Magnesium in PDB 4mgn: Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna

The structure of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna, PDB code: 4mgn was solved by J.C.Grigg, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.29 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.838, 205.182, 161.421, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 27.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna (pdb code 4mgn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 18 binding sites of Magnesium where determined in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna, PDB code: 4mgn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:0.2 occ:1.00 O6 A:G58 2.5 87.7 1.0 C6 A:G58 3.5 63.5 1.0 N7 A:G58 3.8 78.1 1.0 OP1 A:G60 4.0 0.5 1.0 C5 A:G58 4.0 57.4 1.0 N1 A:G58 4.8 49.8 1.0 MG A:MG104 4.8 0.7 1.0 C5 A:U57 4.8 81.6 1.0

Magnesium binding site 2 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:68.9 occ:1.00 O6 A:G55 2.5 84.0 1.0 O2 B:C55 2.8 66.0 1.0 O6 A:G56 3.0 97.9 1.0 O6 A:G62 3.0 64.9 1.0 N7 A:G55 3.2 74.7 1.0 C6 A:G55 3.3 77.5 1.0 C2 B:C55 3.6 71.1 1.0 C5 A:G55 3.6 63.7 1.0 C6 A:G56 3.6 83.5 1.0 C6 A:G62 4.0 80.5 1.0 N7 A:G62 4.0 76.9 1.0 N3 B:C55 4.1 63.3 1.0 N2 B:G18 4.2 86.1 1.0 N1 A:G56 4.3 69.6 1.0 C5 A:G56 4.3 80.5 1.0 C5 A:G62 4.4 65.3 1.0 N1 B:C55 4.4 61.9 1.0 C8 A:G55 4.4 92.9 1.0 C1' B:C55 4.6 60.6 1.0 N7 A:G56 4.6 91.0 1.0 N1 A:G55 4.7 70.3 1.0 O2' A:A61 4.8 87.2 1.0 N1 B:G18 4.8 65.0 1.0 C2 B:G18 4.9 78.3 1.0 C4 A:G55 4.9 63.6 1.0 O2' A:C54 5.0 95.8 1.0

Magnesium binding site 3 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:75.7 occ:1.00 O3' A:C47 2.5 0.2 1.0 OP1 A:C48 3.0 0.8 1.0 P A:C48 3.1 0.8 1.0 N2 A:G60 3.2 0.9 1.0 C5' A:C47 3.2 0.1 1.0 N1 A:G59 3.3 45.5 1.0 C4' A:C47 3.3 1.0 1.0 C3' A:C47 3.3 0.7 1.0 OP2 A:C48 3.6 0.1 1.0 C2 A:G60 3.7 89.1 1.0 N2 A:G59 3.9 81.8 1.0 O6 A:G59 4.0 48.9 1.0 O5' A:C47 4.0 0.5 1.0 N3 A:G60 4.1 51.9 1.0 C2 A:G59 4.1 76.6 1.0 C6 A:G59 4.1 52.8 1.0 N1 A:G60 4.5 53.2 1.0 O5' A:C48 4.6 0.3 1.0 C2' A:C47 4.6 0.6 1.0 OP1 A:C47 4.7 94.2 1.0 O2' A:C47 4.7 0.6 1.0 O4' A:C47 4.8 0.3 1.0 P A:C47 4.9 0.1 1.0

Magnesium binding site 4 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:0.7 occ:1.00 OP2 A:G58 2.5 80.9 1.0 N7 A:G58 3.4 78.1 1.0 C8 A:G58 3.5 85.6 1.0 P A:G58 3.7 0.3 1.0 O5' A:G58 3.8 78.4 1.0 OP2 A:U57 4.0 95.8 1.0 O5' A:U57 4.3 59.0 1.0 C3' A:U57 4.5 0.4 1.0 P A:U57 4.6 1.0 1.0 O3' A:U57 4.6 0.9 1.0 C5 A:G58 4.8 57.4 1.0 MG A:MG101 4.8 0.2 1.0 OP1 A:G58 4.8 0.2 1.0 N9 A:G58 4.8 83.2 1.0 OP1 A:U57 4.9 0.5 1.0

Magnesium binding site 5 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:88.3 occ:1.00 OP2 A:C89 3.8 0.9 1.0 OP1 A:C89 4.4 0.6 1.0 N7 A:A13 4.4 0.4 1.0 O4 A:U14 4.5 0.3 1.0 P A:C89 4.6 0.8 1.0 OP1 A:G88 4.7 0.5 1.0 OP2 A:A13 4.8 0.3 1.0

Magnesium binding site 6 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:83.5 occ:1.00 O2B B:GTP1 3.3 0.3 1.0 O3B B:GTP1 3.4 0.7 1.0 O1B B:GTP1 3.5 0.9 1.0 PB B:GTP1 3.6 0.9 1.0 O1G B:GTP1 4.2 0.6 1.0 PG B:GTP1 4.3 0.2 1.0 O2G B:GTP1 4.8 0.2 1.0

Magnesium binding site 7 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:69.5 occ:1.00 O6 B:G4 3.0 82.5 1.0 O6 B:G3 3.7 88.5 1.0 C6 B:G4 4.1 77.4 1.0 N4 B:C68 4.2 0.5 1.0 O4 B:U67 4.2 94.3 1.0 N7 B:G3 4.4 72.8 1.0 C6 B:G3 4.4 82.4 1.0 N7 B:G4 4.6 75.7 1.0 N6 B:A5 4.7 88.1 1.0 C5 B:G3 4.7 79.4 1.0 C5 B:G4 4.8 71.8 1.0 N4 B:C2 4.9 88.3 1.0

Magnesium binding site 8 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:81.7 occ:1.00 OP1 B:U8 3.4 71.5 1.0 OP2 B:U12 3.5 86.0 1.0 OP2 B:A9 3.5 99.0 1.0 OP2 B:U8 3.5 69.1 1.0 P B:U8 4.0 99.4 1.0 OP2 B:U11 4.0 0.3 1.0 OP1 B:A9 4.2 0.8 1.0 P B:A9 4.4 0.6 1.0 P B:U11 4.7 0.7 1.0 O5' B:U11 4.7 84.5 1.0 OP1 B:U11 4.8 0.2 1.0 O5' B:U8 4.8 0.7 1.0 C5' B:A9 4.9 86.2 1.0 P B:U12 5.0 0.6 1.0

Magnesium binding site 9 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:0.2 occ:1.00 O6 B:G42 3.3 0.4 1.0 O6 B:G41 3.7 0.8 1.0 N4 B:C26 4.2 0.8 1.0 C6 B:G42 4.2 0.3 1.0 C6 B:G41 4.4 0.6 1.0 N7 B:G41 4.6 0.5 1.0 N7 B:G42 4.7 0.2 1.0 C5 B:G41 4.8 0.3 1.0 C5 B:G42 4.8 0.6 1.0

Magnesium binding site 10 out of 18 in the Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Co-Crystal Structure of the G. Kaustophilus Glyqs T Box Riboswitch Stem I in Complex with Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:97.9 occ:1.00 O6 C:G58 2.2 96.8 1.0 C6 C:G58 3.4 0.6 1.0 O2 C:C54 3.9 91.3 1.0 C5 C:G58 4.2 0.8 1.0 O4 C:U57 4.3 0.1 1.0 N7 C:G58 4.3 0.4 1.0 N1 C:G58 4.4 97.5 1.0 OP1 C:G60 4.6 95.8 1.0 C5 C:U57 4.8 89.4 1.0 C4 C:U57 4.9 92.7 1.0 C2 C:C54 5.0 84.0 1.0

J.C.Grigg, A.Ke. Structural Determinants For Geometry and Information Decoding of Trna By T Box Leader Rna. Structure V. 21 2025 2013.
ISSN: ISSN 0969-2126
PubMed: 24095061
DOI: 10.1016/J.STR.2013.09.001