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Fluorine in PDB 3jxq: X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2

Protein crystallography data

The structure of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxq was solved by D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.45
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 21.224, 26.486, 29.310, 97.56, 105.47, 109.38
R / Rfree (%) 17.1 / 20.5

Other elements in 3jxq:

The structure of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 (pdb code 3jxq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2, PDB code: 3jxq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3jxq

Go back to Fluorine Binding Sites List in 3jxq
Fluorine binding site 1 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F5

b:15.6
occ:1.00
F5 A:5CF5 0.0 15.6 1.0
C5 A:5CF5 1.3 13.6 1.0
C6 A:5CF5 2.3 12.5 1.0
C4 A:5CF5 2.4 11.7 1.0
N4 A:5CF5 2.8 13.8 1.0
O A:HOH32 3.3 21.5 1.0
O A:HOH49 3.3 28.1 1.0
O A:HOH31 3.4 21.4 1.0
N1 A:5CF5 3.6 13.3 1.0
C5 A:G4 3.6 11.8 1.0
N7 A:G4 3.6 14.6 1.0
N3 A:5CF5 3.6 11.2 1.0
C4 A:G4 3.6 11.2 1.0
C8 A:G4 3.6 15.1 1.0
N9 A:G4 3.6 13.4 1.0
OP2 A:5CF5 3.8 17.8 1.0
C3' A:G4 4.0 14.6 1.0
C2' A:G4 4.1 12.0 1.0
C2 A:5CF5 4.1 10.8 1.0
O5' A:5CF5 4.2 15.9 1.0
C6 A:G4 4.2 12.0 1.0
N3 A:G4 4.2 12.0 1.0
C1' A:G4 4.4 13.0 1.0
O A:HOH62 4.4 23.8 1.0
P A:5CF5 4.5 16.2 1.0
N7 A:G6 4.5 13.7 1.0
N1 A:G4 4.7 11.1 1.0
C2 A:G4 4.7 13.1 1.0
O3' A:G4 4.7 13.8 1.0
O6 A:G4 4.8 13.7 1.0
C1' A:5CF5 4.8 13.4 1.0
O4' A:5CF5 4.8 12.6 1.0
O A:HOH83 4.9 35.3 1.0

Fluorine binding site 2 out of 4 in 3jxq

Go back to Fluorine Binding Sites List in 3jxq
Fluorine binding site 2 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F5

b:15.1
occ:1.00
F5 B:5CF5 0.0 15.1 1.0
C5 B:5CF5 1.3 12.3 1.0
C6 B:5CF5 2.3 14.5 1.0
C4 B:5CF5 2.4 14.6 1.0
N4 B:5CF5 2.8 14.4 1.0
O B:HOH43 3.0 28.8 1.0
O B:HOH96 3.0 26.9 1.0
O B:HOH53 3.2 34.9 1.0
O B:HOH12 3.3 22.2 1.0
O B:HOH14 3.4 23.3 1.0
N7 B:G4 3.4 13.7 1.0
C8 B:G4 3.5 12.7 1.0
N1 B:5CF5 3.6 13.6 1.0
N3 B:5CF5 3.6 15.1 1.0
OP2 B:5CF5 3.6 16.6 1.0
C5 B:G4 3.8 11.8 1.0
O B:HOH101 3.9 28.6 1.0
N9 B:G4 4.0 11.9 1.0
C2 B:5CF5 4.1 14.1 1.0
C4 B:G4 4.1 11.9 1.0
O5' B:5CF5 4.3 14.4 1.0
C3' B:G4 4.3 14.5 1.0
C6 B:G4 4.5 11.8 1.0
N7 B:G6 4.5 23.4 1.0
P B:5CF5 4.5 16.1 1.0
C2' B:G4 4.6 13.3 1.0
O5' B:G4 4.6 13.7 1.0
OP2 B:G4 4.6 15.7 1.0
O K:HOH41 4.7 24.1 1.0
C1' B:G4 4.8 13.0 1.0
C1' B:5CF5 4.8 15.2 1.0
O6 B:G4 4.8 13.0 1.0
MG K:MG7 4.9 40.0 0.8
O4' B:5CF5 4.9 15.6 1.0
O3' B:G4 5.0 14.9 1.0
N3 B:G4 5.0 13.4 1.0

Fluorine binding site 3 out of 4 in 3jxq

Go back to Fluorine Binding Sites List in 3jxq
Fluorine binding site 3 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:F5

b:15.9
occ:1.00
F5 K:5CF5 0.0 15.9 1.0
C5 K:5CF5 1.3 14.9 1.0
C6 K:5CF5 2.3 15.4 1.0
C4 K:5CF5 2.4 14.6 1.0
N4 K:5CF5 2.8 14.7 1.0
O K:HOH73 3.0 27.1 1.0
O K:HOH64 3.1 31.4 1.0
O K:HOH115 3.3 21.4 1.0
N1 K:5CF5 3.6 14.2 1.0
OP2 K:5CF5 3.6 15.8 1.0
N3 K:5CF5 3.6 13.1 1.0
C5 K:G4 3.6 13.8 1.0
C4 K:G4 3.7 16.0 1.0
N7 K:G4 3.7 16.3 1.0
C8 K:G4 3.7 17.4 1.0
N9 K:G4 3.7 15.4 1.0
O K:HOH8 3.7 17.6 1.0
C2 K:5CF5 4.1 14.0 1.0
C2' K:G4 4.1 16.7 1.0
C3' K:G4 4.1 18.9 1.0
O5' K:5CF5 4.2 13.5 1.0
C6 K:G4 4.3 12.4 1.0
N3 K:G4 4.3 15.7 1.0
N7 K:G6 4.3 14.5 1.0
C1' K:G4 4.4 18.4 1.0
P K:5CF5 4.4 16.1 1.0
O B:HOH94 4.6 30.7 1.0
N1 K:G4 4.7 15.6 1.0
C2 K:G4 4.7 14.4 1.0
MG K:MG7 4.8 40.0 0.8
O3' K:G4 4.8 15.5 1.0
O K:HOH57 4.8 32.0 1.0
C1' K:5CF5 4.8 13.3 1.0
O4' K:5CF5 4.8 15.7 1.0
O6 K:G4 4.9 16.8 1.0

Fluorine binding site 4 out of 4 in 3jxq

Go back to Fluorine Binding Sites List in 3jxq
Fluorine binding site 4 out of 4 in the X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Structure of R[Cgcg(5-Fluoro)Cg]2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:F5

b:18.9
occ:1.00
F5 L:5CF5 0.0 18.9 1.0
C5 L:5CF5 1.3 15.4 1.0
C6 L:5CF5 2.3 14.4 1.0
C4 L:5CF5 2.4 15.0 1.0
N4 L:5CF5 2.8 19.9 1.0
O L:HOH111 3.0 35.5 1.0
O L:HOH131 3.4 40.2 1.0
O L:HOH86 3.5 33.0 1.0
N1 L:5CF5 3.5 16.4 1.0
N3 L:5CF5 3.6 14.1 1.0
C5 L:G4 3.6 15.7 1.0
OP2 L:5CF5 3.6 22.3 1.0
N7 L:G4 3.7 18.7 1.0
C4 L:G4 3.8 16.3 1.0
O L:HOH123 3.8 30.4 1.0
C8 L:G4 3.9 16.8 1.0
N9 L:G4 3.9 19.6 1.0
C2 L:5CF5 4.1 16.8 1.0
C6 L:G4 4.1 16.4 1.0
C3' L:G4 4.2 18.7 1.0
O5' L:5CF5 4.3 18.9 1.0
N3 L:G4 4.3 17.4 1.0
C2' L:G4 4.4 15.9 1.0
N1 L:G4 4.5 17.4 1.0
O L:HOH54 4.5 25.9 1.0
P L:5CF5 4.6 22.2 1.0
O6 L:G4 4.6 21.0 1.0
C2 L:G4 4.6 15.2 1.0
O4' L:5CF5 4.7 17.5 1.0
C1' L:5CF5 4.7 19.5 1.0
C1' L:G4 4.7 20.3 1.0
O3' L:G4 5.0 21.9 1.0

Reference:

D.A.Adamiak, J.Milecki, R.W.Adamiak, W.Rypniewski. The Hydration and Unusual Hydrogen Bonding in the Crystal Structure of An Rna Duplex Containing Alternating Cg Base Pairs New J.Chem. V. 34 903 2010.
ISSN: ISSN 1144-0546
DOI: 10.1039/B9NJ00601J
Page generated: Sun Dec 13 11:49:00 2020

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