Magnesium in PDB 6pmo: Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly

The structure of Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly, PDB code: 6pmo was solved by S.Li, J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.98 / 2.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.851, 139.913, 136.023, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.3

The structure of Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly also contains other interesting chemical elements:

Iridium

(Ir)

13 atoms

The binding sites of Magnesium atom in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly (pdb code 6pmo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly, PDB code: 6pmo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly


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 Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg110 b:79.0 occ:1.00 O B:HOH211 2.4 61.1 1.0 N7 B:G3 4.2 91.8 1.0 N7 B:G4 4.4 92.1 1.0 O6 B:G4 4.5 93.8 1.0 O6 B:G3 4.9 0.9 1.0 C8 B:G3 4.9 0.3 1.0 C5 B:G3 4.9 95.2 1.0

Magnesium binding site 2 out of 4 in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly


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 Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg111 b:57.8 occ:1.00 OP1 B:C48 1.8 99.0 1.0 OP1 B:C50 3.0 69.8 1.0 P B:C48 3.2 67.7 1.0 OP2 B:C48 3.7 60.1 1.0 P B:C50 3.9 69.4 1.0 O5' B:C48 4.0 72.0 1.0 O5' B:C50 4.1 74.0 1.0 O3' B:U47 4.2 68.7 1.0 OP2 B:G51 4.3 80.5 1.0 C3' B:U47 4.3 88.3 1.0 OP2 B:C50 4.3 91.7 1.0 C5' B:C48 4.6 59.1 1.0 C5' B:C50 4.7 79.4 1.0 C5' B:U47 4.9 95.5 1.0

Magnesium binding site 3 out of 4 in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly


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 Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:65.3 occ:1.00 O4 A:U185 2.8 74.4 1.0 OP1 B:A76 2.9 87.7 1.0 O6 A:G167 3.0 71.1 1.0 O6 A:G184 3.1 76.7 1.0 N4 A:C166 3.5 80.9 1.0 C4 A:U185 3.7 61.2 1.0 N3 A:U185 3.9 68.6 1.0 O4 A:U131 4.0 94.3 1.0 C6 A:G184 4.1 72.7 1.0 P B:A76 4.1 79.3 1.0 C6 A:G167 4.1 68.1 1.0 N4 A:C168 4.2 73.5 1.0 C5' B:A76 4.2 71.0 1.0 C4 A:C166 4.4 80.5 1.0 O3' B:C75 4.5 79.4 1.0 O5' B:A76 4.5 69.7 1.0 C4 A:U131 4.6 87.7 1.0 N7 A:G167 4.7 66.2 1.0 N3 A:C166 4.8 82.4 1.0 C5 A:G167 4.8 66.4 1.0 C5 A:G184 4.9 67.6 1.0 N4 A:C183 5.0 62.7 1.0

Magnesium binding site 4 out of 4 in the Co-Crystal Structure of the Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly


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 Geobacillus Kaustophilus Glyq T-Box Riboswitch Discriminator Domain in Complex with Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:84.1 occ:1.00 O6 A:G161 3.6 76.6 1.0 O6 A:G162 3.6 66.0 1.0 N7 A:G161 3.7 70.5 1.0 N7 A:G162 4.1 72.0 1.0 C6 A:G161 4.2 66.7 1.0 C5 A:G161 4.2 66.2 1.0 C6 A:G162 4.5 73.7 1.0 C5 A:G162 4.7 73.3 1.0 C8 A:G161 4.8 71.4 1.0 O4 A:U160 4.8 54.5 1.0

S.Li, Z.Su, J.Lehmann, V.Stamatopoulou, N.Giarimoglou, F.E.Henderson, L.Fan, G.D.Pintilie, K.Zhang, M.Chen, S.J.Ludtke, Y.X.Wang, C.Stathopoulos, W.Chiu, J.Zhang. Structural Basis of Amino Acid Surveillance By Higher-Order Trna-Mrna Interactions. Nat.Struct.Mol.Biol. 2019.
ISSN: ESSN 1545-9985
PubMed: 31740854
DOI: 10.1038/S41594-019-0326-7