Iridium 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:

Magnesium

(Mg)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iridium 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 Iridium atom.
In total 13 binding sites of Iridium 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 Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 13 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 Iridium with other atoms in the Ir 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:Ir101 b:0.8 occ:0.81 O4 B:U65 3.1 67.2 1.0 O6 B:G49 3.7 86.6 1.0 O6 B:G64 3.9 88.0 1.0 O6 B:G7 4.0 60.4 1.0 C4 B:U65 4.2 69.5 1.0 N4 B:C66 4.6 53.3 1.0 N3 B:U65 4.7 74.9 1.0 N4 B:C50 4.7 78.9 1.0 C6 B:G49 4.8 81.0 1.0 C6 B:G64 4.9 94.6 1.0 C6 B:G7 5.0 58.4 1.0

Iridium binding site 2 out of 13 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 Iridium with other atoms in the Ir 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:Ir102 b:0.2 occ:0.84 OP2 B:G51 3.8 80.5 1.0 IR B:IR107 4.6 0.9 1.0 OP2 B:G52 4.8 92.9 1.0 OP2 B:C48 4.9 60.1 1.0 P B:G51 5.0 84.2 1.0

Iridium binding site 3 out of 13 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 Iridium with other atoms in the Ir 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 B:Ir103 b:0.1 occ:1.00 OP1 B:G17 2.7 75.5 1.0 OP2 B:G18 3.8 86.7 1.0 OP2 B:U16 4.0 72.9 1.0 P B:G17 4.1 75.6 1.0 OP1 B:G18 4.3 91.0 1.0 O5' B:G17 4.5 74.9 1.0 P B:G18 4.6 83.0 1.0

Iridium binding site 4 out of 13 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 Iridium with other atoms in the Ir 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 B:Ir104 b:0.5 occ:1.00 OP2 B:G44 3.9 0.8 1.0 N7 B:G45 4.2 69.7 1.0 O6 B:G45 4.5 72.5 1.0 P B:G44 5.0 0.1 1.0

Iridium binding site 5 out of 13 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 Iridium with other atoms in the Ir binding site number 5 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:Ir105 b:0.1 occ:0.69 OP1 B:U47 3.8 0.7 1.0

Iridium binding site 6 out of 13 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 Iridium with other atoms in the Ir binding site number 6 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:Ir106 b:0.4 occ:0.91 N7 B:G15 3.6 52.7 1.0 OP2 B:A14 3.9 76.0 1.0 OP1 B:G7 3.9 78.7 1.0 OP2 B:G15 4.1 71.0 1.0 O4 B:U8 4.4 74.3 1.0 O6 B:G15 4.4 52.4 1.0 C8 B:G15 4.5 51.8 1.0 C5 B:G15 4.6 51.2 1.0 C4 B:U8 4.7 59.1 1.0 P B:A14 4.8 70.3 1.0 OP2 B:G7 4.9 77.7 1.0 P B:G7 4.9 76.2 1.0 C6 B:G15 4.9 59.5 1.0 O5' B:A14 4.9 70.4 1.0

Iridium binding site 7 out of 13 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 Iridium with other atoms in the Ir binding site number 7 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:Ir107 b:0.9 occ:0.98 O6 B:G52 3.6 81.8 1.0 OP1 B:U60 4.2 65.2 1.0 O6 B:G53 4.5 59.9 1.0 N7 B:G52 4.5 83.4 1.0 O6 B:G51 4.6 89.2 1.0 C6 B:G52 4.6 83.8 1.0 IR B:IR102 4.6 0.2 0.8 OP2 B:U60 4.8 61.9 1.0 P B:U60 4.8 60.4 1.0 O2' B:A58 4.9 65.8 1.0 N4 B:C62 4.9 65.7 1.0 N4 B:C61 5.0 62.7 1.0 C5 B:G52 5.0 83.5 1.0 O3' B:A59 5.0 53.2 1.0

Iridium binding site 8 out of 13 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 Iridium with other atoms in the Ir binding site number 8 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:Ir108 b:0.7 occ:0.83 OP2 B:G39 4.5 0.6 1.0 N7 B:G40 4.5 1.0 1.0 N7 B:G39 4.6 0.4 1.0 O6 B:G40 4.7 0.6 1.0 OP2 B:A25 5.0 81.4 1.0

Iridium binding site 9 out of 13 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 Iridium with other atoms in the Ir binding site number 9 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:Ir109 b:0.1 occ:0.88 O6 B:G45 3.9 72.5 1.0 O6 B:G44 4.1 70.4 1.0 OP1 B:A22 4.3 56.5 1.0 N7 B:G43 4.4 87.5 1.0 O6 B:G43 4.6 91.3 1.0 C6 B:G45 4.7 60.4 1.0 OP2 B:A22 4.7 66.1 1.0 N7 B:G44 4.7 81.4 1.0 OP2 B:A23 4.8 61.6 1.0 P B:A22 4.9 56.1 1.0 C5 B:G43 5.0 92.8 1.0 C6 B:G44 5.0 78.3 1.0

Iridium binding site 10 out of 13 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 Iridium with other atoms in the Ir binding site number 10 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:Ir112 b:0.5 occ:1.00 OP2 B:C56 2.4 85.6 1.0 OP2 B:U55 3.4 94.0 1.0 OP1 B:U55 3.6 96.7 1.0 P B:U55 3.7 85.2 1.0 P B:C56 3.8 82.2 1.0 O5' B:U55 3.8 84.5 1.0 O5' B:C56 4.6 71.0 1.0 C5' B:U55 4.6 81.1 1.0 C5' B:C56 4.7 67.3 1.0 OP1 B:C56 4.7 90.5 1.0 O3' B:U55 4.7 74.9 1.0 C3' B:U55 4.8 64.9 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