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Fluorine in PDB 5ci3: Ribonucleotide Reductase Y122 2,3,5-F3Y Variant

Enzymatic activity of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant

All present enzymatic activity of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant:
1.17.4.1;

Protein crystallography data

The structure of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant, PDB code: 5ci3 was solved by M.A.Funk, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.44 / 2.40
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.216, 92.216, 207.044, 90.00, 90.00, 120.00
R / Rfree (%) 16.6 / 21.2

Other elements in 5ci3:

The structure of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant (pdb code 5ci3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant, PDB code: 5ci3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 1 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:91.9
occ:0.55
F2 A:FY3122 0.0 91.9 0.6
CD2 A:FY3122 1.0 87.0 0.5
CD1 A:FY3122 1.3 86.7 0.6
CE2 A:FY3122 2.0 85.4 0.5
CG A:FY3122 2.2 85.4 0.5
CE1 A:FY3122 2.3 85.8 0.6
CG A:FY3122 2.3 84.4 0.6
F5 A:FY3122 2.4 81.9 0.5
F3 A:FY3122 2.7 83.9 0.6
CB A:FY3122 2.8 77.1 0.6
CB A:FY3122 2.8 78.7 0.5
CD1 A:LEU77 2.9 92.3 1.0
CA A:FY3122 3.0 74.8 0.5
CA A:FY3122 3.0 74.6 0.6
CZ A:FY3122 3.2 85.7 0.5
CD1 A:FY3122 3.3 86.7 0.5
CD1 A:ILE125 3.4 68.3 1.0
CZ A:FY3122 3.6 85.6 0.6
CD2 A:FY3122 3.6 86.8 0.6
CE1 A:FY3122 3.7 86.4 0.5
N A:FY3122 3.8 70.3 0.5
N A:FY3122 3.8 69.7 0.6
CE2 A:FY3122 4.1 87.2 0.6
CG A:LEU77 4.1 89.5 1.0
C A:FY3122 4.2 78.6 0.5
C A:FY3122 4.2 79.0 0.6
OH A:FY3122 4.3 85.6 0.5
O A:FY3122 4.4 80.5 0.5
O A:FY3122 4.4 80.7 0.6
C A:SER121 4.4 69.7 1.0
OG1 A:THR81 4.5 73.6 1.0
O A:SER121 4.5 71.6 1.0
F2 A:FY3122 4.5 88.6 0.5
CG1 A:ILE125 4.6 71.7 1.0
CB A:ILE125 4.6 73.1 1.0
OH A:FY3122 4.7 86.3 0.6
OG A:SER121 4.8 73.9 1.0
OD1 A:ASN227 4.8 81.5 1.0
OE1 A:GLN80 4.8 93.1 1.0
CD2 A:LEU77 4.9 90.3 1.0
O A:LEU77 4.9 75.5 1.0
O A:HOH542 4.9 85.9 1.0

Fluorine binding site 2 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 2 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:88.6
occ:0.45
F2 A:FY3122 0.0 88.6 0.5
CD2 A:FY3122 1.0 86.8 0.6
CD1 A:FY3122 1.3 86.7 0.5
CE2 A:FY3122 1.9 87.2 0.6
CG A:FY3122 2.2 84.4 0.6
F5 A:FY3122 2.3 91.3 0.6
CE1 A:FY3122 2.4 86.4 0.5
CG A:FY3122 2.4 85.4 0.5
F3 A:FY3122 2.7 88.5 0.5
CB A:FY3122 2.9 78.7 0.5
CB A:FY3122 2.9 77.1 0.6
CA A:SER119 3.1 73.1 0.6
CA A:SER119 3.1 73.6 0.4
CZ A:FY3122 3.2 85.6 0.6
O A:HIS118 3.3 74.4 1.0
CD1 A:FY3122 3.3 86.7 0.6
CA A:THR81 3.4 82.0 1.0
O A:SER119 3.6 75.8 0.6
O A:SER119 3.6 75.4 0.4
CZ A:FY3122 3.6 85.7 0.5
CD2 A:FY3122 3.6 87.0 0.5
N A:SER119 3.7 72.6 0.6
N A:SER119 3.7 72.8 0.4
CE1 A:FY3122 3.7 85.8 0.6
C A:HIS118 3.8 72.7 1.0
C A:SER119 3.8 74.5 0.6
C A:SER119 3.8 74.1 0.4
CG2 A:THR81 3.8 76.3 1.0
OG1 A:THR81 3.8 73.6 1.0
CB A:THR81 3.9 78.7 1.0
CB A:SER119 4.0 75.2 0.6
CB A:SER119 4.1 75.6 0.4
CE2 A:FY3122 4.1 85.4 0.5
CA A:FY3122 4.1 74.8 0.5
OG A:SER119 4.1 78.0 0.6
CA A:FY3122 4.1 74.6 0.6
N A:FY3122 4.2 70.3 0.5
N A:THR81 4.2 76.9 1.0
N A:FY3122 4.2 69.7 0.6
OH A:FY3122 4.3 86.3 0.6
O A:THR81 4.3 81.5 1.0
O A:GLN80 4.3 82.8 1.0
C A:THR81 4.4 85.0 1.0
F2 A:FY3122 4.5 91.9 0.6
O A:HOH537 4.5 69.2 1.0
C A:GLN80 4.5 76.2 1.0
CB A:ASP84 4.5 70.3 1.0
OH A:FY3122 4.7 85.6 0.5
N A:ARG120 5.0 68.4 1.0

Fluorine binding site 3 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 3 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:83.9
occ:0.55
F3 A:FY3122 0.0 83.9 0.6
F5 A:FY3122 0.7 81.9 0.5
CE2 A:FY3122 1.1 85.4 0.5
CE1 A:FY3122 1.3 85.8 0.6
CZ A:FY3122 1.7 85.7 0.5
OH A:FY3122 2.0 85.6 0.5
CD1 A:FY3122 2.4 86.7 0.6
CZ A:FY3122 2.4 85.6 0.6
CD2 A:FY3122 2.4 87.0 0.5
F2 A:FY3122 2.7 91.9 0.6
OH A:FY3122 2.8 86.3 0.6
CE1 A:FY3122 3.1 86.4 0.5
NE2 A:GLN80 3.2 87.5 1.0
CD A:GLN80 3.4 87.0 1.0
CD1 A:ILE231 3.5 73.2 1.0
CG A:FY3122 3.5 85.4 0.5
OE1 A:GLN80 3.6 93.1 1.0
CE2 A:FY3122 3.6 87.2 0.6
CG A:FY3122 3.6 84.4 0.6
CD1 A:ILE234 3.7 62.6 1.0
CD1 A:FY3122 3.7 86.7 0.5
CB A:GLN80 3.8 72.2 1.0
F3 A:FY3122 4.1 88.5 0.5
CD2 A:FY3122 4.1 86.8 0.6
CG A:GLN80 4.2 78.0 1.0
O A:HOH542 4.3 85.9 1.0
CD1 A:LEU77 4.4 92.3 1.0
F5 A:FY3122 4.7 91.3 0.6
CB A:FY3122 4.8 78.7 0.5
O A:HOH508 4.9 0.8 1.0
CB A:FY3122 4.9 77.1 0.6
CD1 A:ILE125 4.9 68.3 1.0
CG1 A:ILE231 5.0 71.5 1.0

Fluorine binding site 4 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 4 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:88.5
occ:0.45
F3 A:FY3122 0.0 88.5 0.5
F5 A:FY3122 0.9 91.3 0.6
CE2 A:FY3122 1.3 87.2 0.6
CE1 A:FY3122 1.3 86.4 0.5
CZ A:FY3122 1.8 85.6 0.6
OH A:FY3122 2.0 86.3 0.6
CZ A:FY3122 2.3 85.7 0.5
CD1 A:FY3122 2.4 86.7 0.5
CD2 A:FY3122 2.6 86.8 0.6
F2 A:FY3122 2.7 88.6 0.5
OH A:FY3122 2.7 85.6 0.5
CE1 A:FY3122 3.1 85.8 0.6
O A:GLN80 3.1 82.8 1.0
CB A:ASP84 3.2 70.3 1.0
OD2 A:ASP84 3.3 64.9 1.0
CG A:ASP84 3.6 72.0 1.0
CG A:FY3122 3.6 84.4 0.6
CE2 A:FY3122 3.6 85.4 0.5
CG A:FY3122 3.6 85.4 0.5
C A:GLN80 3.7 76.2 1.0
CD1 A:FY3122 3.8 86.7 0.6
CB A:HIS118 4.0 60.7 1.0
F3 A:FY3122 4.1 83.9 0.6
O A:HIS118 4.1 74.4 1.0
CD2 A:FY3122 4.1 87.0 0.5
CB A:GLN80 4.2 72.2 1.0
CZ A:PHE208 4.2 81.2 1.0
N A:THR81 4.2 76.9 1.0
C A:HIS118 4.2 72.7 1.0
CA A:THR81 4.2 82.0 1.0
CE1 A:PHE208 4.4 80.1 1.0
CA A:ASP84 4.4 75.7 1.0
CA A:GLN80 4.5 72.1 1.0
N A:SER119 4.5 72.6 0.6
N A:SER119 4.5 72.8 0.4
N A:ASP84 4.5 70.9 1.0
OD1 A:ASP84 4.7 75.7 1.0
F5 A:FY3122 4.7 81.9 0.5
CA A:HIS118 4.7 67.2 1.0
CA A:SER119 4.7 73.1 0.6
CA A:SER119 4.7 73.6 0.4
CD1 A:ILE234 4.8 62.6 1.0
O A:HOH561 4.9 89.8 1.0
CB A:FY3122 4.9 78.7 0.5
C A:THR81 5.0 85.0 1.0
CB A:FY3122 5.0 77.1 0.6
O A:THR81 5.0 81.5 1.0

Fluorine binding site 5 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 5 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:91.3
occ:0.55
F5 A:FY3122 0.0 91.3 0.6
F3 A:FY3122 0.9 88.5 0.5
CE2 A:FY3122 1.3 87.2 0.6
CE1 A:FY3122 1.8 86.4 0.5
CD1 A:FY3122 2.3 86.7 0.5
CZ A:FY3122 2.3 85.6 0.6
F2 A:FY3122 2.3 88.6 0.5
CD2 A:FY3122 2.3 86.8 0.6
OH A:FY3122 2.7 86.3 0.6
CB A:ASP84 2.9 70.3 1.0
CZ A:FY3122 3.0 85.7 0.5
OD2 A:ASP84 3.2 64.9 1.0
C A:HIS118 3.4 72.7 1.0
CB A:HIS118 3.5 60.7 1.0
O A:HIS118 3.5 74.4 1.0
CG A:ASP84 3.5 72.0 1.0
OH A:FY3122 3.5 85.6 0.5
CG A:FY3122 3.6 84.4 0.6
CE1 A:FY3122 3.6 85.8 0.6
N A:SER119 3.6 72.6 0.6
N A:SER119 3.6 72.8 0.4
CG A:FY3122 3.7 85.4 0.5
O A:GLN80 3.7 82.8 1.0
CA A:SER119 3.8 73.1 0.6
CA A:SER119 3.8 73.6 0.4
CA A:HIS118 4.0 67.2 1.0
CD1 A:FY3122 4.1 86.7 0.6
CE2 A:FY3122 4.1 85.4 0.5
CA A:ASP84 4.2 75.7 1.0
OG A:SER119 4.3 78.0 0.6
C A:GLN80 4.3 76.2 1.0
CD2 A:FY3122 4.4 87.0 0.5
CA A:THR81 4.4 82.0 1.0
N A:ASP84 4.6 70.9 1.0
OD1 A:ASP84 4.7 75.7 1.0
CB A:SER119 4.7 75.2 0.6
N A:THR81 4.7 76.9 1.0
F3 A:FY3122 4.7 83.9 0.6
CG A:HIS118 4.7 62.8 1.0
CB A:SER119 4.7 75.6 0.4
CB A:FY3122 4.8 78.7 0.5
C A:ASP84 4.8 81.2 1.0
CZ A:PHE208 4.8 81.2 1.0
CB A:FY3122 4.8 77.1 0.6
O A:THR81 4.9 81.5 1.0
C A:SER119 5.0 74.5 0.6
C A:SER119 5.0 74.1 0.4
O A:GLU115 5.0 69.9 1.0
CD1 A:ILE234 5.0 62.6 1.0

Fluorine binding site 6 out of 6 in 5ci3

Go back to Fluorine Binding Sites List in 5ci3
Fluorine binding site 6 out of 6 in the Ribonucleotide Reductase Y122 2,3,5-F3Y Variant


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ribonucleotide Reductase Y122 2,3,5-F3Y Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F122

b:81.9
occ:0.45
F5 A:FY3122 0.0 81.9 0.5
F3 A:FY3122 0.7 83.9 0.6
CE2 A:FY3122 1.3 85.4 0.5
CE1 A:FY3122 1.8 85.8 0.6
CZ A:FY3122 2.4 85.7 0.5
CD2 A:FY3122 2.4 87.0 0.5
F2 A:FY3122 2.4 91.9 0.6
CD1 A:FY3122 2.4 86.7 0.6
OH A:FY3122 2.7 85.6 0.5
CZ A:FY3122 3.0 85.6 0.6
CD1 A:ILE231 3.1 73.2 1.0
OH A:FY3122 3.5 86.3 0.6
NE2 A:GLN80 3.5 87.5 1.0
CE1 A:FY3122 3.6 86.4 0.5
CG A:FY3122 3.6 85.4 0.5
OE1 A:GLN80 3.7 93.1 1.0
CD A:GLN80 3.7 87.0 1.0
CG A:FY3122 3.8 84.4 0.6
CD1 A:ILE234 3.8 62.6 1.0
O A:HOH542 4.0 85.9 1.0
CD1 A:LEU77 4.1 92.3 1.0
CD1 A:FY3122 4.1 86.7 0.5
CE2 A:FY3122 4.1 87.2 0.6
CD1 A:ILE125 4.2 68.3 1.0
CB A:GLN80 4.4 72.2 1.0
CD2 A:FY3122 4.5 86.8 0.6
CG1 A:ILE231 4.6 71.5 1.0
OD1 A:ASN227 4.6 81.5 1.0
CG A:GLN80 4.7 78.0 1.0
F3 A:FY3122 4.7 88.5 0.5
CB A:FY3122 4.8 78.7 0.5
CB A:FY3122 4.9 77.1 0.6
O A:HOH508 4.9 0.8 1.0
OG A:SER121 4.9 73.9 1.0

Reference:

P.H.Oyala, K.R.Ravichandran, M.A.Funk, P.A.Stucky, T.A.Stich, C.L.Drennan, R.D.Britt, J.Stubbe. Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated Into Enzymes: E. Coli Ribonucleotide Reductase As An Example. J.Am.Chem.Soc. V. 138 7951 2016.
ISSN: ESSN 1520-5126
PubMed: 27276098
DOI: 10.1021/JACS.6B03605
Page generated: Tue Jul 15 02:52:19 2025

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