Fluorine in PDB 6sc0: Thermolysin in Complex with Fragment J22
Enzymatic activity of Thermolysin in Complex with Fragment J22
All present enzymatic activity of Thermolysin in Complex with Fragment J22:
3.4.24.27;
Protein crystallography data
The structure of Thermolysin in Complex with Fragment J22, PDB code: 6sc0
was solved by
F.Magari,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.29 /
1.53
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
92.572,
92.572,
129.113,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
14.5 /
16.6
|
Other elements in 6sc0:
The structure of Thermolysin in Complex with Fragment J22 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Thermolysin in Complex with Fragment J22
(pdb code 6sc0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Thermolysin in Complex with Fragment J22, PDB code: 6sc0:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6sc0
Go back to
Fluorine Binding Sites List in 6sc0
Fluorine binding site 1 out
of 3 in the Thermolysin in Complex with Fragment J22
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F409
b:35.1
occ:1.00
|
F
|
E:L5Q409
|
0.0
|
35.1
|
1.0
|
C6
|
E:L5Q409
|
1.3
|
36.0
|
1.0
|
F1
|
E:L5Q409
|
2.1
|
37.3
|
1.0
|
F2
|
E:L5Q409
|
2.1
|
38.2
|
1.0
|
C5
|
E:L5Q409
|
2.4
|
31.5
|
1.0
|
N1
|
E:L5Q409
|
2.8
|
28.2
|
1.0
|
O1
|
E:L5Q409
|
2.9
|
23.7
|
1.0
|
HD23
|
E:LEU202
|
3.0
|
25.5
|
1.0
|
HD21
|
E:LEU202
|
3.1
|
25.5
|
1.0
|
C4
|
E:L5Q409
|
3.1
|
26.9
|
1.0
|
CD2
|
E:LEU202
|
3.3
|
21.3
|
1.0
|
HD22
|
E:LEU202
|
3.4
|
25.5
|
1.0
|
HH22
|
E:ARG203
|
3.4
|
19.2
|
1.0
|
HG22
|
E:VAL139
|
3.5
|
19.4
|
1.0
|
HG22
|
E:ILE188
|
4.1
|
21.2
|
1.0
|
NH2
|
E:ARG203
|
4.1
|
16.0
|
1.0
|
HG13
|
E:VAL139
|
4.1
|
18.1
|
1.0
|
HH12
|
E:ARG203
|
4.3
|
21.0
|
1.0
|
C3
|
E:L5Q409
|
4.4
|
30.6
|
1.0
|
CG2
|
E:VAL139
|
4.5
|
16.1
|
1.0
|
HH21
|
E:ARG203
|
4.5
|
19.2
|
1.0
|
HG21
|
E:ILE188
|
4.5
|
21.2
|
1.0
|
HD23
|
E:LEU133
|
4.5
|
23.6
|
1.0
|
HA
|
E:VAL139
|
4.6
|
16.1
|
1.0
|
HG11
|
E:VAL139
|
4.7
|
18.1
|
1.0
|
HG21
|
E:VAL139
|
4.7
|
19.4
|
1.0
|
CG2
|
E:ILE188
|
4.7
|
17.6
|
1.0
|
CG1
|
E:VAL139
|
4.8
|
15.1
|
1.0
|
CG
|
E:LEU202
|
4.8
|
30.3
|
1.0
|
HZ
|
E:PHE130
|
4.8
|
24.8
|
1.0
|
OD1
|
E:ASN112
|
4.8
|
20.2
|
1.0
|
NH1
|
E:ARG203
|
4.9
|
17.5
|
1.0
|
N
|
E:L5Q409
|
4.9
|
32.2
|
1.0
|
CZ
|
E:ARG203
|
4.9
|
16.1
|
1.0
|
OE2
|
E:GLU143
|
4.9
|
21.2
|
1.0
|
HG23
|
E:ILE188
|
5.0
|
21.2
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6sc0
Go back to
Fluorine Binding Sites List in 6sc0
Fluorine binding site 2 out
of 3 in the Thermolysin in Complex with Fragment J22
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F409
b:37.3
occ:1.00
|
F1
|
E:L5Q409
|
0.0
|
37.3
|
1.0
|
C6
|
E:L5Q409
|
1.3
|
36.0
|
1.0
|
F
|
E:L5Q409
|
2.1
|
35.1
|
1.0
|
F2
|
E:L5Q409
|
2.1
|
38.2
|
1.0
|
C5
|
E:L5Q409
|
2.4
|
31.5
|
1.0
|
HD23
|
E:LEU133
|
3.0
|
23.6
|
1.0
|
N1
|
E:L5Q409
|
3.0
|
28.2
|
1.0
|
HB3
|
E:ALA113
|
3.2
|
16.8
|
1.0
|
HG13
|
E:VAL139
|
3.3
|
18.1
|
1.0
|
HD22
|
E:LEU133
|
3.4
|
23.6
|
1.0
|
H
|
E:ALA113
|
3.4
|
16.1
|
1.0
|
HG11
|
E:VAL139
|
3.4
|
18.1
|
1.0
|
CD2
|
E:LEU133
|
3.5
|
19.6
|
1.0
|
OD1
|
E:ASN112
|
3.7
|
20.2
|
1.0
|
HG22
|
E:VAL139
|
3.7
|
19.4
|
1.0
|
HD21
|
E:LEU133
|
3.8
|
23.6
|
1.0
|
CG1
|
E:VAL139
|
3.8
|
15.1
|
1.0
|
N
|
E:ALA113
|
4.0
|
13.4
|
1.0
|
CB
|
E:ALA113
|
4.0
|
14.0
|
1.0
|
C4
|
E:L5Q409
|
4.0
|
26.9
|
1.0
|
HA
|
E:ASN112
|
4.1
|
16.7
|
1.0
|
OE2
|
E:GLU143
|
4.2
|
21.2
|
1.0
|
O
|
E:ALA113
|
4.2
|
14.9
|
1.0
|
HB2
|
E:ALA113
|
4.2
|
16.8
|
1.0
|
HD21
|
E:LEU202
|
4.3
|
25.5
|
1.0
|
HG21
|
E:VAL139
|
4.3
|
19.4
|
1.0
|
O1
|
E:L5Q409
|
4.4
|
23.7
|
1.0
|
CG2
|
E:VAL139
|
4.4
|
16.1
|
1.0
|
HD22
|
E:LEU202
|
4.4
|
25.5
|
1.0
|
CA
|
E:ALA113
|
4.5
|
15.1
|
1.0
|
HB3
|
E:LEU133
|
4.5
|
17.2
|
1.0
|
HG12
|
E:VAL139
|
4.5
|
18.1
|
1.0
|
HD23
|
E:LEU202
|
4.7
|
25.5
|
1.0
|
CD2
|
E:LEU202
|
4.7
|
21.3
|
1.0
|
C
|
E:ALA113
|
4.7
|
12.6
|
1.0
|
CB
|
E:VAL139
|
4.7
|
13.8
|
1.0
|
C
|
E:ASN112
|
4.7
|
14.4
|
1.0
|
HZ
|
E:PHE130
|
4.8
|
24.8
|
1.0
|
HB1
|
E:ALA113
|
4.8
|
16.8
|
1.0
|
CA
|
E:ASN112
|
4.8
|
13.9
|
1.0
|
CG
|
E:ASN112
|
4.8
|
20.4
|
1.0
|
HA
|
E:VAL139
|
4.9
|
16.1
|
1.0
|
CG
|
E:LEU133
|
4.9
|
18.4
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6sc0
Go back to
Fluorine Binding Sites List in 6sc0
Fluorine binding site 3 out
of 3 in the Thermolysin in Complex with Fragment J22
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Thermolysin in Complex with Fragment J22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F409
b:38.2
occ:1.00
|
F2
|
E:L5Q409
|
0.0
|
38.2
|
1.0
|
C6
|
E:L5Q409
|
1.3
|
36.0
|
1.0
|
F1
|
E:L5Q409
|
2.1
|
37.3
|
1.0
|
F
|
E:L5Q409
|
2.1
|
35.1
|
1.0
|
C5
|
E:L5Q409
|
2.4
|
31.5
|
1.0
|
HG13
|
E:VAL139
|
2.5
|
18.1
|
1.0
|
OE2
|
E:GLU143
|
3.2
|
21.2
|
1.0
|
HG22
|
E:VAL139
|
3.3
|
19.4
|
1.0
|
HA
|
E:VAL139
|
3.4
|
16.1
|
1.0
|
CG1
|
E:VAL139
|
3.4
|
15.1
|
1.0
|
HG11
|
E:VAL139
|
3.6
|
18.1
|
1.0
|
N1
|
E:L5Q409
|
3.7
|
28.2
|
1.0
|
HB3
|
E:ALA113
|
3.7
|
16.8
|
1.0
|
HB3
|
E:HIS142
|
3.8
|
15.6
|
1.0
|
HG2
|
E:GLU143
|
3.8
|
20.0
|
1.0
|
HD2
|
E:HIS142
|
3.9
|
14.5
|
1.0
|
CD2
|
E:HIS142
|
4.0
|
12.1
|
1.0
|
CB
|
E:VAL139
|
4.0
|
13.8
|
1.0
|
CG2
|
E:VAL139
|
4.1
|
16.1
|
1.0
|
HG12
|
E:VAL139
|
4.1
|
18.1
|
1.0
|
CA
|
E:VAL139
|
4.1
|
13.4
|
1.0
|
CD
|
E:GLU143
|
4.1
|
16.5
|
1.0
|
CG
|
E:HIS142
|
4.1
|
13.3
|
1.0
|
O1
|
E:L5Q409
|
4.2
|
23.7
|
1.0
|
O
|
E:VAL139
|
4.2
|
13.8
|
1.0
|
C4
|
E:L5Q409
|
4.4
|
26.9
|
1.0
|
O2
|
E:BCT410
|
4.4
|
16.9
|
0.8
|
HG21
|
E:VAL139
|
4.4
|
19.4
|
1.0
|
CB
|
E:HIS142
|
4.5
|
13.0
|
1.0
|
CG
|
E:GLU143
|
4.5
|
16.6
|
1.0
|
NE2
|
E:HIS142
|
4.5
|
15.7
|
1.0
|
HH22
|
E:ARG203
|
4.5
|
19.2
|
1.0
|
C
|
E:VAL139
|
4.6
|
12.7
|
1.0
|
O
|
E:ALA113
|
4.6
|
14.9
|
1.0
|
HD23
|
E:LEU133
|
4.6
|
23.6
|
1.0
|
CB
|
E:ALA113
|
4.7
|
14.0
|
1.0
|
ND1
|
E:HIS142
|
4.8
|
12.9
|
1.0
|
HG3
|
E:GLU143
|
4.8
|
20.0
|
1.0
|
H
|
E:ALA113
|
4.8
|
16.1
|
1.0
|
HG23
|
E:VAL139
|
4.8
|
19.4
|
1.0
|
HB2
|
E:HIS142
|
4.8
|
15.6
|
1.0
|
C
|
E:BCT410
|
4.9
|
17.2
|
0.8
|
CE1
|
E:HIS142
|
4.9
|
14.9
|
1.0
|
HB
|
E:VAL139
|
5.0
|
16.6
|
1.0
|
|
Reference:
F.Magari,
A.Heine,
G.Klebe.
Thermolysin in Complex with Fragment J22 To Be Published.
Page generated: Fri Aug 2 01:41:34 2024
|