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Fluorine in PDB 7dug: Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound

Protein crystallography data

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound, PDB code: 7dug was solved by H.Demirci, E.Destan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.78 / 3.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 400, 400, 173, 90, 90, 90
R / Rfree (%) 18.6 / 22.5

Other elements in 7dug:

The structure of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 249 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound (pdb code 7dug). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound, PDB code: 7dug:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7dug

Go back to Fluorine Binding Sites List in 7dug
Fluorine binding site 1 out of 3 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1601

b:244.6
occ:1.00
F2 A:HJR1601 0.0 244.6 1.0
C6 A:HJR1601 1.4 243.1 1.0
F1 A:HJR1601 2.2 243.5 1.0
F3 A:HJR1601 2.2 242.3 1.0
S A:HJR1601 2.6 242.5 1.0
O2 A:HJR1601 3.1 241.8 1.0
C12 A:HJR1601 3.2 169.7 1.0
N12 A:HJR1601 3.3 204.6 1.0
C62 A:HJR1601 3.9 151.7 1.0
O1 A:HJR1601 4.0 251.9 1.0
O62 A:HJR1601 4.4 140.1 1.0
C22 A:HJR1601 4.4 162.4 1.0

Fluorine binding site 2 out of 3 in 7dug

Go back to Fluorine Binding Sites List in 7dug
Fluorine binding site 2 out of 3 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1601

b:243.5
occ:1.00
F1 A:HJR1601 0.0 243.5 1.0
C6 A:HJR1601 1.4 243.1 1.0
F2 A:HJR1601 2.2 244.6 1.0
F3 A:HJR1601 2.2 242.3 1.0
S A:HJR1601 2.6 242.5 1.0
O1 A:HJR1601 3.0 251.9 1.0
O2 A:HJR1601 3.3 241.8 1.0
N12 A:HJR1601 4.0 204.6 1.0
N4 A:5MC1404 4.3 127.5 1.0
N4 A:C1403 4.6 130.8 1.0
C12 A:HJR1601 4.7 169.7 1.0
O6 A:G1497 4.8 157.9 1.0
CM5 A:5MC1404 4.8 145.4 1.0

Fluorine binding site 3 out of 3 in 7dug

Go back to Fluorine Binding Sites List in 7dug
Fluorine binding site 3 out of 3 in the Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Thermus Thermophilus (HB8) 30S Ribosomal Subunit with Mrna and Cognate Transfer Rna Anticodon Stem-Loop and Sisomicin Derivative N1''Tfms Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1601

b:242.3
occ:1.00
F3 A:HJR1601 0.0 242.3 1.0
C6 A:HJR1601 1.4 243.1 1.0
F2 A:HJR1601 2.2 244.6 1.0
F1 A:HJR1601 2.2 243.5 1.0
S A:HJR1601 2.6 242.5 1.0
N12 A:HJR1601 3.1 204.6 1.0
N4 A:5MC1404 3.2 127.5 1.0
O1 A:HJR1601 3.2 251.9 1.0
CM5 A:5MC1404 3.6 145.4 1.0
C12 A:HJR1601 3.7 169.7 1.0
O62 A:HJR1601 3.9 140.1 1.0
O2 A:HJR1601 4.0 241.8 1.0
C93 A:HJR1601 4.0 89.1 1.0
C62 A:HJR1601 4.1 151.7 1.0
C4 A:5MC1404 4.1 138.5 1.0
C5 A:5MC1404 4.3 136.2 1.0
C23 A:HJR1601 4.5 126.2 1.0
N33 A:HJR1601 4.5 104.7 1.0
C13 A:HJR1601 4.7 129.6 1.0
O6 A:G1405 4.8 147.3 1.0
O6 A:G1497 4.9 157.9 1.0

Reference:

H.Demirci, H.Demirci, E.Destan. N/A N/A.
Page generated: Tue Jul 15 19:11:45 2025

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