Fluorine in PDB 6jfr: K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
Enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
All present enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus:
3.5.1.88;
Protein crystallography data
The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr
was solved by
I.H.Lee,
T.H.Ho,
L.W.Kang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.99 /
2.40
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.792,
120.709,
47.281,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20 /
25.4
|
Other elements in 6jfr:
The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
(pdb code 6jfr). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6jfr
Go back to
Fluorine Binding Sites List in 6jfr
Fluorine binding site 1 out
of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F203
b:77.7
occ:1.00
|
F1
|
A:K3U203
|
0.0
|
77.7
|
1.0
|
C12
|
A:K3U203
|
1.3
|
88.2
|
1.0
|
F2
|
A:K3U203
|
2.2
|
93.6
|
1.0
|
F
|
A:K3U203
|
2.3
|
70.8
|
1.0
|
C11
|
A:K3U203
|
2.3
|
86.5
|
1.0
|
N
|
A:LEU112
|
2.6
|
35.4
|
1.0
|
C3
|
A:K3U203
|
2.9
|
89.5
|
1.0
|
NI
|
A:NI201
|
3.0
|
58.2
|
1.0
|
CA
|
A:CYS111
|
3.1
|
33.1
|
1.0
|
C
|
A:CYS111
|
3.3
|
36.0
|
1.0
|
CB
|
A:LEU112
|
3.4
|
29.3
|
1.0
|
C4
|
A:K3U203
|
3.5
|
94.3
|
1.0
|
CA
|
A:LEU112
|
3.5
|
32.2
|
1.0
|
NE2
|
A:GLN65
|
3.6
|
26.7
|
1.0
|
CD2
|
A:LEU112
|
3.7
|
33.1
|
1.0
|
SG
|
A:CYS111
|
3.8
|
26.5
|
1.0
|
CB
|
A:CYS111
|
3.9
|
32.5
|
1.0
|
CG
|
A:LEU112
|
4.0
|
31.5
|
1.0
|
N
|
A:CYS111
|
4.2
|
32.9
|
1.0
|
C2
|
A:K3U203
|
4.2
|
89.8
|
1.0
|
OE2
|
A:GLU155
|
4.2
|
51.8
|
1.0
|
O
|
A:GLY60
|
4.3
|
28.6
|
1.0
|
O
|
A:GLY110
|
4.3
|
35.2
|
1.0
|
NE2
|
A:HIS154
|
4.4
|
29.6
|
1.0
|
OE1
|
A:GLN65
|
4.4
|
30.2
|
1.0
|
CD
|
A:GLN65
|
4.4
|
29.4
|
1.0
|
N
|
A:SER113
|
4.5
|
33.7
|
1.0
|
CD1
|
A:LEU112
|
4.5
|
30.2
|
1.0
|
O
|
A:CYS111
|
4.5
|
31.7
|
1.0
|
C
|
A:LEU112
|
4.6
|
31.7
|
1.0
|
C
|
A:GLY110
|
4.7
|
32.3
|
1.0
|
O1
|
A:K3U203
|
4.8
|
88.2
|
1.0
|
C5
|
A:K3U203
|
5.0
|
91.5
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6jfr
Go back to
Fluorine Binding Sites List in 6jfr
Fluorine binding site 2 out
of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F203
b:70.8
occ:1.00
|
F
|
A:K3U203
|
0.0
|
70.8
|
1.0
|
C12
|
A:K3U203
|
1.4
|
88.2
|
1.0
|
OE2
|
A:GLU155
|
2.0
|
51.8
|
1.0
|
F2
|
A:K3U203
|
2.1
|
93.6
|
1.0
|
F1
|
A:K3U203
|
2.3
|
77.7
|
1.0
|
NI
|
A:NI201
|
2.3
|
58.2
|
1.0
|
C11
|
A:K3U203
|
2.5
|
86.5
|
1.0
|
CD
|
A:GLU155
|
3.2
|
51.4
|
1.0
|
C4
|
A:K3U203
|
3.3
|
94.3
|
1.0
|
NE2
|
A:HIS154
|
3.3
|
29.6
|
1.0
|
C3
|
A:K3U203
|
3.4
|
89.5
|
1.0
|
CD2
|
A:HIS154
|
3.4
|
27.8
|
1.0
|
O
|
A:GLY60
|
3.5
|
28.6
|
1.0
|
OE1
|
A:GLN65
|
3.5
|
30.2
|
1.0
|
OE1
|
A:GLU155
|
3.6
|
55.9
|
1.0
|
NE2
|
A:GLN65
|
3.8
|
26.7
|
1.0
|
NE2
|
A:HIS158
|
3.9
|
40.7
|
1.0
|
O
|
A:HOH315
|
3.9
|
53.5
|
1.0
|
CD
|
A:GLN65
|
4.0
|
29.4
|
1.0
|
CD2
|
A:HIS158
|
4.1
|
38.0
|
1.0
|
C
|
A:GLY60
|
4.2
|
32.6
|
1.0
|
SG
|
A:CYS111
|
4.4
|
26.5
|
1.0
|
CG
|
A:GLU155
|
4.5
|
44.7
|
1.0
|
CE1
|
A:HIS154
|
4.6
|
26.6
|
1.0
|
CA
|
A:CYS111
|
4.7
|
33.1
|
1.0
|
CG
|
A:HIS154
|
4.7
|
27.4
|
1.0
|
C5
|
A:K3U203
|
4.7
|
91.5
|
1.0
|
C2
|
A:K3U203
|
4.7
|
89.8
|
1.0
|
N
|
A:LEU112
|
4.8
|
35.4
|
1.0
|
CA
|
A:LEU61
|
4.8
|
30.4
|
1.0
|
N
|
A:LEU61
|
4.9
|
30.7
|
1.0
|
O1
|
A:K3U203
|
4.9
|
88.2
|
1.0
|
CD2
|
A:LEU112
|
5.0
|
33.1
|
1.0
|
CB
|
A:CYS111
|
5.0
|
32.5
|
1.0
|
CA
|
A:GLY60
|
5.0
|
34.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6jfr
Go back to
Fluorine Binding Sites List in 6jfr
Fluorine binding site 3 out
of 3 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F203
b:93.6
occ:1.00
|
F2
|
A:K3U203
|
0.0
|
93.6
|
1.0
|
C12
|
A:K3U203
|
1.3
|
88.2
|
1.0
|
F
|
A:K3U203
|
2.1
|
70.8
|
1.0
|
F1
|
A:K3U203
|
2.2
|
77.7
|
1.0
|
C11
|
A:K3U203
|
2.3
|
86.5
|
1.0
|
O
|
A:GLY60
|
2.4
|
28.6
|
1.0
|
CD2
|
A:LEU112
|
3.0
|
33.1
|
1.0
|
OE1
|
A:GLN65
|
3.4
|
30.2
|
1.0
|
OE2
|
A:GLU155
|
3.4
|
51.8
|
1.0
|
C
|
A:GLY60
|
3.5
|
32.6
|
1.0
|
NE2
|
A:GLN65
|
3.6
|
26.7
|
1.0
|
C3
|
A:K3U203
|
3.7
|
89.5
|
1.0
|
CB
|
A:LEU112
|
3.8
|
29.3
|
1.0
|
CD
|
A:GLN65
|
3.9
|
29.4
|
1.0
|
CD1
|
A:LEU61
|
4.0
|
34.3
|
1.0
|
CG
|
A:LEU112
|
4.0
|
31.5
|
1.0
|
CA
|
A:LEU61
|
4.0
|
30.4
|
1.0
|
NI
|
A:NI201
|
4.0
|
58.2
|
1.0
|
N
|
A:LEU61
|
4.2
|
30.7
|
1.0
|
CD
|
A:GLU155
|
4.3
|
51.4
|
1.0
|
N
|
A:LEU112
|
4.3
|
35.4
|
1.0
|
C4
|
A:K3U203
|
4.4
|
94.3
|
1.0
|
OE1
|
A:GLU155
|
4.5
|
55.9
|
1.0
|
CB
|
A:LEU61
|
4.5
|
32.3
|
1.0
|
CA
|
A:GLY60
|
4.6
|
34.0
|
1.0
|
C2
|
A:K3U203
|
4.6
|
89.8
|
1.0
|
O1
|
A:K3U203
|
4.7
|
88.2
|
1.0
|
CA
|
A:LEU112
|
4.7
|
32.2
|
1.0
|
N
|
A:GLY60
|
4.8
|
33.9
|
1.0
|
CG
|
A:LEU61
|
4.8
|
34.5
|
1.0
|
O
|
A:HOH315
|
4.8
|
53.5
|
1.0
|
CD1
|
A:LEU112
|
4.9
|
30.2
|
1.0
|
|
Reference:
I.H.Lee,
T.H.Ho,
L.W.Kang.
K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus To Be Published.
Page generated: Thu Aug 1 21:34:41 2024
|