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Iodine 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:

Rhodium (Rh) 5 atoms

Iodine Binding Sites:

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

Iodine binding site 1 out of 10 in 454d

Go back to Iodine Binding Sites List in 454d
Iodine binding site 1 out of 10 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 Iodine with other atoms in the I 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
A:I2

b:21.1
occ:1.00
 I5 A:5IU2 0.0 21.1 1.0
C5 A:5IU2 1.9 20.8 1.0
C6 A:5IU2 2.9 19.4 1.0
C4 A:5IU2 3.0 20.3 1.0
O A:HOH182 3.2 38.4 1.0
O4 A:5IU2 3.2 21.6 1.0
O A:HOH431 3.6 47.9 1.0
O A:HOH369 3.7 34.9 1.0
C8 A:DG1 3.8 21.4 1.0
O A:HOH475 3.8 35.0 1.0
C2' A:DG1 3.9 21.0 1.0
N9 A:DG1 3.9 19.6 1.0
O A:HOH180 4.0 23.4 1.0
O A:HOH368 4.0 26.6 1.0
N7 A:DG1 4.1 21.2 1.0
N1 A:5IU2 4.2 18.5 1.0
N3 A:5IU2 4.2 18.4 1.0
C4 A:DG1 4.3 18.9 1.0
C5 A:DG1 4.4 20.1 1.0
C1' A:DG1 4.4 19.8 1.0
O4 A:DT3 4.4 20.5 1.0
C7 A:DT3 4.6 20.7 1.0
C2 A:5IU2 4.8 19.1 1.0

Iodine binding site 2 out of 10 in 454d

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Iodine binding site 2 out of 10 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 Iodine with other atoms in the I 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
B:I10

b:21.1
occ:1.00
 I5 B:5IU10 0.0 21.1 1.0
C5 B:5IU10 1.9 22.0 1.0
C6 B:5IU10 2.9 22.6 1.0
C4 B:5IU10 2.9 22.7 1.0
OP1 G:DA54 3.1 22.2 1.0
O4 B:5IU10 3.2 23.4 1.0
O G:HOH315 3.5 35.6 1.0
O B:HOH238 3.7 24.4 1.0
O G:HOH194 3.8 26.4 1.0
C2' B:DG9 3.8 23.6 1.0
C8 B:DG9 3.8 24.3 1.0
P G:DA54 3.9 22.1 1.0
N9 B:DG9 3.9 23.0 1.0
O B:HOH153 3.9 23.0 1.0
O B:HOH104 4.0 26.5 1.0
OP2 G:DA54 4.1 25.2 1.0
O5' G:DA54 4.2 23.6 1.0
N7 B:DG9 4.2 23.6 1.0
N1 B:5IU10 4.2 21.8 1.0
N3 B:5IU10 4.2 23.5 1.0
C1' B:DG9 4.2 22.2 1.0
O G:HOH193 4.3 25.7 1.0
O4 B:DT11 4.4 20.9 1.0
C4 B:DG9 4.4 22.0 1.0
C5 B:DG9 4.5 22.7 1.0
C5' G:DA54 4.5 24.4 1.0
C7 B:DT11 4.6 23.6 1.0
C2 B:5IU10 4.8 23.1 1.0
O G:HOH284 4.9 29.3 1.0
O B:HOH195 5.0 28.7 1.0

Iodine binding site 3 out of 10 in 454d

Go back to Iodine Binding Sites List in 454d
Iodine binding site 3 out of 10 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 Iodine with other atoms in the I 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
C:I18

b:46.7
occ:1.00
 I5 C:5IU18 0.0 46.7 1.0
C5 C:5IU18 1.9 43.5 1.0
C6 C:5IU18 2.9 44.1 1.0
C4 C:5IU18 2.9 45.4 1.0
O4 C:5IU18 3.1 45.1 1.0
C2' C:DG17 3.7 42.6 1.0
C8 C:DG17 3.8 34.8 1.0
N9 C:DG17 3.9 33.3 1.0
O4 C:DT19 3.9 40.7 1.0
N3 C:5IU18 4.2 40.1 1.0
N1 C:5IU18 4.2 42.0 1.0
N7 C:DG17 4.2 33.0 1.0
C1' C:DG17 4.3 37.6 1.0
C4 C:DG17 4.4 30.7 1.0
C7 C:DT19 4.5 42.2 1.0
C5 C:DG17 4.5 28.4 1.0
C4 C:DT19 4.7 32.9 1.0
C2 C:5IU18 4.7 39.3 1.0
C5 C:DT19 5.0 32.8 1.0

Iodine binding site 4 out of 10 in 454d

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Iodine binding site 4 out of 10 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 Iodine with other atoms in the I 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
D:I26

b:43.9
occ:1.00
 I5 D:5IU26 0.0 43.9 1.0
C5 D:5IU26 1.9 40.0 1.0
C6 D:5IU26 2.9 40.5 1.0
C4 D:5IU26 2.9 42.7 1.0
O4 D:5IU26 3.1 49.7 1.0
O D:HOH248 3.8 36.3 1.0
C2' D:DG25 3.9 45.5 1.0
C8 D:DG25 3.9 41.4 1.0
O4 D:DT27 3.9 40.7 1.0
N9 D:DG25 3.9 39.3 1.0
N1 D:5IU26 4.1 42.2 1.0
N3 D:5IU26 4.2 41.8 1.0
N7 D:DG25 4.2 37.5 1.0
C4 D:DG25 4.3 36.6 1.0
C1' D:DG25 4.4 40.8 1.0
C5 D:DG25 4.4 38.4 1.0
C4 D:DT27 4.7 40.6 1.0
C7 D:DT27 4.7 43.6 1.0
N6 C:DA22 4.7 43.7 1.0
C2 D:5IU26 4.7 42.9 1.0
OP2 D:5IU26 4.8 59.4 1.0

Iodine binding site 5 out of 10 in 454d

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Iodine binding site 5 out of 10 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 Iodine with other atoms in the I 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
E:I34

b:20.1
occ:1.00
 I5 E:5IU34 0.0 20.1 1.0
C5 E:5IU34 2.0 18.2 1.0
C6 E:5IU34 2.9 18.7 1.0
C4 E:5IU34 3.0 18.7 1.0
O4 E:5IU34 3.2 18.7 1.0
C8 E:DG33 3.7 19.1 1.0
O E:HOH115 3.8 43.2 1.0
O E:HOH181 3.9 29.1 1.0
N7 E:DG33 3.9 20.1 1.0
N9 E:DG33 4.0 20.1 1.0
C2' E:DG33 4.0 22.7 1.0
N3 E:5IU34 4.3 18.4 1.0
N1 E:5IU34 4.3 18.9 1.0
C5 E:DG33 4.3 18.2 1.0
C4 E:DG33 4.4 18.9 1.0
C1' E:DG33 4.5 20.8 1.0
C7 E:DT35 4.5 19.1 1.0
O4 E:DT35 4.6 17.1 1.0
C2 E:5IU34 4.8 19.1 1.0

Iodine binding site 6 out of 10 in 454d

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Iodine binding site 6 out of 10 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 Iodine with other atoms in the I binding site number 6 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
F:I42

b:21.7
occ:1.00
 I5 F:5IU42 0.0 21.7 1.0
C5 F:5IU42 2.0 19.8 1.0
C6 F:5IU42 3.0 19.0 1.0
C4 F:5IU42 3.0 19.6 1.0
O4 F:5IU42 3.2 20.0 1.0
O F:HOH187 3.3 31.9 1.0
O F:HOH354 3.3 55.0 1.0
O F:HOH186 3.6 25.3 1.0
C2' F:DG41 3.7 19.6 1.0
O F:HOH357 3.8 41.2 1.0
O F:HOH355 3.8 27.5 1.0
N9 F:DG41 3.9 19.5 1.0
O F:HOH124 3.9 25.2 1.0
C8 F:DG41 3.9 21.0 1.0
O F:HOH185 4.1 23.1 1.0
C1' F:DG41 4.2 19.8 1.0
N3 F:5IU42 4.3 18.1 1.0
N1 F:5IU42 4.3 18.3 1.0
C4 F:DG41 4.3 18.9 1.0
N7 F:DG41 4.3 20.4 1.0
O4 F:DT43 4.4 18.0 1.0
C5 F:DG41 4.5 18.7 1.0
C2 F:5IU42 4.8 18.1 1.0
C7 F:DT43 4.8 19.3 1.0
O A:HOH446 4.9 36.4 1.0
O F:HOH356 4.9 41.2 1.0
N3 F:DG41 4.9 18.0 1.0
OP2 F:5IU42 5.0 21.3 1.0

Iodine binding site 7 out of 10 in 454d

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Iodine binding site 7 out of 10 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 Iodine with other atoms in the I binding site number 7 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:I50

b:25.6
occ:1.00
 I5 G:5IU50 0.0 25.6 1.0
C5 G:5IU50 1.9 28.4 1.0
C6 G:5IU50 2.9 28.4 1.0
C4 G:5IU50 3.0 26.7 1.0
O4 G:5IU50 3.3 27.2 1.0
O G:HOH159 3.7 31.5 1.0
C8 G:DG49 3.9 27.1 1.0
C2' G:DG49 3.9 27.1 1.0
O G:HOH158 4.0 19.5 1.0
N9 G:DG49 4.0 26.6 1.0
N1 G:5IU50 4.2 25.4 1.0
O4 G:DT51 4.2 21.5 1.0
N3 G:5IU50 4.2 25.2 1.0
O G:HOH225 4.2 29.2 1.0
N7 G:DG49 4.2 26.8 1.0
C1' G:DG49 4.4 26.0 1.0
C4 G:DG49 4.5 25.6 1.0
C7 G:DT51 4.5 22.9 1.0
C5 G:DG49 4.6 26.4 1.0
C2 G:5IU50 4.8 27.8 1.0
C4 G:DT51 4.9 20.5 1.0

Iodine binding site 8 out of 10 in 454d

Go back to Iodine Binding Sites List in 454d
Iodine binding site 8 out of 10 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 Iodine with other atoms in the I binding site number 8 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
H:I58

b:24.4
occ:1.00
 I5 H:5IU58 0.0 24.4 1.0
C5 H:5IU58 2.0 24.5 1.0
C6 H:5IU58 2.9 24.8 1.0
C4 H:5IU58 3.0 23.8 1.0
O4 H:5IU58 3.2 24.0 1.0
O H:HOH358 3.6 41.6 1.0
C2' H:DG57 3.7 24.1 1.0
O H:HOH449 3.9 36.4 1.0
C8 H:DG57 3.9 21.7 1.0
N9 H:DG57 4.0 21.6 1.0
O H:HOH344 4.0 28.2 1.0
O H:HOH458 4.1 28.1 1.0
N1 H:5IU58 4.2 23.4 1.0
N3 H:5IU58 4.3 22.0 1.0
N7 H:DG57 4.3 22.8 1.0
C1' H:DG57 4.3 22.8 1.0
O4 H:DT59 4.3 22.0 1.0
C4 H:DG57 4.4 20.4 1.0
C5 H:DG57 4.5 21.9 1.0
C7 H:DT59 4.7 22.1 1.0
C2 H:5IU58 4.8 24.1 1.0

Iodine binding site 9 out of 10 in 454d

Go back to Iodine Binding Sites List in 454d
Iodine binding site 9 out of 10 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 Iodine with other atoms in the I binding site number 9 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
I:I66

b:51.7
occ:1.00
 I5 I:5IU66 0.0 51.7 1.0
C5 I:5IU66 1.9 39.4 1.0
C4 I:5IU66 2.9 42.5 1.0
C6 I:5IU66 2.9 43.9 1.0
O4 I:5IU66 3.0 47.8 1.0
C8 I:DG65 3.8 42.3 1.0
C2' I:DG65 3.8 42.0 1.0
N9 I:DG65 4.0 37.2 1.0
N7 I:DG65 4.2 41.2 1.0
N3 I:5IU66 4.2 41.5 1.0
O4 I:DT67 4.2 49.8 1.0
N1 I:5IU66 4.2 43.0 1.0
C1' I:DG65 4.4 39.7 1.0
C4 I:DG65 4.5 36.8 1.0
C5 I:DG65 4.6 39.0 1.0
C2 I:5IU66 4.8 43.9 1.0
C7 I:DT67 4.9 46.6 1.0

Iodine binding site 10 out of 10 in 454d

Go back to Iodine Binding Sites List in 454d
Iodine binding site 10 out of 10 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 Iodine with other atoms in the I binding site number 10 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:I74

b:38.8
occ:1.00
 I5 J:5IU74 0.0 38.8 1.0
C5 J:5IU74 1.9 38.0 1.0
C6 J:5IU74 2.8 38.8 1.0
C4 J:5IU74 3.0 35.3 1.0
O4 J:5IU74 3.3 37.3 1.0
C8 J:DG73 3.6 36.0 1.0
N9 J:DG73 3.8 38.1 1.0
O J:HOH481 3.8 48.8 1.0
N7 J:DG73 3.9 34.7 1.0
C2' J:DG73 4.0 43.8 1.0
N1 J:5IU74 4.1 40.7 1.0
O4 J:DT75 4.1 54.1 1.0
C4 J:DG73 4.2 34.4 1.0
C7 J:DT75 4.2 57.4 1.0
C5 J:DG73 4.2 32.1 1.0
N3 J:5IU74 4.2 33.4 1.0
C1' J:DG73 4.3 38.9 1.0
C4 J:DT75 4.7 49.3 1.0
C2 J:5IU74 4.7 35.4 1.0
C5 J:DT75 4.8 49.3 1.0
N3 J:DG73 4.9 32.6 1.0
O J:HOH479 5.0 48.3 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: Sun Aug 11 17:20:28 2024

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