Magnesium in PDB 4lck: Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna

The structure of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna, PDB code: 4lck was solved by J.Zhang, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.42 / 3.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	100.382, 108.474, 266.886, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.1

The structure of Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna also contains other interesting chemical elements:

Strontium

(Sr)

79 atoms

The binding sites of Magnesium atom in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna (pdb code 4lck). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna, PDB code: 4lck:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg223 b:77.5 occ:1.00 MG C:MG224 4.2 0.2 1.0 N7 C:G20 4.4 0.8 1.0

Magnesium binding site 2 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg224 b:0.2 occ:1.00 O6 C:G20 2.3 0.5 1.0 C6 C:G20 3.3 0.2 1.0 N7 C:G20 3.7 0.8 1.0 C5 C:G20 3.9 0.9 1.0 MG C:MG223 4.2 77.5 1.0 N1 C:G20 4.6 0.1 1.0 C8 C:G20 5.0 0.0 1.0

Magnesium binding site 3 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg225 b:0.4 occ:1.00 N6 C:A29 2.3 0.4 1.0 O6 C:G28 3.1 0.3 1.0 C6 C:A29 3.2 0.1 1.0 N1 C:A29 3.5 0.2 1.0 C6 C:G28 4.2 0.8 1.0 C5 C:A29 4.4 0.9 1.0 N7 C:G28 4.6 0.8 1.0 O6 C:G27 4.7 0.7 1.0 C2 C:A29 4.8 0.8 1.0 C5 C:G28 4.8 0.8 1.0

Magnesium binding site 4 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg116 b:81.1 occ:1.00 O4' E:A20 2.3 0.0 1.0 C1' E:A20 2.5 0.9 1.0 C4' E:A20 3.0 0.8 1.0 O3' E:A20 3.3 94.7 1.0 N3 E:A20 3.5 0.8 1.0 O4' E:G21 3.5 0.6 1.0 N9 E:A20 3.5 0.6 1.0 C3' E:A20 3.5 0.1 1.0 C2' E:A20 3.6 0.5 1.0 N1 E:A14 3.7 87.5 1.0 C8 E:G21 3.8 82.8 1.0 C4 E:A20 3.8 0.6 1.0 C1' E:G21 4.1 98.5 1.0 N9 E:G21 4.1 88.5 1.0 N2 E:G15 4.2 91.8 1.0 C5' E:A20 4.3 0.6 1.0 O2' E:A20 4.3 0.5 1.0 C2 E:A14 4.4 88.1 1.0 N6 E:A14 4.5 0.1 1.0 C6 E:A14 4.6 96.1 1.0 N7 E:G21 4.6 81.6 1.0 C2 E:A20 4.6 0.1 1.0 P E:G21 4.7 1.0 1.0 N3 E:G15 4.7 0.6 1.0 OP1 E:G21 4.7 0.9 1.0 C2 E:G15 4.8 97.0 1.0 C8 E:A20 4.8 0.2 1.0 C4' E:G21 4.8 0.4 1.0 O5' E:A20 4.8 0.1 1.0

Magnesium binding site 5 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg117 b:0.5 occ:1.00 O3' E:C79 4.0 0.6 1.0 OP1 E:G5 4.2 0.5 1.0

Magnesium binding site 6 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg220 b:69.0 occ:1.00 OP2 F:U21 3.5 1.0 1.0 OP2 F:A22 4.1 0.1 1.0 O4 F:U23 4.5 0.3 1.0 P F:U21 4.6 0.5 1.0 O5' F:U21 4.8 0.8 1.0

Magnesium binding site 7 out of 7 in the Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate 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 A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg221 b:94.0 occ:1.00 C8 F:A54 3.2 0.9 1.0 O2' F:A54 3.3 0.2 1.0 C2' F:A54 3.5 1.0 1.0 OP2 F:A54 3.6 0.3 1.0 N7 F:A54 3.9 0.3 1.0 N9 F:A54 4.1 0.2 1.0 C5 F:U55 4.2 0.7 1.0 C1' F:A54 4.4 0.5 1.0 O5' F:A54 4.4 0.4 1.0 C6 F:U55 4.5 0.1 1.0 P F:A54 4.7 0.5 1.0 C3' F:A54 4.7 0.1 1.0

J.Zhang, A.R.Ferre-D'amare. Co-Crystal Structure of A T-Box Riboswitch Stem I Domain in Complex with Its Cognate Trna. Nature V. 500 363 2013.
ISSN: ISSN 0028-0836
PubMed: 23892783
DOI: 10.1038/NATURE12440