Magnesium in PDB 6ufg: Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh

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

Resolution Low / High (Å)	77.21 / 2.93
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	77.209, 77.209, 172.754, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.5

The structure of Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh also contains other interesting chemical elements:

Potassium

(K)

4 atoms

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh (pdb code 6ufg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh, PDB code: 6ufg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:0.9 occ:1.00 OP2 B:U12 3.2 0.9 1.0 OP2 B:U8 3.4 91.0 1.0 OP2 B:A9 4.1 0.7 1.0 OP1 B:A9 4.3 0.2 1.0 P B:U8 4.4 0.6 1.0 C5 B:U12 4.5 0.6 1.0 OP1 B:U8 4.5 0.8 1.0 P B:U12 4.7 0.1 1.0 P B:A9 4.7 0.3 1.0 OP2 B:C11 4.8 0.5 1.0 C5 B:C13 4.8 0.9 1.0

Magnesium binding site 2 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:0.8 occ:1.00 N7 B:G69 3.6 83.1 1.0 O6 B:G70 3.8 82.8 1.0 O6 B:G69 3.8 90.8 1.0 C5 B:G69 4.1 81.4 1.0 C6 B:G69 4.2 78.7 1.0 C8 B:G69 4.6 85.5 1.0 N7 B:G70 4.6 85.5 1.0 C6 B:G70 4.7 81.9 1.0

Magnesium binding site 3 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:78.1 occ:1.00 OP1 B:A77 2.4 95.4 1.0 O4 A:U160 2.8 79.2 1.0 O6 A:G132 3.0 77.4 1.0 N4 A:C131 3.2 0.5 1.0 P B:A77 3.7 78.6 1.0 O6 A:G96 3.7 83.6 1.0 C5' B:A77 3.7 72.4 1.0 C4 A:U160 3.9 71.9 1.0 O6 A:G159 4.0 77.2 1.0 O3' B:C76 4.1 91.5 1.0 O5' B:A77 4.2 71.1 1.0 C6 A:G132 4.2 84.2 1.0 N3 A:U160 4.2 64.6 1.0 C4 A:C131 4.3 87.1 1.0 C6 A:G96 4.8 74.0 1.0 N7 A:G132 4.8 83.0 1.0 N4 A:C133 4.9 70.2 1.0 C5 A:G132 4.9 85.7 1.0 OP2 B:A77 4.9 68.0 1.0 C6 A:G159 5.0 69.1 1.0 C5 A:C131 5.0 80.3 1.0

Magnesium binding site 4 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:96.3 occ:1.00 N7 A:G70 3.6 0.3 1.0 OP2 A:C82 3.6 0.1 1.0 O6 A:G70 3.9 0.5 1.0 O6 A:G84 3.9 0.5 1.0 C5 A:G70 4.2 0.8 1.0 C6 A:G70 4.4 0.6 1.0 C8 A:G70 4.5 0.3 1.0 P A:C82 4.7 0.0 1.0 N7 A:G84 4.7 0.5 1.0 N2 A:G69 4.7 98.2 1.0 N7 A:A83 4.8 0.1 1.0 OP2 A:A83 4.8 0.6 1.0 C2 A:G69 4.9 97.1 1.0 C6 A:G84 4.9 0.3 1.0 N3 A:G69 4.9 97.7 1.0 N6 A:A83 5.0 0.9 1.0

Magnesium binding site 5 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:61.4 occ:1.00 O6 A:G135 2.5 85.3 1.0 O4 A:U157 2.8 68.6 1.0 O6 A:G134 3.0 77.8 1.0 O6 A:G156 3.2 80.9 1.0 C6 A:G135 3.6 71.3 1.0 N4 A:C136 3.7 91.2 1.0 C6 A:G134 3.7 71.7 1.0 C4 A:U157 3.8 66.1 1.0 N3 A:U157 4.0 73.8 1.0 N4 A:C158 4.1 71.6 1.0 C6 A:G156 4.2 67.3 1.0 N7 A:G135 4.3 83.4 1.0 C5 A:G135 4.3 69.6 1.0 C5 A:G134 4.5 59.5 1.0 N1 A:G134 4.5 64.4 1.0 C4 A:C136 4.6 67.7 1.0 N7 A:G134 4.7 77.6 1.0 N1 A:G135 4.7 75.2 1.0 C4 A:C158 5.0 60.8 1.0 N1 A:G156 5.0 64.4 1.0

Magnesium binding site 6 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:95.0 occ:1.00 OP2 A:G94 2.4 80.9 1.0 P A:G94 3.9 97.0 1.0 O5' A:G96 4.1 99.0 1.0 OP1 A:G96 4.3 0.7 1.0 OP1 A:G94 4.5 0.2 1.0 O3' A:C93 4.6 0.6 1.0 C4' A:G96 4.7 0.2 1.0 O4' A:G96 4.8 0.2 1.0 O5' A:G94 4.9 88.1 1.0 C5' A:G94 4.9 58.6 1.0 P A:G96 4.9 0.2 1.0

Magnesium binding site 7 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:88.3 occ:1.00 OP1 A:G94 2.0 0.2 1.0 P A:G94 3.5 97.0 1.0 OP1 A:C93 3.6 0.5 1.0 C3' A:C93 4.1 0.3 1.0 O5' A:G94 4.1 88.1 1.0 O3' A:C93 4.2 0.6 1.0 OP2 A:G94 4.5 80.9 1.0 OP2 A:C161 4.6 64.8 1.0 P A:C93 4.8 0.5 1.0 O2' A:C161 4.8 95.5 1.0 O3' A:C161 4.9 75.2 1.0 C4' A:C93 4.9 0.9 1.0 C5' A:C93 5.0 0.8 1.0

Magnesium binding site 8 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:83.6 occ:1.00 O6 A:G121 3.3 64.0 1.0 N7 A:G121 3.4 61.9 1.0 O6 A:G122 3.7 76.4 1.0 C6 A:G121 3.8 65.4 1.0 C5 A:G121 3.9 53.8 1.0 N7 A:G122 4.1 56.8 1.0 C6 A:G122 4.5 62.2 1.0 C8 A:G121 4.5 55.6 1.0 N4 A:C120 4.6 77.4 1.0 C5 A:G122 4.6 52.5 1.0 OP1 A:G159 4.6 78.8 1.0

Magnesium binding site 9 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:93.7 occ:1.00 O6 A:G127 3.7 84.7 1.0 O6 A:G126 4.1 88.5 1.0 N7 A:G126 4.1 81.7 1.0 N7 A:G127 4.4 79.0 1.0 C6 A:G126 4.7 72.2 1.0 C6 A:G127 4.7 76.7 1.0 C5 A:G126 4.7 79.4 1.0 O4 A:U125 4.7 62.4 1.0 C5 A:G127 5.0 68.8 1.0

Magnesium binding site 10 out of 11 in the Co-Crystal Structure of M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh


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 M. Tuberculosis Iles T-Box in Complex with Trna-3'-Oh within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:0.8 occ:1.00 OP1 A:A90 2.9 0.7 1.0 OP1 A:C88 3.1 0.6 1.0 N7 A:G91 3.8 96.5 1.0 P A:A90 4.2 0.9 1.0 OP2 A:G91 4.2 0.5 1.0 O5' A:A90 4.3 0.1 1.0 P A:C88 4.4 0.4 1.0 C8 A:G91 4.5 80.9 1.0 OP2 A:C88 4.8 0.7 1.0 C5 A:G91 4.9 86.7 1.0 O6 A:G91 4.9 82.3 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