Magnesium in PDB 6ufh: Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate

The structure of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate, PDB code: 6ufh was solved by R.A.Battaglia, J.A.Grigg, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.68 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.276, 61.430, 122.520, 90.00, 93.97, 90.00
R / Rfree (%)	22 / 26.9

The binding sites of Magnesium atom in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate (pdb code 6ufh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate, PDB code: 6ufh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.0 occ:1.00 OP2 B:U8 3.2 0.3 1.0 OP2 B:U12 3.6 0.2 1.0 OP1 B:U8 3.9 0.2 1.0 OP2 B:A9 3.9 0.9 1.0 P B:U8 3.9 0.3 1.0 OP1 B:A9 4.0 1.0 1.0 OP2 B:C11 4.1 0.8 1.0 P B:A9 4.5 0.2 1.0 O5' B:U8 4.8 0.0 1.0 OP1 B:C11 4.8 0.7 1.0 P B:C11 4.8 0.8 1.0

Magnesium binding site 2 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.3 occ:1.00 OP2 B:A14 2.6 0.2 1.0 OP1 B:A7 2.9 0.4 1.0 O3' B:U6 2.9 0.1 1.0 P B:A7 3.3 0.6 1.0 O5' B:A7 3.3 0.6 1.0 P B:A14 3.8 0.8 1.0 O2' B:U6 3.9 0.9 1.0 OP1 B:A14 4.1 0.7 1.0 C3' B:U6 4.1 0.8 1.0 C5' B:A7 4.2 0.6 1.0 O3' B:C13 4.4 0.5 1.0 O4 B:U8 4.5 0.8 1.0 C2' B:U6 4.6 0.2 1.0 C4' B:U6 4.6 0.4 1.0 C3' B:C13 4.7 0.9 1.0 OP2 B:A7 4.7 0.2 1.0 C5 B:U8 4.7 0.6 1.0 C5' B:C13 5.0 0.7 1.0

Magnesium binding site 3 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:95.4 occ:1.00 OP1 A:A119 2.1 85.5 1.0 P A:A119 3.5 96.5 1.0 O5' A:A119 4.0 0.7 1.0 OP2 A:A119 4.3 71.7 1.0 OP1 A:G120 4.4 99.0 1.0 C5' A:A119 4.5 0.4 1.0 O5' A:G120 4.5 56.1 1.0 O3' A:A118 4.6 69.2 1.0

Magnesium binding site 4 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:88.1 occ:1.00 OP1 A:A118 2.7 0.4 1.0 P A:A118 4.1 0.1 1.0 O3' A:C117 4.6 81.9 1.0 O5' A:A118 5.0 0.1 1.0

Magnesium binding site 5 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:75.4 occ:1.00 OP1 B:A2377 2.4 0.1 1.0 O6 A:G160 3.2 84.2 1.0 O4 A:U161 3.3 72.9 1.0 O6 A:G133 3.3 69.0 1.0 N4 A:C132 3.4 70.4 1.0 P B:A2377 3.9 81.6 1.0 N4 A:C134 4.0 75.1 1.0 N3 A:U161 4.1 51.5 1.0 C4 A:U161 4.1 64.0 1.0 C5' B:A2377 4.1 85.8 1.0 C6 A:G160 4.3 64.3 1.0 C6 A:G133 4.3 88.2 1.0 C4 A:C132 4.3 82.9 1.0 N7 A:G133 4.5 63.3 1.0 O5' B:A2377 4.5 68.3 1.0 O3' B:C76 4.5 0.5 1.0 O6 A:G97 4.8 77.1 1.0 C5 A:G133 4.8 76.7 1.0 C5 A:C132 4.9 92.0 1.0 OP2 B:A2377 4.9 80.0 1.0

Magnesium binding site 6 out of 6 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-2'3'Cyclic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:0.3 occ:1.00 N7 A:G41 4.0 0.0 1.0 N7 A:G42 4.3 0.2 1.0 C5 A:G41 4.5 0.8 1.0 OP2 A:G41 4.6 0.9 1.0 C8 A:G41 4.6 0.6 1.0 O6 A:G41 4.6 0.3 1.0 O6 A:G42 4.6 0.8 1.0 OP2 A:C40 4.8 0.7 1.0 C6 A:G41 4.8 0.5 1.0

R.A.Battaglia, J.C.Grigg, A.Ke. Structural Basis For Trna Decoding and Aminoacylation Sensing By T-Box Riboregulators. Nat.Struct.Mol.Biol. 2019.
ISSN: ESSN 1545-9985
PubMed: 31740853
DOI: 10.1038/S41594-019-0327-6