Rhodium in PDB 454d: Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'

The structure of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3', PDB code: 454d was solved by C.L.Kielkopf, K.E.Erkkila, B.P.Hudson, J.K.Barton, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.00 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.740, 23.980, 96.520, 90.00, 93.24, 90.00
R / Rfree (%)	17 / 21

The structure of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' also contains other interesting chemical elements:

Iodine

(I)

10 atoms

The binding sites of Rhodium atom in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' (pdb code 454d). This binding sites where shown within 5.0 Angstroms radius around Rhodium atom.
In total 5 binding sites of Rhodium where determined in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3', PDB code: 454d:
Jump to Rhodium binding site number: 1; 2; 3; 4; 5;

Rhodium binding site 1 out of 5 in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 1 of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' within 5.0Å range: probe atom residue distance (Å) B Occ B:Rh81 b:20.3 occ:1.00 RH B:RHM81 0.0 20.3 1.0 N14 B:RHM81 2.0 21.8 1.0 N13 B:RHM81 2.0 20.5 1.0 N12 B:RHM81 2.1 22.3 1.0 N5 B:RHM81 2.1 21.3 1.0 N8 B:RHM81 2.1 22.9 1.0 N1 B:RHM81 2.1 19.5 1.0 C25 B:RHM81 2.8 20.0 1.0 C24 B:RHM81 2.8 20.6 1.0 C10 B:RHM81 2.9 22.9 1.0 C6 B:RHM81 2.9 24.1 1.0 C7 B:RHM81 2.9 25.5 1.0 C9 B:RHM81 3.0 25.0 1.0 C4 B:RHM81 3.0 23.4 1.0 C3 B:RHM81 3.0 19.5 1.0 O A:HOH94 3.9 27.6 1.0 O B:HOH246 4.0 30.7 1.0 O B:HOH276 4.0 32.2 1.0 C11 B:RHM81 4.1 28.8 1.0 O6 B:DG12 4.1 19.6 1.0 O6 A:DG4 4.2 21.1 1.0 O B:HOH95 4.2 31.8 1.0 C21 B:RHM81 4.2 21.6 1.0 C2 B:RHM81 4.2 20.6 1.0 C23 B:RHM81 4.3 20.5 1.0 O B:HOH275 4.3 33.9 1.0 N7 B:DG12 4.8 21.4 1.0 C6 B:DG12 4.8 19.7 1.0 C16 B:RHM81 4.8 23.6 1.0 C29 B:RHM81 4.9 21.4 1.0 C6 A:DG4 4.9 20.0 1.0 N7 A:DG4 5.0 20.7 1.0

Rhodium binding site 2 out of 5 in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 2 of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' within 5.0Å range: probe atom residue distance (Å) B Occ D:Rh82 b:41.6 occ:1.00 RH D:RHM82 0.0 41.6 1.0 N13 D:RHM82 2.0 35.8 1.0 N14 D:RHM82 2.0 36.8 1.0 N8 D:RHM82 2.0 38.4 1.0 N5 D:RHM82 2.1 39.3 1.0 N12 D:RHM82 2.1 40.8 1.0 N1 D:RHM82 2.1 34.4 1.0 C25 D:RHM82 2.7 36.6 1.0 C24 D:RHM82 2.7 37.1 1.0 C3 D:RHM82 2.8 33.8 1.0 C7 D:RHM82 2.8 42.7 1.0 C6 D:RHM82 2.8 42.8 1.0 C10 D:RHM82 2.8 41.4 1.0 C9 D:RHM82 2.9 40.2 1.0 C4 D:RHM82 3.0 33.0 1.0 O D:HOH340 3.1 38.7 0.5 O6 D:DG28 3.8 23.3 0.5 C2 D:RHM82 4.0 38.0 1.0 C11 D:RHM82 4.0 42.6 1.0 C21 D:RHM82 4.1 38.3 1.0 C23 D:RHM82 4.1 37.7 1.0 O D:HOH247 4.3 50.3 1.0 N7 D:DG28 4.3 26.8 0.5 O6 D:DG28 4.4 25.7 0.5 C6 D:DG28 4.4 24.5 0.5 O6 C:DG20 4.4 29.6 1.0 N7 D:DG28 4.5 25.8 0.5 C5 D:DG28 4.6 24.7 0.5 C16 D:RHM82 4.7 38.5 1.0 C29 D:RHM82 4.8 40.0 1.0 O D:HOH199 4.8 43.0 1.0 C6 D:DG28 4.9 25.0 0.5 C5 D:DG28 5.0 23.6 0.5

Rhodium binding site 3 out of 5 in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 3 of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' within 5.0Å range: probe atom residue distance (Å) B Occ E:Rh83 b:15.9 occ:1.00 RH E:RHM83 0.0 15.9 1.0 N13 E:RHM83 2.0 15.8 1.0 N14 E:RHM83 2.0 16.6 1.0 N5 E:RHM83 2.0 17.3 1.0 N8 E:RHM83 2.1 16.5 1.0 N1 E:RHM83 2.1 16.4 1.0 N12 E:RHM83 2.1 16.8 1.0 C25 E:RHM83 2.9 16.3 1.0 C24 E:RHM83 2.9 15.5 1.0 C9 E:RHM83 2.9 18.3 1.0 C4 E:RHM83 2.9 19.0 1.0 C7 E:RHM83 2.9 18.7 1.0 C3 E:RHM83 2.9 18.3 1.0 C6 E:RHM83 2.9 18.7 1.0 C10 E:RHM83 3.0 17.8 1.0 O E:HOH142 3.9 28.6 1.0 O E:HOH138 4.1 26.7 1.0 O E:HOH119 4.1 26.8 1.0 O6 E:DG36 4.1 16.9 1.0 O6 F:DG44 4.1 16.3 1.0 C2 E:RHM83 4.2 19.5 1.0 O E:HOH161 4.2 25.5 1.0 C11 E:RHM83 4.2 18.1 1.0 C23 E:RHM83 4.3 16.6 1.0 C21 E:RHM83 4.3 16.0 1.0 N7 F:DG44 4.7 17.0 1.0 C6 F:DG44 4.8 15.7 1.0 C6 E:DG36 4.9 15.5 1.0 C29 E:RHM83 4.9 17.4 1.0 C16 E:RHM83 4.9 16.6 1.0 N7 E:DG36 4.9 17.9 1.0 C5 F:DG44 5.0 15.6 1.0

Rhodium binding site 4 out of 5 in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 4 of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' within 5.0Å range: probe atom residue distance (Å) B Occ G:Rh84 b:18.6 occ:1.00 RH G:RHM84 0.0 18.6 1.0 N13 G:RHM84 2.0 18.5 1.0 N14 G:RHM84 2.0 18.3 1.0 N5 G:RHM84 2.1 19.5 1.0 N12 G:RHM84 2.1 19.2 1.0 N8 G:RHM84 2.1 19.9 1.0 N1 G:RHM84 2.1 19.4 1.0 C25 G:RHM84 2.9 17.4 1.0 C24 G:RHM84 2.9 18.0 1.0 C10 G:RHM84 2.9 20.5 1.0 C7 G:RHM84 2.9 23.2 1.0 C3 G:RHM84 2.9 21.5 1.0 C4 G:RHM84 2.9 20.1 1.0 C6 G:RHM84 2.9 22.6 1.0 C9 G:RHM84 3.0 22.9 1.0 O G:HOH455 4.0 35.6 1.0 O6 H:DG60 4.1 19.1 1.0 O6 G:DG52 4.2 19.0 1.0 C2 G:RHM84 4.2 21.4 1.0 C11 G:RHM84 4.2 23.4 1.0 O G:HOH250 4.2 22.4 1.0 O G:HOH253 4.2 28.5 1.0 C21 G:RHM84 4.3 17.5 1.0 C23 G:RHM84 4.3 18.3 1.0 O G:HOH131 4.3 29.9 1.0 O G:HOH113 4.3 18.8 1.0 O G:HOH254 4.5 42.2 1.0 N7 G:DG52 4.8 22.0 1.0 C6 G:DG52 4.8 19.7 1.0 N7 H:DG60 4.8 20.9 1.0 C6 H:DG60 4.8 17.9 1.0 C29 G:RHM84 4.9 18.6 1.0 C16 G:RHM84 4.9 18.8 1.0

Rhodium binding site 5 out of 5 in the Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3'


Mono view


Stereo pair view

A full contact list of Rhodium with other atoms in the Rh binding site number 5 of Intercalation and Major Groove Recognition in the 1.2 A Resolution Crystal Structure of Rh[ME2TRIEN]Phi Bound to 5'-G(5IU)Tgcaac-3' within 5.0Å range: probe atom residue distance (Å) B Occ J:Rh85 b:37.5 occ:1.00 RH J:RHM85 0.0 37.5 1.0 N14 J:RHM85 2.0 35.9 1.0 N13 J:RHM85 2.0 33.3 1.0 N5 J:RHM85 2.1 42.8 1.0 N8 J:RHM85 2.1 43.9 1.0 N1 J:RHM85 2.1 34.4 1.0 N12 J:RHM85 2.1 38.7 1.0 C3 J:RHM85 2.5 41.0 1.0 C4 J:RHM85 2.5 42.7 1.0 C25 J:RHM85 2.8 33.1 1.0 C24 J:RHM85 2.8 31.4 1.0 C10 J:RHM85 2.8 40.7 1.0 C9 J:RHM85 2.8 40.6 1.0 C6 J:RHM85 3.1 42.8 1.0 C7 J:RHM85 3.1 42.1 1.0 C2 J:RHM85 3.7 40.0 1.0 C11 J:RHM85 3.8 46.4 1.0 O6 J:DG76 4.1 41.6 1.0 O6 I:DG68 4.1 35.4 1.0 C21 J:RHM85 4.2 29.8 1.0 C23 J:RHM85 4.2 30.9 1.0 O J:HOH201 4.3 33.6 1.0 O J:HOH301 4.6 51.6 1.0 C16 J:RHM85 4.8 33.1 1.0 C29 J:RHM85 4.8 31.7 1.0 C6 I:DG68 4.8 32.1 1.0 C6 J:DG76 4.8 35.1 1.0 N7 I:DG68 4.9 31.2 1.0

C.L.Kielkopf, K.E.Erkkila, B.P.Hudson, J.K.Barton, D.C.Rees. Structure of A Photoactive Rhodium Complex Intercalated Into Dna. Nat.Struct.Biol. V. 7 117 2000.
ISSN: ISSN 1072-8368
PubMed: 10655613
DOI: 10.1038/72385