Magnesium in PDB 4nya: Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine

The structure of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine, PDB code: 4nya 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 / 2.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.730, 29.890, 95.430, 90.00, 93.94, 90.00
R / Rfree (%)	22.5 / 27.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine (pdb code 4nya). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine, PDB code: 4nya:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:58.4 occ:1.00 O3' A:C55 2.4 73.2 1.0 P A:A56 3.1 67.2 1.0 OP1 A:A56 3.1 67.9 1.0 O5' A:A56 3.1 63.8 1.0 O2' A:C55 3.5 81.9 1.0 C3' A:C55 3.6 79.8 1.0 C5' A:A56 4.0 55.0 1.0 OP2 A:C57 4.1 48.2 1.0 C4' A:C55 4.1 82.8 1.0 C2' A:C55 4.1 81.4 1.0 C5 A:C57 4.2 40.2 1.0 O5' A:C55 4.5 89.2 1.0 N4 A:C57 4.5 39.5 1.0 OP2 A:A56 4.5 65.8 1.0 C4 A:C57 4.9 41.9 1.0 C5' A:C55 5.0 85.7 1.0

Magnesium binding site 2 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:74.5 occ:1.00 OP1 A:C63 2.0 70.8 1.0 O3' A:U62 3.1 69.6 1.0 P A:C63 3.1 70.2 1.0 OP2 A:U64 3.4 65.8 1.0 C5' A:C63 3.9 64.6 1.0 O5' A:C63 3.9 68.1 1.0 O2' A:U62 3.9 71.9 1.0 P A:U64 4.2 65.6 1.0 O3' A:C63 4.3 64.4 1.0 OP2 A:C63 4.4 70.0 1.0 OP1 A:U64 4.5 65.8 1.0 C3' A:U62 4.5 68.8 1.0 C3' A:C63 4.6 63.7 1.0 C2' A:U62 4.8 69.6 1.0 C4' A:C63 4.8 63.8 1.0

Magnesium binding site 3 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:68.7 occ:1.00 OP1 A:C77 2.9 45.6 1.0 OP1 A:U79 3.0 60.0 1.0 OP2 A:C77 3.2 47.5 1.0 P A:C77 3.5 46.9 1.0 O3' A:G78 3.5 57.9 1.0 P A:U79 3.6 61.0 1.0 OP2 A:U79 3.8 58.4 1.0 C3' A:G78 4.3 53.0 1.0 O3' A:G76 4.7 46.2 1.0 O5' A:C77 4.7 47.5 1.0

Magnesium binding site 4 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:37.8 occ:1.00 O A:HOH201 2.3 46.2 1.0 OP1 A:G37 3.5 49.2 1.0 P A:G37 4.9 48.1 1.0

Magnesium binding site 5 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:57.2 occ:1.00 N7 A:G81 3.4 51.0 1.0 N7 A:G82 3.4 46.9 1.0 O6 A:G82 3.7 41.0 1.0 O6 A:G83 3.7 40.3 1.0 O6 A:G81 3.8 51.6 1.0 C5 A:G81 4.0 51.3 1.0 C6 A:G81 4.2 50.6 1.0 C5 A:G82 4.2 46.0 1.0 C6 A:G82 4.3 44.6 1.0 C8 A:G81 4.3 50.4 1.0 C6 A:G83 4.3 41.4 1.0 OP2 A:A80 4.3 74.0 1.0 C8 A:G82 4.5 47.7 1.0 OP2 A:G81 4.8 60.0 1.0 N1 A:G83 5.0 42.5 1.0

Magnesium binding site 6 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg106 b:62.7 occ:1.00 O2A A:GTP10 3.3 89.3 1.0 O2B A:GTP10 4.7 91.4 1.0 PA A:GTP10 4.7 89.2 1.0

Magnesium binding site 7 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg107 b:51.4 occ:1.00 O6 A:G60 2.6 41.5 1.0 O4 A:U59 3.1 40.9 1.0 O6 A:G78 3.1 38.8 1.0 O6 A:G72 3.1 62.2 1.0 C6 A:G60 3.7 37.5 1.0 C4 A:U59 3.8 40.7 1.0 C6 A:G78 3.9 40.0 1.0 N1 A:G78 3.9 41.4 1.0 C5 A:U59 3.9 41.3 1.0 C5 A:C58 4.1 42.5 1.0 N1 A:G60 4.2 36.9 1.0 C6 A:G72 4.3 65.8 1.0 N4 A:C58 4.3 42.1 1.0 C4 A:C58 4.4 42.6 1.0 OP2 A:C58 4.6 44.0 1.0 C6 A:C58 4.8 43.8 1.0 N6 A:A80 4.8 47.0 1.0 N7 A:G72 4.9 66.2 1.0 C5 A:G60 4.9 38.7 1.0 C5 A:G72 5.0 65.7 1.0

Magnesium binding site 8 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg108 b:41.4 occ:1.00 O2' A:C77 2.2 45.0 1.0 C2' A:C77 2.8 47.2 1.0 N2 A:G60 2.9 34.6 1.0 OP1 A:G78 2.9 50.9 1.0 O3' A:C77 3.4 48.5 1.0 C3' A:C77 3.7 48.2 1.0 P A:G78 3.7 51.4 1.0 C2 A:G60 3.9 37.6 1.0 N3 A:G60 4.1 38.5 1.0 N7 A:G78 4.1 43.6 1.0 N3 A:A80 4.2 52.1 1.0 C1' A:C77 4.2 47.4 1.0 C8 A:G78 4.2 44.2 1.0 C2 A:A80 4.4 51.1 1.0 C4 A:A80 4.5 51.6 1.0 OP2 A:G78 4.5 52.2 1.0 C4' A:C77 4.8 47.8 1.0 N1 A:A80 4.9 52.0 1.0 N9 A:A80 5.0 52.8 1.0 N1 A:C77 5.0 46.9 1.0

Magnesium binding site 9 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg109 b:40.9 occ:1.00 O2' A:G40 2.4 43.7 1.0 O3' A:G40 3.0 46.7 1.0 C2' A:G40 3.4 40.9 1.0 C3' A:G40 3.5 42.9 1.0 C4' A:G40 3.6 42.6 1.0 N7 A:A41 3.7 45.5 1.0 O6 A:G42 3.9 47.7 1.0 C8 A:A41 4.1 45.6 1.0 C1' A:G40 4.3 40.5 1.0 P A:A41 4.3 50.9 1.0 O4' A:G40 4.4 40.7 1.0 OP1 A:A41 4.4 50.5 1.0 O5' A:A41 4.7 50.2 1.0 C5' A:G40 4.7 44.2 1.0 C5 A:A41 4.8 45.3 1.0 N7 A:G42 4.8 43.6 1.0 C6 A:G42 4.9 44.5 1.0

Magnesium binding site 10 out of 15 in the Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the E. Coli Thim Riboswitch in Complex with 5- (Azidomethyl)-2-Methylpyrimidin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:76.3 occ:1.00 N2 B:G82 3.5 64.5 1.0 C1' B:C58 3.6 59.8 1.0 O4' B:C58 3.7 60.9 1.0 O2 B:C57 4.1 45.6 1.0 O2' B:C58 4.3 58.5 1.0 C5' B:G18 4.4 59.1 1.0 N1 B:C58 4.5 57.6 1.0 O2 B:C58 4.6 59.9 1.0 C2' B:C58 4.6 61.0 1.0 C4' B:C58 4.7 59.9 1.0 C2 B:G82 4.8 64.5 1.0 O2' B:C57 4.8 47.3 1.0 C2 B:C58 4.9 58.1 1.0 O2' B:G83 4.9 63.6 1.0 O4' B:G83 4.9 64.2 1.0 C4' B:G18 4.9 55.4 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