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Fluorine in PDB 1id9: Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++

Protein crystallography data

The structure of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++, PDB code: 1id9 was solved by W.Cruse, P.Saludjian, A.Neuman, T.Prange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 11.00 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.730, 19.390, 45.830, 90.00, 105.70, 90.00
R / Rfree (%) 15.3 / 19.5

Other elements in 1id9:

The structure of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++ also contains other interesting chemical elements:

Rhodium (Rh) 2 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++ (pdb code 1id9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++, PDB code: 1id9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1id9

Go back to Fluorine Binding Sites List in 1id9
Fluorine binding site 1 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9

b:27.5
occ:1.00
F5 A:UFP9 0.0 27.5 1.0
C5 A:UFP9 1.5 18.6 1.0
O A:HOH116 2.3 31.6 1.0
C6 A:UFP9 2.5 11.1 1.0
C4 A:UFP9 2.5 14.8 1.0
O4 A:UFP9 2.8 21.4 1.0
O A:HOH147 3.0 62.5 1.0
O A:HOH136 3.1 35.9 1.0
O1P A:UFP9 3.6 16.8 1.0
N1 A:UFP9 3.7 12.3 1.0
N3 A:UFP9 3.8 12.7 1.0
C2 A:UFP9 4.3 17.0 1.0
O2P A:UFP9 4.4 17.2 1.0
P A:UFP9 4.5 18.4 1.0
C1' A:UFP9 5.0 10.2 1.0

Fluorine binding site 2 out of 3 in 1id9

Go back to Fluorine Binding Sites List in 1id9
Fluorine binding site 2 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9

b:43.9
occ:0.50
F5 B:UFP9 0.0 43.9 0.5
C5 B:UFP9 1.5 39.9 0.5
C5 B:UFP9 2.1 38.8 0.5
F5 B:UFP9 2.4 41.1 0.5
C4 B:UFP9 2.4 35.6 0.5
C6 B:UFP9 2.5 36.2 0.5
C4 B:UFP9 2.5 38.2 0.5
C6 B:UFP9 2.7 41.0 0.5
OP1 B:C8 2.8 35.4 1.0
O4 B:UFP9 2.8 32.5 0.5
O4 B:UFP9 2.8 35.6 0.5
N3 B:UFP9 3.2 34.7 0.5
N1 B:UFP9 3.4 40.4 0.5
O B:HOH108 3.5 41.4 1.0
C2 B:UFP9 3.6 38.0 0.5
N1 B:UFP9 3.8 41.5 0.5
N3 B:UFP9 3.8 44.2 0.5
O1P B:UFP9 4.0 40.2 1.0
P B:C8 4.1 36.0 1.0
C2 B:UFP9 4.3 38.5 0.5
OP2 B:C8 4.5 37.0 1.0
C1' B:UFP9 4.6 37.6 0.5
O2 B:UFP9 4.7 36.1 0.5
O5' B:C8 4.7 37.0 1.0
C2' B:UFP9 4.9 39.5 0.5
O4' B:UFP9 4.9 38.9 0.5
C1' B:UFP9 5.0 39.5 0.5

Fluorine binding site 3 out of 3 in 1id9

Go back to Fluorine Binding Sites List in 1id9
Fluorine binding site 3 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[F]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F9

b:41.1
occ:0.50
F5 B:UFP9 0.0 41.1 0.5
C5 B:UFP9 1.5 38.8 0.5
C4 B:UFP9 1.6 38.2 0.5
O4 B:UFP9 1.6 32.5 0.5
C5 B:UFP9 2.0 39.9 0.5
F5 B:UFP9 2.4 43.9 0.5
C6 B:UFP9 2.5 41.0 0.5
C4 B:UFP9 2.5 35.6 0.5
N3 B:UFP9 2.6 44.2 0.5
O4 B:UFP9 2.8 35.6 0.5
C6 B:UFP9 3.0 36.2 0.5
C2 B:UFP9 3.5 38.5 0.5
N1 B:UFP9 3.7 41.5 0.5
N1 B:UFP9 3.8 40.4 0.5
N3 B:UFP9 3.8 34.7 0.5
OP1 B:C8 4.0 35.4 1.0
C2 B:UFP9 4.3 38.0 0.5
OP2 B:C8 4.3 37.0 1.0
O1P B:UFP9 4.4 40.2 1.0
O2 B:UFP9 4.6 37.6 0.5
P B:C8 4.7 36.0 1.0
C1' B:UFP9 5.0 37.6 0.5

Reference:

W.Cruse, P.Saludjian, A.Neuman, T.Prange. Destabilizing Effect of A Fluorouracil Extra Base in A Hybrid Rna Duplex Compared with Bromo and Chloro Analogues. Acta Crystallogr.,Sect.D V. 57 1609 2001.
ISSN: ISSN 0907-4449
PubMed: 11679725
DOI: 10.1107/S0907444901012318
Page generated: Sun Dec 13 11:30:18 2020

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