Atomistry » Rhodium » PDB 165d-6wrm » 454d
Atomistry »
  Rhodium »
    PDB 165d-6wrm »
      454d »

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'

Protein crystallography data

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

Other elements in 454d:

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

Rhodium Binding Sites:

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 454d

Go back to Rhodium Binding Sites List in 454d
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 454d

Go back to Rhodium Binding Sites List in 454d
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 454d

Go back to Rhodium Binding Sites List in 454d
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 454d

Go back to Rhodium Binding Sites List in 454d
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 454d

Go back to Rhodium Binding Sites List in 454d
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

Reference:

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
Page generated: Wed Dec 16 02:07:36 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy