Iridium in PDB 5kpy: Structure of A 5-Hydroxytryptophan Aptamer

The structure of Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy was solved by R.T.Batey, E.Porter, M.Merck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.33 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.553, 26.594, 63.367, 90.00, 106.32, 90.00
R / Rfree (%)	21.7 / 25.8

The structure of Structure of A 5-Hydroxytryptophan Aptamer also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iridium atom in the Structure of A 5-Hydroxytryptophan Aptamer (pdb code 5kpy). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 12 binding sites of Iridium where determined in the Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy:
Jump to Iridium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iridium binding site 1 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir102 b:97.6 occ:1.00 IR A:IRI102 0.0 97.6 1.0 N1 A:IRI102 2.3 56.0 1.0 N6 A:IRI102 2.3 65.0 1.0 N2 A:IRI102 2.3 43.2 1.0 N4 A:IRI102 2.3 60.3 1.0 N5 A:IRI102 2.3 35.5 1.0 N3 A:IRI102 2.3 49.5 1.0 HN13 A:IRI102 2.7 67.2 1.0 HN11 A:IRI102 2.7 67.2 1.0 HN12 A:IRI102 2.7 67.2 1.0 HN22 A:IRI102 2.7 51.9 1.0 HN21 A:IRI102 2.7 51.9 1.0 HN23 A:IRI102 2.7 51.9 1.0 HN63 A:IRI102 2.7 78.0 1.0 HN62 A:IRI102 2.7 78.0 1.0 HN61 A:IRI102 2.7 78.0 1.0 HN42 A:IRI102 2.7 72.4 1.0 HN41 A:IRI102 2.7 72.4 1.0 HN43 A:IRI102 2.7 72.4 1.0 HN52 A:IRI102 2.7 42.6 1.0 HN53 A:IRI102 2.7 42.6 1.0 HN51 A:IRI102 2.7 42.6 1.0 HN32 A:IRI102 2.7 59.4 1.0 HN31 A:IRI102 2.7 59.4 1.0 HN33 A:IRI102 2.7 59.4 1.0 O A:HOH242 4.0 25.2 0.8 O A:HOH213 4.2 22.5 1.0

Iridium binding site 2 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir103 b:70.7 occ:1.00 IR A:IRI103 0.0 70.7 1.0 N5 A:IRI103 2.3 42.8 1.0 N3 A:IRI103 2.3 44.9 1.0 N1 A:IRI103 2.3 47.9 1.0 N2 A:IRI103 2.3 48.2 1.0 N4 A:IRI103 2.3 44.7 1.0 N6 A:IRI103 2.3 45.2 1.0 HN53 A:IRI103 2.7 51.3 1.0 HN52 A:IRI103 2.7 51.3 1.0 HN51 A:IRI103 2.7 51.3 1.0 HN12 A:IRI103 2.7 57.4 1.0 HN31 A:IRI103 2.7 53.9 1.0 HN13 A:IRI103 2.7 57.4 1.0 HN11 A:IRI103 2.7 57.4 1.0 HN32 A:IRI103 2.7 53.9 1.0 HN33 A:IRI103 2.7 53.9 1.0 HN21 A:IRI103 2.7 57.9 1.0 HN23 A:IRI103 2.7 57.9 1.0 HN22 A:IRI103 2.7 57.9 1.0 HN41 A:IRI103 2.7 53.6 1.0 HN42 A:IRI103 2.7 53.6 1.0 HN43 A:IRI103 2.7 53.6 1.0 HN63 A:IRI103 2.7 54.3 1.0 HN62 A:IRI103 2.7 54.3 1.0 HN61 A:IRI103 2.7 54.3 1.0 O4 A:U81 4.4 38.3 1.0 O6 A:G14 4.4 41.9 1.0 O6 A:G80 4.9 35.1 1.0

Iridium binding site 3 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir104 b:55.1 occ:1.00 IR A:IRI104 0.0 55.1 1.0 N4 A:IRI104 2.3 37.9 1.0 N5 A:IRI104 2.3 35.1 1.0 N3 A:IRI104 2.3 38.1 1.0 N6 A:IRI104 2.3 33.5 1.0 N1 A:IRI104 2.3 29.3 1.0 N2 A:IRI104 2.3 29.4 1.0 HN41 A:IRI104 2.7 45.5 1.0 HN43 A:IRI104 2.7 45.5 1.0 HN42 A:IRI104 2.7 45.5 1.0 HN53 A:IRI104 2.7 42.1 1.0 HN51 A:IRI104 2.7 42.1 1.0 HN52 A:IRI104 2.7 42.1 1.0 HN33 A:IRI104 2.7 45.7 1.0 HN31 A:IRI104 2.7 45.7 1.0 HN32 A:IRI104 2.7 45.7 1.0 HN61 A:IRI104 2.7 40.1 1.0 HN62 A:IRI104 2.7 40.1 1.0 HN63 A:IRI104 2.7 40.1 1.0 HN13 A:IRI104 2.7 35.1 1.0 HN12 A:IRI104 2.7 35.1 1.0 HN11 A:IRI104 2.7 35.1 1.0 HN23 A:IRI104 2.7 35.2 1.0 HN21 A:IRI104 2.7 35.2 1.0 HN22 A:IRI104 2.7 35.2 1.0 O2' A:A21 4.4 23.6 1.0 O A:HOH246 4.5 19.4 0.8 N3 A:A21 4.6 19.5 1.0 O3' A:A21 4.8 21.6 1.0 OP2 A:U22 4.9 23.1 1.0 OP2 A:A73 4.9 19.7 1.0

Iridium binding site 4 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir105 b:34.0 occ:1.00 IR A:IRI105 0.0 34.0 1.0 N2 A:IRI105 2.2 23.9 1.0 N4 A:IRI105 2.2 21.7 1.0 N1 A:IRI105 2.2 23.5 1.0 N3 A:IRI105 2.3 21.8 1.0 N6 A:IRI105 2.3 20.4 1.0 N5 A:IRI105 2.3 20.4 1.0 HN23 A:IRI105 2.7 28.7 1.0 HN21 A:IRI105 2.7 28.7 1.0 HN22 A:IRI105 2.7 28.7 1.0 HN43 A:IRI105 2.7 26.1 1.0 HN12 A:IRI105 2.7 28.2 1.0 HN11 A:IRI105 2.7 28.2 1.0 HN42 A:IRI105 2.7 26.1 1.0 HN13 A:IRI105 2.7 28.2 1.0 HN41 A:IRI105 2.7 26.1 1.0 HN32 A:IRI105 2.7 26.2 1.0 HN31 A:IRI105 2.7 26.2 1.0 HN33 A:IRI105 2.7 26.2 1.0 HN62 A:IRI105 2.7 24.4 1.0 HN61 A:IRI105 2.7 24.4 1.0 HN63 A:IRI105 2.7 24.4 1.0 HN51 A:IRI105 2.7 24.5 1.0 HN53 A:IRI105 2.7 24.5 1.0 HN52 A:IRI105 2.7 24.5 1.0 O A:HOH218 3.4 20.3 0.9 O A:HOH210 3.4 21.8 0.8 O6 A:G23 3.9 17.8 1.0 O4 A:U53 4.3 18.7 1.0 O2' A:G55 4.8 16.1 1.0 O4' A:A73 4.9 16.1 1.0

Iridium binding site 5 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir106 b:17.4 occ:1.00 IR A:IRI106 0.0 17.4 1.0 N4 A:IRI106 2.2 18.2 1.0 N2 A:IRI106 2.2 16.8 1.0 N6 A:IRI106 2.2 15.2 1.0 N5 A:IRI106 2.2 16.5 1.0 N1 A:IRI106 2.3 13.8 1.0 N3 A:IRI106 2.3 15.6 1.0 HN41 A:IRI106 2.6 21.8 1.0 HN42 A:IRI106 2.6 21.8 1.0 HN43 A:IRI106 2.6 21.8 1.0 HN23 A:IRI106 2.6 20.2 1.0 HN22 A:IRI106 2.6 20.2 1.0 HN21 A:IRI106 2.6 20.2 1.0 HN61 A:IRI106 2.7 18.2 1.0 HN63 A:IRI106 2.7 18.2 1.0 HN62 A:IRI106 2.7 18.2 1.0 HN51 A:IRI106 2.7 19.8 1.0 HN53 A:IRI106 2.7 19.8 1.0 HN52 A:IRI106 2.7 19.8 1.0 HN11 A:IRI106 2.7 16.6 1.0 HN12 A:IRI106 2.7 16.6 1.0 HN13 A:IRI106 2.7 16.6 1.0 HN33 A:IRI106 2.7 18.7 1.0 HN32 A:IRI106 2.7 18.7 1.0 HN31 A:IRI106 2.7 18.7 1.0 O A:HOH234 3.5 15.8 1.0 O A:HOH245 3.5 18.1 0.8 O A:HOH236 3.8 22.2 0.8 O2 A:U25 4.0 17.0 1.0 OXT A:4PQ101 4.1 16.1 1.0 O2' A:U45 4.1 18.7 1.0 O A:HOH264 4.2 17.7 1.0 MG A:MG119 4.3 25.6 1.0 O A:HOH224 4.5 19.4 0.8

Iridium binding site 6 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 6 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir107 b:27.4 occ:1.00 IR A:IRI107 0.0 27.4 1.0 N3 A:IRI107 2.2 21.6 1.0 N1 A:IRI107 2.2 25.2 1.0 N6 A:IRI107 2.3 24.0 1.0 N4 A:IRI107 2.3 20.4 1.0 N5 A:IRI107 2.3 23.7 1.0 N2 A:IRI107 2.3 25.1 1.0 HN33 A:IRI107 2.7 25.9 1.0 HN32 A:IRI107 2.7 25.9 1.0 HN31 A:IRI107 2.7 25.9 1.0 HN13 A:IRI107 2.7 30.3 1.0 HN12 A:IRI107 2.7 30.3 1.0 HN11 A:IRI107 2.7 30.3 1.0 HN61 A:IRI107 2.7 28.8 1.0 HN63 A:IRI107 2.7 28.8 1.0 HN62 A:IRI107 2.7 28.8 1.0 HN43 A:IRI107 2.7 24.4 1.0 HN41 A:IRI107 2.7 24.4 1.0 HN42 A:IRI107 2.7 24.4 1.0 HN53 A:IRI107 2.7 28.4 1.0 HN21 A:IRI107 2.7 30.1 1.0 HN51 A:IRI107 2.7 28.4 1.0 HN52 A:IRI107 2.7 28.4 1.0 HN23 A:IRI107 2.7 30.1 1.0 HN22 A:IRI107 2.7 30.1 1.0 OP2 A:C71 3.5 18.9 1.0 O4 A:U72 3.7 19.4 1.0 OP2 A:C70 3.9 17.4 1.0 OP1 A:C70 4.0 15.7 1.0 P A:C70 4.4 19.4 1.0 O5' A:C70 4.8 18.1 1.0 C4 A:U72 4.9 20.5 1.0 P A:C71 5.0 17.6 1.0

Iridium binding site 7 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 7 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir108 b:23.9 occ:1.00 IR A:IRI108 0.0 23.9 1.0 N3 A:IRI108 2.2 19.1 1.0 N2 A:IRI108 2.2 23.2 1.0 N4 A:IRI108 2.2 16.0 1.0 N1 A:IRI108 2.2 21.4 1.0 N5 A:IRI108 2.3 16.9 1.0 N6 A:IRI108 2.3 17.3 1.0 HN33 A:IRI108 2.7 22.9 1.0 HN31 A:IRI108 2.7 22.9 1.0 HN32 A:IRI108 2.7 22.9 1.0 HN21 A:IRI108 2.7 27.8 1.0 HN22 A:IRI108 2.7 27.8 1.0 HN23 A:IRI108 2.7 27.8 1.0 HN42 A:IRI108 2.7 19.2 1.0 HN41 A:IRI108 2.7 19.2 1.0 HN43 A:IRI108 2.7 19.2 1.0 HN13 A:IRI108 2.7 25.7 1.0 HN11 A:IRI108 2.7 25.7 1.0 HN12 A:IRI108 2.7 25.7 1.0 HN53 A:IRI108 2.7 20.2 1.0 HN51 A:IRI108 2.7 20.2 1.0 HN52 A:IRI108 2.7 20.2 1.0 HN61 A:IRI108 2.7 20.7 1.0 HN63 A:IRI108 2.7 20.7 1.0 HN62 A:IRI108 2.7 20.7 1.0 O A:HOH206 3.2 22.4 1.0 O A:HOH265 3.7 14.8 1.0 O A:HOH254 3.9 17.9 0.8 O2' A:A24 4.0 15.6 1.0 O A:HOH260 4.5 15.4 0.9 O6 A:G52 4.5 16.6 1.0 O4 A:U54 4.8 18.2 1.0 O A:HOH276 4.8 17.3 0.6

Iridium binding site 8 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 8 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir109 b:39.0 occ:1.00 IR A:IRI109 0.0 39.0 1.0 N5 A:IRI109 2.2 32.3 1.0 N6 A:IRI109 2.3 35.1 1.0 N2 A:IRI109 2.3 35.9 1.0 N4 A:IRI109 2.3 35.7 1.0 N3 A:IRI109 2.3 37.2 1.0 N1 A:IRI109 2.3 28.8 1.0 HN53 A:IRI109 2.7 38.8 1.0 HN51 A:IRI109 2.7 38.8 1.0 HN52 A:IRI109 2.7 38.8 1.0 HN62 A:IRI109 2.7 42.1 1.0 HN63 A:IRI109 2.7 42.1 1.0 HN61 A:IRI109 2.7 42.1 1.0 HN21 A:IRI109 2.7 43.0 1.0 HN23 A:IRI109 2.7 43.0 1.0 HN22 A:IRI109 2.7 43.0 1.0 HN42 A:IRI109 2.7 42.8 1.0 HN43 A:IRI109 2.7 42.8 1.0 HN33 A:IRI109 2.7 44.7 1.0 HN31 A:IRI109 2.7 44.7 1.0 HN41 A:IRI109 2.7 42.8 1.0 HN32 A:IRI109 2.7 44.7 1.0 HN12 A:IRI109 2.7 34.5 1.0 HN11 A:IRI109 2.7 34.5 1.0 HN13 A:IRI109 2.7 34.5 1.0 O A:HOH272 3.9 25.3 1.0 O6 A:G29 4.0 31.7 1.0 O A:HOH278 4.2 27.5 0.8 N7 A:G29 4.3 30.2 1.0 O4 A:U30 4.7 34.5 1.0 C6 A:G29 4.8 31.7 1.0 O A:HOH286 4.9 39.4 1.0 C5 A:G29 4.9 30.3 1.0

Iridium binding site 9 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 9 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir110 b:23.6 occ:1.00 IR A:IRI110 0.0 23.6 1.0 N3 A:IRI110 2.2 22.1 1.0 N6 A:IRI110 2.2 22.7 1.0 N2 A:IRI110 2.2 28.5 1.0 N4 A:IRI110 2.2 18.6 1.0 N5 A:IRI110 2.2 23.1 1.0 N1 A:IRI110 2.3 20.9 1.0 HN31 A:IRI110 2.7 26.5 1.0 HN62 A:IRI110 2.7 27.2 1.0 HN63 A:IRI110 2.7 27.2 1.0 HN32 A:IRI110 2.7 26.5 1.0 HN33 A:IRI110 2.7 26.5 1.0 HN61 A:IRI110 2.7 27.2 1.0 HN21 A:IRI110 2.7 34.2 1.0 HN23 A:IRI110 2.7 34.2 1.0 HN22 A:IRI110 2.7 34.2 1.0 HN41 A:IRI110 2.7 22.3 1.0 HN43 A:IRI110 2.7 22.3 1.0 HN42 A:IRI110 2.7 22.3 1.0 HN51 A:IRI110 2.7 27.7 1.0 HN52 A:IRI110 2.7 27.7 1.0 HN53 A:IRI110 2.7 27.7 1.0 HN12 A:IRI110 2.7 25.0 1.0 HN11 A:IRI110 2.7 25.0 1.0 HN13 A:IRI110 2.7 25.0 1.0 O A:HOH225 3.4 30.9 1.0 OP2 A:G55 3.9 20.9 1.0 O2 A:U54 4.0 17.2 1.0 OP2 A:A24 4.1 16.0 1.0 OP1 A:A40 4.4 35.5 1.0 OP2 A:A40 4.5 36.9 1.0 O2' A:U54 4.6 19.7 1.0 OP1 A:A24 4.7 16.4 1.0 P A:A40 4.8 38.0 1.0 P A:A24 5.0 17.8 1.0

Iridium binding site 10 out of 12 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 10 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir111 b:72.8 occ:1.00 IR A:IRI111 0.0 72.8 1.0 N4 A:IRI111 2.3 46.7 1.0 N1 A:IRI111 2.3 39.7 1.0 N6 A:IRI111 2.3 44.3 1.0 N2 A:IRI111 2.3 46.7 1.0 N3 A:IRI111 2.3 49.9 1.0 N5 A:IRI111 2.3 56.7 1.0 HN43 A:IRI111 2.7 56.1 1.0 HN41 A:IRI111 2.7 56.1 1.0 HN42 A:IRI111 2.7 56.1 1.0 HN12 A:IRI111 2.7 47.6 1.0 HN11 A:IRI111 2.7 47.6 1.0 HN13 A:IRI111 2.7 47.6 1.0 HN63 A:IRI111 2.7 53.1 1.0 HN61 A:IRI111 2.7 53.1 1.0 HN62 A:IRI111 2.7 53.1 1.0 HN23 A:IRI111 2.7 56.0 1.0 HN22 A:IRI111 2.7 56.0 1.0 HN21 A:IRI111 2.7 56.0 1.0 HN31 A:IRI111 2.7 59.9 1.0 HN33 A:IRI111 2.7 59.9 1.0 HN32 A:IRI111 2.7 59.9 1.0 HN53 A:IRI111 2.7 68.1 1.0 HN52 A:IRI111 2.7 68.1 1.0 HN51 A:IRI111 2.7 68.1 1.0 N7 A:G38 4.3 38.2 1.0 OP2 A:G37 4.6 47.8 1.0 O6 A:G38 4.7 38.7 1.0

E.B.Porter, J.T.Polaski, M.M.Morck, R.T.Batey. Recurrent Rna Motifs As Scaffolds For Genetically Encodable Small-Molecule Biosensors. Nat. Chem. Biol. V. 13 295 2017.
ISSN: ESSN 1552-4469
PubMed: 28092358
DOI: 10.1038/NCHEMBIO.2278