine, PDB code: 4nyd 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)	50.00 / 2.90
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	65.436, 65.436, 101.110, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 25.7

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Manganese atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine (pdb code 4nyd). 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 Hypoxanthine, PDB code: 4nyd:
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 Hypoxanthine


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 Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:60.8 occ:1.00 OP2 A:U64 2.2 70.1 1.0 OP1 A:C63 2.3 70.3 1.0 P A:C63 3.2 68.7 1.0 OP2 A:C63 3.2 70.1 1.0 P A:U64 3.4 70.7 1.0 O3' A:C63 3.8 68.3 1.0 C3' A:C63 4.3 63.5 1.0 OP1 A:U64 4.3 66.6 1.0 O5' A:C63 4.3 67.9 1.0 O3' A:U62 4.4 69.2 1.0 O5' A:U64 4.6 70.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine


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 Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn108 b:0.8 occ:1.00 OP2 A:A80 2.8 0.6 1.0 N7 A:G81 3.7 88.9 1.0 OP2 A:G81 3.8 92.3 1.0 P A:A80 3.9 0.2 1.0 OP1 A:A80 4.1 0.3 1.0 N7 A:G82 4.3 84.0 1.0 O6 A:G83 4.4 85.6 1.0 C8 A:G81 4.4 90.1 1.0 N7 A:A80 4.6 89.0 1.0 C8 A:A80 4.7 91.4 1.0 C5 A:G81 4.7 88.5 1.0 O6 A:G81 4.7 87.3 1.0 O3' A:U79 4.8 0.3 1.0 C3' A:A80 5.0 95.8 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine


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 Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn110 b:50.5 occ:1.00 O A:HOH206 2.1 45.3 1.0 O A:HOH208 2.1 43.9 1.0 N7 A:G40 2.3 61.6 1.0 O A:HOH207 3.1 53.5 1.0 O6 A:G40 3.2 63.0 1.0 C5 A:G40 3.2 61.2 1.0 C8 A:G40 3.4 61.8 1.0 C6 A:G40 3.5 61.6 1.0 C4 A:G40 4.4 60.3 1.0 OP2 A:G40 4.5 56.9 1.0 N9 A:G40 4.5 60.4 1.0 OP2 A:U39 4.7 57.9 1.0 N1 A:G40 4.9 59.7 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with Hypoxanthine


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 Hypoxanthine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn111 b:80.7 occ:1.00 O6 A:G78 2.0 96.7 1.0 O6 A:G72 2.1 90.6 1.0 O6 A:G60 2.2 75.3 1.0 C6 A:G72 3.0 88.9 1.0 C6 A:G78 3.1 95.0 1.0 C6 A:G60 3.2 74.1 1.0 N1 A:G72 3.5 90.8 1.0 N1 A:G60 3.6 73.9 1.0 N1 A:G78 3.6 94.9 1.0 N3 A:C77 3.9 78.2 1.0 O4 A:U59 4.1 69.3 1.0 C2 A:A61 4.1 72.9 1.0 N1 A:A61 4.1 74.6 1.0 C5 A:G72 4.2 86.9 1.0 C5 A:G78 4.4 95.3 1.0 N4 A:C77 4.4 77.6 1.0 C5 A:G60 4.5 74.2 1.0 C4 A:C77 4.6 77.9 1.0 O2 A:C77 4.7 81.0 1.0 C2 A:C77 4.8 79.4 1.0 C2 A:G72 4.8 90.3 1.0 O6 A:G76 4.8 84.2 1.0 C2 A:G60 4.9 73.5 1.0 N7 A:G72 4.9 85.3 1.0 C4 A:U59 4.9 69.9 1.0 C2 A:G78 4.9 94.4 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