Fluorine in PDB 3zww: Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
Enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
All present enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom:
3.2.2.5;
Protein crystallography data
The structure of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom, PDB code: 3zww
was solved by
M.Kotaka,
R.Graeff,
L.H.Zhang,
H.C.Lee,
Q.Hao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.86 /
2.30
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.962,
77.522,
140.503,
88.00,
89.16,
88.29
|
R / Rfree (%)
|
19.977 /
25.736
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
(pdb code 3zww). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom, PDB code: 3zww:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 3zww
Go back to
Fluorine Binding Sites List in 3zww
Fluorine binding site 1 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:60.4
occ:1.00
|
F2R
|
A:AVU301
|
0.0
|
60.4
|
1.0
|
C2R
|
A:AVU301
|
1.4
|
55.6
|
1.0
|
C1R
|
A:AVU301
|
2.3
|
55.9
|
1.0
|
C3R
|
A:AVU301
|
2.4
|
54.9
|
1.0
|
OE2
|
A:GLU179
|
3.3
|
55.4
|
1.0
|
O4R
|
A:AVU301
|
3.3
|
56.9
|
1.0
|
CD2
|
A:LEU97
|
3.3
|
40.6
|
1.0
|
C4R
|
A:AVU301
|
3.3
|
56.1
|
1.0
|
O3R
|
A:AVU301
|
3.4
|
50.5
|
1.0
|
CB
|
A:LEU97
|
4.0
|
35.6
|
1.0
|
C5R
|
A:AVU301
|
4.0
|
58.1
|
1.0
|
NE1
|
A:TRP77
|
4.1
|
41.1
|
1.0
|
OG
|
A:SER144
|
4.2
|
43.4
|
1.0
|
CG
|
A:LEU97
|
4.3
|
39.5
|
1.0
|
CE2
|
A:TRP77
|
4.4
|
38.8
|
1.0
|
CZ2
|
A:TRP77
|
4.4
|
43.3
|
1.0
|
CD
|
A:GLU179
|
4.4
|
51.3
|
1.0
|
O2'
|
A:AVU301
|
4.5
|
90.2
|
1.0
|
OE1
|
A:GLU179
|
4.9
|
51.0
|
1.0
|
CD1
|
A:TRP77
|
4.9
|
37.0
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 2 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:34.2
occ:1.00
|
F2R
|
B:AVU301
|
0.0
|
34.2
|
1.0
|
C2R
|
B:AVU301
|
1.4
|
35.2
|
1.0
|
C1R
|
B:AVU301
|
2.3
|
33.5
|
1.0
|
C3R
|
B:AVU301
|
2.3
|
35.1
|
1.0
|
O4R
|
B:AVU301
|
2.8
|
34.6
|
1.0
|
C4R
|
B:AVU301
|
3.1
|
36.3
|
1.0
|
O3R
|
B:AVU301
|
3.4
|
30.8
|
1.0
|
CD2
|
B:LEU97
|
3.5
|
27.5
|
1.0
|
OE2
|
B:GLU179
|
3.6
|
35.0
|
1.0
|
C5R
|
B:AVU301
|
3.7
|
40.3
|
1.0
|
CB
|
B:LEU97
|
3.9
|
25.8
|
1.0
|
NE1
|
B:TRP77
|
4.2
|
33.8
|
1.0
|
CZ2
|
B:TRP77
|
4.3
|
35.2
|
1.0
|
CE2
|
B:TRP77
|
4.3
|
30.9
|
1.0
|
CG
|
B:LEU97
|
4.3
|
27.8
|
1.0
|
CD
|
B:GLU179
|
4.6
|
33.2
|
1.0
|
OG
|
B:SER144
|
4.7
|
28.1
|
1.0
|
OE1
|
B:GLU179
|
4.7
|
39.9
|
1.0
|
C3'
|
B:AVU301
|
4.8
|
81.9
|
1.0
|
OE2
|
B:GLU98
|
4.9
|
35.6
|
1.0
|
O5R
|
B:AVU301
|
4.9
|
44.6
|
1.0
|
O3'
|
B:AVU301
|
4.9
|
80.4
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 3 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F301
b:43.0
occ:1.00
|
F2R
|
C:AVU301
|
0.0
|
43.0
|
1.0
|
C2R
|
C:AVU301
|
1.4
|
41.0
|
1.0
|
C1R
|
C:AVU301
|
2.2
|
39.9
|
1.0
|
C3R
|
C:AVU301
|
2.3
|
43.0
|
1.0
|
O4R
|
C:AVU301
|
3.0
|
43.0
|
1.0
|
C4R
|
C:AVU301
|
3.1
|
43.4
|
1.0
|
OE2
|
C:GLU179
|
3.4
|
37.9
|
1.0
|
O3R
|
C:AVU301
|
3.5
|
38.5
|
1.0
|
CD2
|
C:LEU97
|
3.6
|
27.5
|
1.0
|
C5R
|
C:AVU301
|
3.6
|
43.3
|
1.0
|
NE1
|
C:TRP77
|
3.9
|
34.1
|
1.0
|
CZ2
|
C:TRP77
|
4.0
|
36.4
|
1.0
|
CB
|
C:LEU97
|
4.0
|
29.2
|
1.0
|
CE2
|
C:TRP77
|
4.1
|
32.3
|
1.0
|
CG
|
C:LEU97
|
4.4
|
31.0
|
1.0
|
CD
|
C:GLU179
|
4.4
|
32.5
|
1.0
|
OE1
|
C:GLU179
|
4.6
|
36.5
|
1.0
|
OE2
|
C:GLU98
|
4.7
|
39.2
|
1.0
|
OG
|
C:SER144
|
4.8
|
27.4
|
1.0
|
O5R
|
C:AVU301
|
4.8
|
45.9
|
1.0
|
CD1
|
C:TRP77
|
4.9
|
29.0
|
1.0
|
CH2
|
C:TRP77
|
4.9
|
38.4
|
1.0
|
OE1
|
C:GLU98
|
5.0
|
33.2
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 4 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F301
b:51.4
occ:1.00
|
F2R
|
D:AVU301
|
0.0
|
51.4
|
1.0
|
C2R
|
D:AVU301
|
1.4
|
49.4
|
1.0
|
C1R
|
D:AVU301
|
2.4
|
46.6
|
1.0
|
C3R
|
D:AVU301
|
2.4
|
47.3
|
1.0
|
CD2
|
D:LEU97
|
3.2
|
34.3
|
1.0
|
O4R
|
D:AVU301
|
3.2
|
46.8
|
1.0
|
O3R
|
D:AVU301
|
3.2
|
42.8
|
1.0
|
C4R
|
D:AVU301
|
3.4
|
46.5
|
1.0
|
OE2
|
D:GLU179
|
3.6
|
40.7
|
1.0
|
CB
|
D:LEU97
|
3.8
|
31.0
|
1.0
|
NE1
|
D:TRP77
|
3.9
|
31.4
|
1.0
|
C5R
|
D:AVU301
|
4.1
|
49.0
|
1.0
|
CG
|
D:LEU97
|
4.2
|
34.4
|
1.0
|
CE2
|
D:TRP77
|
4.3
|
31.3
|
1.0
|
CZ2
|
D:TRP77
|
4.4
|
38.9
|
1.0
|
CD
|
D:GLU179
|
4.5
|
40.3
|
1.0
|
OG
|
D:SER144
|
4.5
|
34.2
|
1.0
|
CD1
|
D:TRP77
|
4.6
|
27.9
|
1.0
|
N7
|
D:AVU301
|
4.7
|
85.9
|
1.0
|
CE2
|
D:TYR147
|
4.8
|
26.2
|
1.0
|
OE1
|
D:GLU179
|
4.8
|
42.3
|
1.0
|
CD2
|
D:TYR147
|
4.8
|
25.3
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 5 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F301
b:39.8
occ:1.00
|
F2R
|
E:AVU301
|
0.0
|
39.8
|
1.0
|
C2R
|
E:AVU301
|
1.4
|
38.2
|
1.0
|
C1R
|
E:AVU301
|
2.2
|
36.8
|
1.0
|
C3R
|
E:AVU301
|
2.3
|
39.7
|
1.0
|
O4R
|
E:AVU301
|
3.1
|
41.2
|
1.0
|
C4R
|
E:AVU301
|
3.2
|
40.8
|
1.0
|
OE2
|
E:GLU179
|
3.4
|
32.4
|
1.0
|
O3R
|
E:AVU301
|
3.4
|
37.3
|
1.0
|
CD2
|
E:LEU97
|
3.8
|
32.8
|
1.0
|
CB
|
E:LEU97
|
3.8
|
27.2
|
1.0
|
C5R
|
E:AVU301
|
3.8
|
42.6
|
1.0
|
NE1
|
E:TRP77
|
4.2
|
32.6
|
1.0
|
CD
|
E:GLU179
|
4.3
|
31.8
|
1.0
|
CZ2
|
E:TRP77
|
4.4
|
32.1
|
1.0
|
CG
|
E:LEU97
|
4.4
|
29.3
|
1.0
|
CE2
|
E:TRP77
|
4.4
|
31.5
|
1.0
|
OE1
|
E:GLU179
|
4.5
|
35.7
|
1.0
|
OG
|
E:SER144
|
4.6
|
22.2
|
1.0
|
CE2
|
E:TYR147
|
4.9
|
25.8
|
1.0
|
CD2
|
E:TYR147
|
5.0
|
25.2
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 6 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F301
b:67.4
occ:1.00
|
F2R
|
F:AVU301
|
0.0
|
67.4
|
1.0
|
C2R
|
F:AVU301
|
1.3
|
67.0
|
1.0
|
C1R
|
F:AVU301
|
2.2
|
68.5
|
1.0
|
C3R
|
F:AVU301
|
2.3
|
66.8
|
1.0
|
O4R
|
F:AVU301
|
2.7
|
69.0
|
1.0
|
C4R
|
F:AVU301
|
3.1
|
68.4
|
1.0
|
OE2
|
F:GLU179
|
3.4
|
67.4
|
1.0
|
O3R
|
F:AVU301
|
3.4
|
68.4
|
1.0
|
CD2
|
F:LEU97
|
3.6
|
54.7
|
1.0
|
OG
|
F:SER144
|
3.8
|
55.8
|
1.0
|
NE1
|
F:TRP77
|
4.0
|
47.4
|
1.0
|
C5R
|
F:AVU301
|
4.0
|
67.2
|
1.0
|
CB
|
F:LEU97
|
4.2
|
51.5
|
1.0
|
CE2
|
F:TRP77
|
4.3
|
48.3
|
1.0
|
CD
|
F:GLU179
|
4.4
|
67.0
|
1.0
|
CZ2
|
F:TRP77
|
4.4
|
51.4
|
1.0
|
CG
|
F:LEU97
|
4.5
|
53.1
|
1.0
|
OE1
|
F:GLU179
|
4.6
|
67.6
|
1.0
|
C8
|
F:AVU301
|
4.7
|
93.5
|
1.0
|
CD1
|
F:TRP77
|
4.7
|
46.9
|
1.0
|
CB
|
F:SER144
|
4.8
|
55.3
|
1.0
|
N7
|
F:AVU301
|
4.9
|
93.2
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 3zww
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Fluorine Binding Sites List in 3zww
Fluorine binding site 7 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F301
b:44.5
occ:1.00
|
F2R
|
G:AVU301
|
0.0
|
44.5
|
1.0
|
C2R
|
G:AVU301
|
1.4
|
40.9
|
1.0
|
C1R
|
G:AVU301
|
2.3
|
36.9
|
1.0
|
C3R
|
G:AVU301
|
2.3
|
40.4
|
1.0
|
O4R
|
G:AVU301
|
3.1
|
38.5
|
1.0
|
C4R
|
G:AVU301
|
3.1
|
39.7
|
1.0
|
O3R
|
G:AVU301
|
3.4
|
37.0
|
1.0
|
OE2
|
G:GLU179
|
3.5
|
34.3
|
1.0
|
CD2
|
G:LEU97
|
3.7
|
31.0
|
1.0
|
C5R
|
G:AVU301
|
3.7
|
40.0
|
1.0
|
CB
|
G:LEU97
|
3.8
|
27.4
|
1.0
|
NE1
|
G:TRP77
|
3.9
|
32.4
|
1.0
|
CE2
|
G:TRP77
|
4.3
|
30.3
|
1.0
|
CZ2
|
G:TRP77
|
4.3
|
33.0
|
1.0
|
CG
|
G:LEU97
|
4.4
|
30.7
|
1.0
|
CD
|
G:GLU179
|
4.5
|
29.6
|
1.0
|
OE1
|
G:GLU179
|
4.6
|
32.0
|
1.0
|
OG
|
G:SER144
|
4.7
|
27.1
|
1.0
|
CD1
|
G:TRP77
|
4.8
|
27.6
|
1.0
|
O5R
|
G:AVU301
|
4.9
|
44.4
|
1.0
|
OE1
|
G:GLU98
|
4.9
|
42.1
|
1.0
|
CE2
|
G:TYR147
|
5.0
|
25.4
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 3zww
Go back to
Fluorine Binding Sites List in 3zww
Fluorine binding site 8 out
of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:F301
b:62.3
occ:1.00
|
F2R
|
H:AVU301
|
0.0
|
62.3
|
1.0
|
C2R
|
H:AVU301
|
1.4
|
57.9
|
1.0
|
C3R
|
H:AVU301
|
2.3
|
57.0
|
1.0
|
C1R
|
H:AVU301
|
2.4
|
59.1
|
1.0
|
C4R
|
H:AVU301
|
3.3
|
57.2
|
1.0
|
O4R
|
H:AVU301
|
3.3
|
59.1
|
1.0
|
O3R
|
H:AVU301
|
3.3
|
55.2
|
1.0
|
NE1
|
H:TRP77
|
3.5
|
41.3
|
1.0
|
OE2
|
H:GLU179
|
3.6
|
56.6
|
1.0
|
CD2
|
H:LEU97
|
3.7
|
46.5
|
1.0
|
C5R
|
H:AVU301
|
3.8
|
55.9
|
1.0
|
CB
|
H:LEU97
|
3.8
|
42.4
|
1.0
|
CE2
|
H:TRP77
|
4.0
|
40.2
|
1.0
|
CZ2
|
H:TRP77
|
4.2
|
43.8
|
1.0
|
CD1
|
H:TRP77
|
4.2
|
39.9
|
1.0
|
C2
|
H:AVU301
|
4.3
|
79.1
|
1.0
|
OG
|
H:SER144
|
4.4
|
47.7
|
1.0
|
CG
|
H:LEU97
|
4.4
|
44.5
|
1.0
|
CD
|
H:GLU179
|
4.5
|
53.5
|
1.0
|
OE1
|
H:GLU179
|
4.6
|
52.3
|
1.0
|
N1
|
H:AVU301
|
4.8
|
79.8
|
1.0
|
CD2
|
H:TRP77
|
4.9
|
38.2
|
1.0
|
O5R
|
H:AVU301
|
4.9
|
54.9
|
1.0
|
|
Reference:
M.Kotaka,
R.Graeff,
Z.Chen,
L.H.Zhang,
H.C.Lee,
Q.Hao.
Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase. J.Mol.Biol. V. 415 514 2012.
ISSN: ISSN 0022-2836
PubMed: 22138343
DOI: 10.1016/J.JMB.2011.11.022
Page generated: Wed Jul 31 23:50:53 2024
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