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Iron 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:

Fluorine (F) 6 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of 5-Methylcytosine Deaminase From Klebsiella Pneumoniae Liganded with 5-Fluorocytosine, PDB code: 4r88:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe502

b:27.5
occ:0.56
NE2 A:HIS56 2.3 18.7 1.0
NE2 A:HIS58 2.4 18.8 1.0
NE2 A:HIS209 2.5 14.3 1.0
OD2 A:ASP308 2.6 35.9 1.0
NE2 A:HIS241 3.0 22.6 1.0
CD2 A:HIS209 3.2 16.1 1.0
CD2 A:HIS58 3.2 22.4 1.0
CE1 A:HIS56 3.2 22.3 1.0
CD2 A:HIS56 3.3 20.4 1.0
CG A:ASP308 3.4 34.5 1.0
OD1 A:ASP308 3.5 38.9 1.0
CE1 A:HIS209 3.5 18.0 1.0
CE1 A:HIS58 3.5 18.0 1.0
C4 A:1LD501 3.6 30.3 1.0
CE1 A:HIS241 3.8 28.0 1.0
N4 A:1LD501 3.8 24.2 1.0
C5 A:1LD501 3.8 22.8 1.0
N3 A:1LD501 4.0 26.2 1.0
CD2 A:HIS241 4.0 19.5 1.0
F A:1LD501 4.2 23.6 1.0
ND1 A:HIS56 4.3 18.4 1.0
CG A:HIS209 4.3 15.7 1.0
C6 A:1LD501 4.4 19.5 1.0
CG A:HIS56 4.4 19.9 1.0
CG A:HIS58 4.5 22.0 1.0
ND1 A:HIS209 4.5 16.1 1.0
C2 A:1LD501 4.5 24.7 1.0
ND1 A:HIS58 4.6 20.0 1.0
N1 A:1LD501 4.7 21.5 1.0
CB A:ASP308 4.7 17.3 1.0
OE2 A:GLU212 4.9 20.3 1.0
ND1 A:HIS241 5.0 22.8 1.0

Iron binding site 2 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe502

b:34.3
occ:0.58
NE2 B:HIS56 2.3 23.9 1.0
NE2 B:HIS58 2.4 22.9 1.0
NE2 B:HIS209 2.5 14.8 1.0
OD2 B:ASP308 2.6 38.4 1.0
NE2 B:HIS241 3.0 23.4 1.0
CE1 B:HIS56 3.2 21.0 1.0
CD2 B:HIS58 3.2 17.9 1.0
CD2 B:HIS209 3.2 13.1 1.0
CD2 B:HIS56 3.3 18.1 1.0
CG B:ASP308 3.3 34.5 1.0
OD1 B:ASP308 3.3 44.3 1.0
CE1 B:HIS58 3.5 19.6 1.0
CE1 B:HIS209 3.5 15.2 1.0
C4 B:1LD501 3.7 29.0 1.0
CE1 B:HIS241 3.8 25.4 1.0
C5 B:1LD501 3.8 26.9 1.0
N4 B:1LD501 3.9 26.0 1.0
N3 B:1LD501 4.0 25.1 1.0
CD2 B:HIS241 4.1 22.2 1.0
F B:1LD501 4.2 30.4 1.0
ND1 B:HIS56 4.3 18.9 1.0
C6 B:1LD501 4.3 23.1 1.0
CG B:HIS56 4.4 21.4 1.0
CG B:HIS209 4.4 11.9 1.0
CG B:HIS58 4.4 18.8 1.0
C2 B:1LD501 4.5 16.8 1.0
ND1 B:HIS209 4.5 15.7 1.0
ND1 B:HIS58 4.5 19.7 1.0
N1 B:1LD501 4.6 17.1 1.0
CB B:ASP308 4.7 21.3 1.0
OE2 B:GLU212 4.9 20.4 1.0

Iron binding site 3 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe502

b:31.8
occ:0.62
NE2 C:HIS56 2.3 23.5 1.0
NE2 C:HIS58 2.4 22.1 1.0
NE2 C:HIS209 2.5 23.0 1.0
OD2 C:ASP308 2.6 41.8 1.0
NE2 C:HIS241 3.1 25.4 1.0
CD2 C:HIS209 3.2 19.4 1.0
CE1 C:HIS56 3.2 18.2 1.0
CD2 C:HIS58 3.3 19.1 1.0
CD2 C:HIS56 3.3 23.0 1.0
CG C:ASP308 3.4 32.8 1.0
CE1 C:HIS209 3.5 24.7 1.0
CE1 C:HIS58 3.5 26.4 1.0
OD1 C:ASP308 3.5 36.9 1.0
C4 C:1LD501 3.7 28.1 1.0
C5 C:1LD501 3.9 25.2 1.0
CE1 C:HIS241 3.9 27.9 1.0
N4 C:1LD501 3.9 24.0 1.0
N3 C:1LD501 4.0 24.9 1.0
CD2 C:HIS241 4.1 20.0 1.0
F C:1LD501 4.2 29.3 1.0
C6 C:1LD501 4.3 21.3 1.0
CG C:HIS209 4.4 21.9 1.0
ND1 C:HIS56 4.4 26.1 1.0
CG C:HIS56 4.4 25.3 1.0
C2 C:1LD501 4.4 23.4 1.0
ND1 C:HIS209 4.4 19.8 1.0
CG C:HIS58 4.5 13.5 1.0
ND1 C:HIS58 4.6 25.4 1.0
N1 C:1LD501 4.6 26.9 1.0
CB C:ASP308 4.7 24.0 1.0
OE2 C:GLU212 4.9 23.9 1.0

Iron binding site 4 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe502

b:35.3
occ:0.69
NE2 D:HIS56 2.4 23.5 1.0
NE2 D:HIS58 2.4 23.0 1.0
NE2 D:HIS209 2.5 19.2 1.0
OD2 D:ASP308 2.5 41.0 1.0
NE2 D:HIS241 3.0 19.7 1.0
CD2 D:HIS209 3.2 17.0 1.0
CG D:ASP308 3.3 41.1 1.0
CE1 D:HIS56 3.3 23.6 1.0
OD1 D:ASP308 3.3 51.2 1.0
CD2 D:HIS58 3.3 24.2 1.0
CD2 D:HIS56 3.4 20.1 1.0
CE1 D:HIS58 3.4 20.8 1.0
CE1 D:HIS209 3.5 18.9 1.0
C4 D:1LD501 3.6 26.2 1.0
CE1 D:HIS241 3.8 21.2 1.0
N4 D:1LD501 3.8 29.0 1.0
C5 D:1LD501 3.9 26.8 1.0
N3 D:1LD501 4.0 18.3 1.0
CD2 D:HIS241 4.0 23.2 1.0
F D:1LD501 4.2 28.0 1.0
CG D:HIS209 4.3 17.5 1.0
C6 D:1LD501 4.4 20.1 1.0
ND1 D:HIS56 4.4 22.1 1.0
C2 D:1LD501 4.4 22.9 1.0
ND1 D:HIS209 4.5 20.2 1.0
CG D:HIS56 4.5 19.3 1.0
CG D:HIS58 4.5 22.9 1.0
ND1 D:HIS58 4.5 16.9 1.0
N1 D:1LD501 4.6 20.8 1.0
CB D:ASP308 4.7 28.3 1.0
OE2 D:GLU212 4.8 21.3 1.0
ND1 D:HIS241 5.0 21.9 1.0

Iron binding site 5 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe502

b:27.4
occ:0.55
NE2 E:HIS56 2.4 22.5 1.0
NE2 E:HIS58 2.4 23.6 1.0
OD2 E:ASP308 2.5 38.6 1.0
NE2 E:HIS209 2.5 18.6 1.0
NE2 E:HIS241 3.0 26.9 1.0
CD2 E:HIS209 3.2 20.0 1.0
CD2 E:HIS58 3.2 20.2 1.0
CG E:ASP308 3.3 33.4 1.0
CE1 E:HIS56 3.3 20.1 1.0
CD2 E:HIS56 3.3 20.3 1.0
OD1 E:ASP308 3.4 34.3 1.0
CE1 E:HIS58 3.5 25.4 1.0
CE1 E:HIS209 3.6 18.8 1.0
C4 E:1LD501 3.6 31.8 1.0
C5 E:1LD501 3.8 29.0 1.0
CE1 E:HIS241 3.8 23.3 1.0
N4 E:1LD501 3.8 20.1 1.0
N3 E:1LD501 4.0 27.8 1.0
CD2 E:HIS241 4.0 24.6 1.0
F E:1LD501 4.1 31.0 1.0
C6 E:1LD501 4.3 22.1 1.0
CG E:HIS209 4.4 20.2 1.0
CG E:HIS58 4.4 20.6 1.0
ND1 E:HIS56 4.5 20.7 1.0
C2 E:1LD501 4.5 23.8 1.0
CG E:HIS56 4.5 23.6 1.0
ND1 E:HIS209 4.5 18.0 1.0
ND1 E:HIS58 4.5 22.5 1.0
N1 E:1LD501 4.6 20.9 1.0
CB E:ASP308 4.7 19.0 1.0
OE2 E:GLU212 4.9 20.8 1.0
ND1 E:HIS241 5.0 22.8 1.0

Iron binding site 6 out of 6 in 4r88

Go back to Iron Binding Sites List in 4r88
Iron 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 Iron with other atoms in the Fe 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:Fe503

b:31.3
occ:0.60
NE2 F:HIS56 2.4 22.1 1.0
NE2 F:HIS209 2.5 15.0 1.0
NE2 F:HIS58 2.5 28.4 1.0
OD2 F:ASP308 2.6 50.1 1.0
NE2 F:HIS241 3.0 26.4 1.0
CD2 F:HIS209 3.2 23.6 1.0
OD1 F:ASP308 3.2 47.0 1.0
CG F:ASP308 3.2 44.9 1.0
CD2 F:HIS56 3.3 18.5 1.0
CE1 F:HIS56 3.3 24.8 1.0
CD2 F:HIS58 3.4 25.9 1.0
CE1 F:HIS209 3.5 21.8 1.0
C4 F:1LD502 3.6 33.2 1.0
CE1 F:HIS58 3.6 27.6 1.0
CE1 F:HIS241 3.7 28.4 1.0
N4 F:1LD502 3.8 35.1 1.0
C5 F:1LD502 3.8 28.6 1.0
N3 F:1LD502 3.9 30.2 1.0
CD2 F:HIS241 4.1 30.7 1.0
F F:1LD502 4.2 29.0 1.0
CG F:HIS209 4.3 19.9 1.0
C6 F:1LD502 4.4 23.0 1.0
ND1 F:HIS56 4.4 22.1 1.0
C2 F:1LD502 4.4 27.4 1.0
CG F:HIS56 4.4 20.1 1.0
ND1 F:HIS209 4.5 21.9 1.0
CG F:HIS58 4.6 27.6 1.0
N1 F:1LD502 4.6 23.2 1.0
CB F:ASP308 4.6 34.7 1.0
ND1 F:HIS58 4.7 27.6 1.0
OE2 F:GLU212 4.9 27.7 1.0
ND1 F:HIS241 5.0 27.7 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: Mon Aug 5 09:09:59 2024

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