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:
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
|