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Fluorine in PDB 6w4x: Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp

Enzymatic activity of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp

All present enzymatic activity of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp:
1.17.4.1;

Other elements in 6w4x:

The structure of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp (pdb code 6w4x). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp, PDB code: 6w4x:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 1 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F122

b:38.8
occ:1.00
 F2 C:FY3122 0.0 38.8 1.0
CD1 C:FY3122 1.3 38.8 1.0
CG C:FY3122 2.3 38.8 1.0
CE1 C:FY3122 2.3 38.8 1.0
F3 C:FY3122 2.7 38.8 1.0
CB C:FY3122 2.9 38.8 1.0
CA C:FY3122 3.1 38.8 1.0
CG C:LEU77 3.4 46.1 1.0
CD2 C:FY3122 3.6 38.8 1.0
CZ C:FY3122 3.6 38.8 1.0
CD1 C:ILE125 3.7 40.4 1.0
CD1 C:LEU77 4.0 46.1 1.0
CG1 C:ILE125 4.0 40.4 1.0
N C:FY3122 4.0 38.8 1.0
CE2 C:FY3122 4.0 38.8 1.0
CD2 C:LEU77 4.1 46.1 1.0
C C:FY3122 4.1 38.8 1.0
O C:FY3122 4.3 38.8 1.0
CB C:LEU77 4.4 46.1 1.0
CA C:LEU77 4.6 46.1 1.0
CD1 C:ILE231 4.6 37.4 1.0
OH C:FY3122 4.8 38.8 1.0
C C:SER121 4.8 34.9 1.0
O C:LEU77 4.8 46.1 1.0
CG1 C:ILE231 4.8 37.4 1.0
O C:SER121 4.8 34.9 1.0

Fluorine binding site 2 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 2 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F122

b:38.8
occ:1.00
 F3 C:FY3122 0.0 38.8 1.0
CE1 C:FY3122 1.3 38.8 1.0
CD1 C:FY3122 2.3 38.8 1.0
CZ C:FY3122 2.3 38.8 1.0
F2 C:FY3122 2.7 38.8 1.0
OH C:FY3122 2.8 38.8 1.0
NE2 C:GLN80 3.3 44.3 1.0
OE1 C:GLN80 3.4 44.3 1.0
CD C:GLN80 3.5 44.3 1.0
CD1 C:ILE231 3.6 37.4 1.0
CE2 C:FY3122 3.6 38.8 1.0
CG1 C:ILE231 3.6 37.4 1.0
CG C:FY3122 3.6 38.8 1.0
CD2 C:FY3122 4.1 38.8 1.0
CE1 C:PHE212 4.1 42.7 1.0
CG2 C:ILE231 4.3 37.4 1.0
CD1 C:ILE234 4.3 34.1 1.0
CB C:GLN80 4.5 44.3 1.0
CB C:ILE231 4.5 37.4 1.0
CG C:GLN80 4.6 44.3 1.0
F5 C:FY3122 4.7 38.8 1.0
CG2 C:ILE234 4.8 34.1 1.0
CD1 C:LEU77 4.8 46.1 1.0
CD1 C:PHE212 4.8 42.7 1.0
CB C:FY3122 4.9 38.8 1.0

Fluorine binding site 3 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 3 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F122

b:38.8
occ:1.00
 F5 C:FY3122 0.0 38.8 1.0
CE2 C:FY3122 1.4 38.8 1.0
OD2 C:ASP84 2.2 43.1 1.0
CZ C:FY3122 2.3 38.8 1.0
CD2 C:FY3122 2.4 38.8 1.0
OH C:FY3122 2.7 38.8 1.0
CG C:ASP84 2.9 43.1 1.0
CB C:HIS118 3.5 33.7 1.0
CB C:ASP84 3.6 43.1 1.0
CE1 C:FY3122 3.6 38.8 1.0
CG C:FY3122 3.6 38.8 1.0
OD1 C:ASP84 3.7 43.1 1.0
FE2 C:FEO501 3.8 43.5 1.0
O C:HOH602 3.9 38.5 1.0
O C:HIS118 3.9 33.7 1.0
C C:HIS118 4.0 33.7 1.0
CD1 C:FY3122 4.1 38.8 1.0
O C:GLN80 4.2 44.3 1.0
OE1 C:GLN80 4.2 44.3 1.0
CA C:HIS118 4.3 33.7 1.0
CG C:HIS118 4.4 33.7 1.0
N C:SER119 4.4 37.6 1.0
ND1 C:HIS118 4.4 33.7 1.0
CB C:GLN80 4.5 44.3 1.0
C C:GLN80 4.7 44.3 1.0
F3 C:FY3122 4.7 38.8 1.0
CG2 C:ILE234 4.7 34.1 1.0
CD1 C:ILE234 4.8 34.1 1.0
CA C:SER119 4.9 37.6 1.0
CB C:FY3122 4.9 38.8 1.0
CA C:ASP84 5.0 43.1 1.0
CD C:GLN80 5.0 44.3 1.0

Fluorine binding site 4 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 4 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F122

b:62.9
occ:1.00
 F2 D:FY3122 0.0 62.9 1.0
CD1 D:FY3122 1.3 62.9 1.0
CG D:FY3122 2.3 62.9 1.0
CE1 D:FY3122 2.3 62.9 1.0
F3 D:FY3122 2.7 62.9 1.0
CB D:FY3122 2.9 62.9 1.0
CA D:FY3122 3.0 62.9 1.0
CD2 D:LEU77 3.2 78.6 1.0
CG D:LEU77 3.4 78.6 1.0
CD2 D:FY3122 3.6 62.9 1.0
CZ D:FY3122 3.6 62.9 1.0
NE2 D:GLN80 3.7 75.0 1.0
CD1 D:ILE125 3.8 64.8 1.0
CD1 D:LEU77 3.9 78.6 1.0
C D:FY3122 4.0 62.9 1.0
N D:FY3122 4.0 62.9 1.0
O D:FY3122 4.0 62.9 1.0
CE2 D:FY3122 4.0 62.9 1.0
CB D:ILE125 4.5 64.8 1.0
CD D:GLN80 4.6 75.0 1.0
CG1 D:ILE125 4.6 64.8 1.0
OG1 D:THR81 4.6 72.8 1.0
O D:SER121 4.7 55.0 1.0
CG D:GLN80 4.7 75.0 1.0
C D:SER121 4.7 55.0 1.0
OH D:FY3122 4.8 62.9 1.0
CB D:LEU77 4.8 78.6 1.0
CG2 D:ILE125 4.9 64.8 1.0
O D:LEU77 4.9 78.6 1.0

Fluorine binding site 5 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 5 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F122

b:62.9
occ:1.00
 F3 D:FY3122 0.0 62.9 1.0
CE1 D:FY3122 1.3 62.9 1.0
NE2 D:GLN80 2.3 75.0 1.0
CD1 D:FY3122 2.3 62.9 1.0
CZ D:FY3122 2.4 62.9 1.0
F2 D:FY3122 2.7 62.9 1.0
OH D:FY3122 2.8 62.9 1.0
CD D:GLN80 2.9 75.0 1.0
CD1 D:ILE231 3.1 68.7 1.0
OE1 D:GLN80 3.5 75.0 1.0
CE2 D:FY3122 3.6 62.9 1.0
CG D:FY3122 3.6 62.9 1.0
CG D:GLN80 3.7 75.0 1.0
CD2 D:FY3122 4.1 62.9 1.0
CG1 D:ILE231 4.4 68.7 1.0
CB D:GLN80 4.5 75.0 1.0
CD1 D:ILE234 4.5 58.1 1.0
F5 D:FY3122 4.7 62.9 1.0
CD1 D:ILE125 4.7 64.8 1.0
CG D:LEU77 4.7 78.6 1.0
CB D:FY3122 4.9 62.9 1.0

Fluorine binding site 6 out of 6 in 6w4x

Go back to Fluorine Binding Sites List in 6w4x
Fluorine binding site 6 out of 6 in the Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Holocomplex of E. Coli Class Ia Ribonucleotide Reductase with Gdp and Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F122

b:62.9
occ:1.00
 F5 D:FY3122 0.0 62.9 1.0
CE2 D:FY3122 1.3 62.9 1.0
OD2 D:ASP84 2.1 65.3 1.0
CZ D:FY3122 2.3 62.9 1.0
CD2 D:FY3122 2.3 62.9 1.0
OH D:FY3122 2.7 62.9 1.0
CG D:ASP84 2.9 65.3 1.0
CB D:ASP84 3.1 65.3 1.0
CE1 D:FY3122 3.6 62.9 1.0
CG D:FY3122 3.6 62.9 1.0
CB D:HIS118 3.7 51.8 1.0
O D:HOH601 3.7 65.3 1.0
O D:GLN80 3.8 75.0 1.0
CE1 D:PHE208 4.0 76.0 1.0
O D:HIS118 4.0 51.8 1.0
CD1 D:FY3122 4.1 62.9 1.0
OD1 D:ASP84 4.1 65.3 1.0
C D:HIS118 4.2 51.8 1.0
FE2 D:FEO501 4.4 62.5 1.0
C D:GLN80 4.4 75.0 1.0
CA D:HIS118 4.5 51.8 1.0
CG D:HIS118 4.5 51.8 1.0
CA D:ASP84 4.5 65.3 1.0
ND1 D:HIS118 4.6 51.8 1.0
CZ D:PHE208 4.6 76.0 1.0
N D:SER119 4.7 54.0 1.0
F3 D:FY3122 4.7 62.9 1.0
CB D:GLN80 4.7 75.0 1.0
N D:ASP84 4.8 65.3 1.0
CB D:FY3122 4.9 62.9 1.0
CD1 D:ILE234 4.9 58.1 1.0
CG2 D:ILE234 4.9 58.1 1.0
CD1 D:PHE208 4.9 76.0 1.0

Reference:

G.Kang, A.T.Taguchi, J.Stubbe, C.L.Drennan. Structure of A Trapped Radical Transfer Pathway Within A Ribonucleotide Reductase Holocomplex. Science 2020.
ISSN: ESSN 1095-9203
PubMed: 32217749
DOI: 10.1126/SCIENCE.ABA6794
Page generated: Fri Aug 2 03:34:28 2024

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