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Fluorine in PDB 4r88: Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine

Enzymatic activity of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine

All present enzymatic activity of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine:
3.5.4.1;

Protein crystallography data

The structure of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine, PDB code: 4r88 was solved by A.A.Fedorov, E.V.Fedorov, D.S.Hitchcock, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.66 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.954, 162.419, 184.047, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.1

Other elements in 4r88:

The structure of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine also contains other interesting chemical elements:

Iron (Fe) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine (pdb code 4r88). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine, PDB code: 4r88:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 1 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


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 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:23.6
occ:1.00
F A:1LD501 0.0 23.6 1.0
C5 A:1LD501 1.3 22.8 1.0
C6 A:1LD501 2.4 19.5 1.0
C4 A:1LD501 2.4 30.3 1.0
N4 A:1LD501 2.8 24.2 1.0
OE2 A:GLU273 3.0 30.3 1.0
OG A:SER309 3.1 24.2 1.0
CE3 A:TRP314 3.5 20.4 1.0
CD2 A:TRP314 3.5 22.2 1.0
N3 A:1LD501 3.6 26.2 1.0
N1 A:1LD501 3.6 21.5 1.0
OD2 A:ASP308 3.6 35.9 1.0
CG A:TRP314 3.7 25.1 1.0
CD2 A:HIS58 3.8 22.4 1.0
OD1 A:ASP308 3.8 38.9 1.0
CB A:TRP314 3.8 15.2 1.0
CG A:ASP308 3.9 34.5 1.0
NE2 A:HIS58 4.0 18.8 1.0
C2 A:1LD501 4.1 24.7 1.0
CD A:GLU273 4.1 31.6 1.0
CZ3 A:TRP314 4.2 26.6 1.0
FE A:FE2502 4.2 27.5 0.6
CE2 A:TRP314 4.2 23.1 1.0
OD1 A:ASP312 4.3 24.0 1.0
CD1 A:TRP314 4.4 27.2 1.0
CG A:HIS58 4.5 22.0 1.0
CB A:SER309 4.5 20.2 1.0
CE1 A:HIS58 4.7 18.0 1.0
NE1 A:TRP314 4.7 27.2 1.0
CH2 A:TRP314 4.8 23.0 1.0
OE1 A:GLU273 4.9 33.8 1.0
CZ2 A:TRP314 4.9 24.5 1.0
OD2 A:ASP312 4.9 27.1 1.0
O A:ASP308 4.9 23.0 1.0
ND1 A:HIS58 5.0 20.0 1.0
CG A:ASP312 5.0 23.9 1.0

Fluorine binding site 2 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 2 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


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 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:30.4
occ:1.00
F B:1LD501 0.0 30.4 1.0
C5 B:1LD501 1.3 26.9 1.0
C6 B:1LD501 2.4 23.1 1.0
C4 B:1LD501 2.4 29.0 1.0
N4 B:1LD501 2.8 26.0 1.0
OE2 B:GLU273 3.0 26.5 1.0
OG B:SER309 3.2 21.7 1.0
CE3 B:TRP314 3.4 17.8 1.0
CD2 B:TRP314 3.4 14.6 1.0
CG B:TRP314 3.6 18.6 1.0
N1 B:1LD501 3.6 17.1 1.0
N3 B:1LD501 3.6 25.1 1.0
OD2 B:ASP308 3.7 38.4 1.0
CB B:TRP314 3.7 18.2 1.0
CD2 B:HIS58 3.8 17.9 1.0
OD1 B:ASP308 3.9 44.3 1.0
NE2 B:HIS58 4.0 22.9 1.0
CG B:ASP308 4.0 34.5 1.0
C2 B:1LD501 4.0 16.8 1.0
CD B:GLU273 4.1 31.9 1.0
CZ3 B:TRP314 4.2 21.2 1.0
FE B:FE2502 4.2 34.3 0.6
CE2 B:TRP314 4.2 20.9 1.0
OD1 B:ASP312 4.3 23.9 1.0
CD1 B:TRP314 4.4 21.1 1.0
CG B:HIS58 4.4 18.8 1.0
CB B:SER309 4.6 20.7 1.0
CE1 B:HIS58 4.7 19.6 1.0
NE1 B:TRP314 4.7 26.7 1.0
CH2 B:TRP314 4.8 21.0 1.0
OD2 B:ASP312 4.8 23.3 1.0
CZ2 B:TRP314 4.9 21.8 1.0
OE1 B:GLU273 4.9 29.2 1.0
ND1 B:HIS58 4.9 19.7 1.0
CG B:GLU273 4.9 27.5 1.0
O B:ASP308 5.0 21.9 1.0
CG B:ASP312 5.0 24.0 1.0

Fluorine binding site 3 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 3 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


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 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:29.3
occ:1.00
F C:1LD501 0.0 29.3 1.0
C5 C:1LD501 1.3 25.2 1.0
C4 C:1LD501 2.4 28.1 1.0
C6 C:1LD501 2.4 21.3 1.0
N4 C:1LD501 2.8 24.0 1.0
OE2 C:GLU273 3.1 28.3 1.0
OG C:SER309 3.1 28.7 1.0
CD2 C:TRP314 3.4 21.9 1.0
CE3 C:TRP314 3.4 20.4 1.0
CG C:TRP314 3.5 22.8 1.0
N3 C:1LD501 3.6 24.9 1.0
N1 C:1LD501 3.6 26.9 1.0
CB C:TRP314 3.7 20.0 1.0
OD1 C:ASP308 3.8 36.9 1.0
CD2 C:HIS58 3.8 19.1 1.0
OD2 C:ASP308 3.8 41.8 1.0
NE2 C:HIS58 3.9 22.1 1.0
CG C:ASP308 4.0 32.8 1.0
C2 C:1LD501 4.0 23.4 1.0
CE2 C:TRP314 4.1 24.6 1.0
CZ3 C:TRP314 4.2 22.5 1.0
CD C:GLU273 4.2 33.3 1.0
FE C:FE2502 4.2 31.8 0.6
OD1 C:ASP312 4.3 29.4 1.0
CD1 C:TRP314 4.3 20.4 1.0
CG C:HIS58 4.4 13.5 1.0
CB C:SER309 4.6 24.6 1.0
CE1 C:HIS58 4.6 26.4 1.0
NE1 C:TRP314 4.6 25.1 1.0
CH2 C:TRP314 4.8 26.4 1.0
CZ2 C:TRP314 4.8 22.5 1.0
ND1 C:HIS58 4.9 25.4 1.0
O C:ASP308 4.9 24.9 1.0
OD2 C:ASP312 5.0 20.9 1.0

Fluorine binding site 4 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 4 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:28.0
occ:1.00
F D:1LD501 0.0 28.0 1.0
C5 D:1LD501 1.3 26.8 1.0
C6 D:1LD501 2.4 20.1 1.0
C4 D:1LD501 2.4 26.2 1.0
N4 D:1LD501 2.8 29.0 1.0
OE2 D:GLU273 3.0 30.1 1.0
OG D:SER309 3.1 30.1 1.0
CD2 D:TRP314 3.4 19.3 1.0
CE3 D:TRP314 3.5 23.1 1.0
CG D:TRP314 3.5 25.8 1.0
N3 D:1LD501 3.6 18.3 1.0
N1 D:1LD501 3.6 20.8 1.0
CB D:TRP314 3.7 20.8 1.0
OD2 D:ASP308 3.8 41.0 1.0
CD2 D:HIS58 4.0 24.2 1.0
C2 D:1LD501 4.1 22.9 1.0
NE2 D:HIS58 4.1 23.0 1.0
CG D:ASP308 4.1 41.1 1.0
CD D:GLU273 4.2 31.6 1.0
OD1 D:ASP308 4.2 51.2 1.0
CE2 D:TRP314 4.2 19.9 1.0
FE D:FE2502 4.2 35.3 0.7
CZ3 D:TRP314 4.3 24.2 1.0
OD1 D:ASP312 4.3 23.4 1.0
CD1 D:TRP314 4.3 21.3 1.0
CB D:SER309 4.5 19.9 1.0
CG D:HIS58 4.5 22.9 1.0
CE1 D:HIS58 4.6 20.8 1.0
NE1 D:TRP314 4.6 21.5 1.0
ND1 D:HIS58 4.8 16.9 1.0
CZ2 D:TRP314 4.9 21.8 1.0
OD2 D:ASP312 4.9 26.8 1.0
CH2 D:TRP314 4.9 18.1 1.0
OE1 D:GLU273 4.9 29.1 1.0
CG D:GLU273 5.0 22.2 1.0

Fluorine binding site 5 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 5 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:31.0
occ:1.00
F E:1LD501 0.0 31.0 1.0
C5 E:1LD501 1.3 29.0 1.0
C6 E:1LD501 2.4 22.1 1.0
C4 E:1LD501 2.4 31.8 1.0
N4 E:1LD501 2.8 20.1 1.0
OE2 E:GLU273 3.0 39.2 1.0
OG E:SER309 3.1 24.9 1.0
CD2 E:TRP314 3.4 18.9 1.0
CE3 E:TRP314 3.4 17.9 1.0
CG E:TRP314 3.6 25.1 1.0
N1 E:1LD501 3.6 20.9 1.0
N3 E:1LD501 3.6 27.8 1.0
OD1 E:ASP308 3.7 34.3 1.0
CB E:TRP314 3.7 20.1 1.0
CD2 E:HIS58 3.8 20.2 1.0
OD2 E:ASP308 3.9 38.6 1.0
NE2 E:HIS58 4.0 23.6 1.0
C2 E:1LD501 4.0 23.8 1.0
CG E:ASP308 4.0 33.4 1.0
FE E:FE2502 4.1 27.4 0.6
CD E:GLU273 4.1 35.1 1.0
CZ3 E:TRP314 4.2 18.2 1.0
CE2 E:TRP314 4.2 25.5 1.0
OD1 E:ASP312 4.2 31.2 1.0
CD1 E:TRP314 4.3 27.9 1.0
CG E:HIS58 4.4 20.6 1.0
CB E:SER309 4.5 26.3 1.0
CE1 E:HIS58 4.6 25.4 1.0
NE1 E:TRP314 4.7 26.7 1.0
CH2 E:TRP314 4.8 19.2 1.0
CZ2 E:TRP314 4.8 21.7 1.0
ND1 E:HIS58 4.8 22.5 1.0
OE1 E:GLU273 4.8 33.1 1.0
O E:ASP308 4.9 24.6 1.0
OD2 E:ASP312 4.9 33.5 1.0
CG E:ASP312 5.0 33.4 1.0
CG E:GLU273 5.0 24.4 1.0

Fluorine binding site 6 out of 6 in 4r88

Go back to Fluorine Binding Sites List in 4r88
Fluorine binding site 6 out of 6 in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F502

b:29.0
occ:1.00
F F:1LD502 0.0 29.0 1.0
C5 F:1LD502 1.3 28.6 1.0
C6 F:1LD502 2.4 23.0 1.0
C4 F:1LD502 2.4 33.2 1.0
N4 F:1LD502 2.8 35.1 1.0
OG F:SER309 3.0 31.6 1.0
OE2 F:GLU273 3.1 26.6 1.0
CE3 F:TRP314 3.4 19.1 1.0
CD2 F:TRP314 3.4 21.2 1.0
CG F:TRP314 3.5 21.6 1.0
N3 F:1LD502 3.6 30.2 1.0
N1 F:1LD502 3.6 23.2 1.0
CB F:TRP314 3.7 18.4 1.0
CD2 F:HIS58 3.8 25.9 1.0
OD1 F:ASP308 3.8 47.0 1.0
OD2 F:ASP308 3.8 50.1 1.0
NE2 F:HIS58 3.9 28.4 1.0
C2 F:1LD502 4.0 27.4 1.0
CG F:ASP308 4.1 44.9 1.0
CZ3 F:TRP314 4.1 23.6 1.0
CE2 F:TRP314 4.1 24.4 1.0
FE F:FE2503 4.2 31.3 0.6
CD F:GLU273 4.2 30.7 1.0
CD1 F:TRP314 4.3 21.2 1.0
OD1 F:ASP312 4.4 24.6 1.0
CB F:SER309 4.5 22.2 1.0
CG F:HIS58 4.5 27.6 1.0
CE1 F:HIS58 4.6 27.6 1.0
NE1 F:TRP314 4.6 24.2 1.0
CH2 F:TRP314 4.8 24.2 1.0
CZ2 F:TRP314 4.8 20.1 1.0
OD2 F:ASP312 4.9 28.4 1.0
ND1 F:HIS58 4.9 27.6 1.0
OE1 F:GLU273 5.0 30.1 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, D.S.Hitchcock, F.M.Raushel, S.C.Almo. Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine To Be Published.
Page generated: Tue Jul 15 00:36:40 2025

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