Chlorine in PDB 7yax: Hydroxynitrile Lyase From the Millipede,
Protein crystallography data
The structure of Hydroxynitrile Lyase From the Millipede,, PDB code: 7yax
was solved by
S.Chaikaew,
Y.Watanabe,
D.Zheng,
F.Motojima,
Y.Asano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.97 /
2.01
|
|
Space group
|
P 63
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.63,
123.63,
129.13,
90,
90,
120
|
|
R / Rfree (%)
|
14.5 /
18
|
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Hydroxynitrile Lyase From the Millipede,
(pdb code 7yax). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Hydroxynitrile Lyase From the Millipede,, PDB code: 7yax:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 7yax
Go back to
Chlorine Binding Sites List in 7yax
Chlorine binding site 1 out
of 4 in the Hydroxynitrile Lyase From the Millipede,
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Hydroxynitrile Lyase From the Millipede, within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl204
b:39.2
occ:1.00
|
HH
|
A:TYR125
|
2.2
|
16.0
|
0.0
|
|
O2
|
A:SO4203
|
2.4
|
51.4
|
1.0
|
|
HH21
|
A:ARG60
|
2.6
|
17.9
|
1.0
|
|
HH12
|
A:ARG60
|
2.7
|
14.4
|
0.0
|
|
HE1
|
A:TYR125
|
2.8
|
14.3
|
1.0
|
|
HD2
|
A:LYS139
|
2.9
|
19.5
|
1.0
|
|
HB2
|
A:LYS139
|
3.0
|
16.7
|
1.0
|
|
OH
|
A:TYR125
|
3.0
|
16.0
|
1.0
|
|
NH1
|
A:ARG60
|
3.2
|
14.2
|
1.0
|
|
HB3
|
A:ALA127
|
3.2
|
13.4
|
1.0
|
|
NH2
|
A:ARG60
|
3.2
|
17.6
|
1.0
|
|
O
|
A:HOH331
|
3.4
|
19.0
|
1.0
|
|
CZ
|
A:ARG60
|
3.5
|
18.3
|
1.0
|
|
CE1
|
A:TYR125
|
3.5
|
13.7
|
1.0
|
|
HD3
|
A:LYS139
|
3.5
|
19.5
|
1.0
|
|
HB3
|
A:LYS139
|
3.6
|
16.7
|
1.0
|
|
CD
|
A:LYS139
|
3.6
|
20.2
|
1.0
|
|
S
|
A:SO4203
|
3.6
|
75.4
|
1.0
|
|
HZ
|
A:PHE47
|
3.7
|
16.2
|
1.0
|
|
HE1
|
A:PHE47
|
3.7
|
15.8
|
1.0
|
|
CB
|
A:LYS139
|
3.7
|
17.2
|
1.0
|
|
CZ
|
A:TYR125
|
3.7
|
15.7
|
1.0
|
|
HH11
|
A:ARG60
|
3.8
|
14.4
|
0.0
|
|
HB2
|
A:ALA127
|
3.9
|
13.4
|
1.0
|
|
CB
|
A:ALA127
|
3.9
|
13.7
|
1.0
|
|
HH22
|
A:ARG60
|
4.0
|
17.9
|
1.0
|
|
O1
|
A:SO4203
|
4.0
|
37.4
|
1.0
|
|
HH
|
A:TYR62
|
4.1
|
17.8
|
0.0
|
|
CZ
|
A:PHE47
|
4.1
|
15.1
|
1.0
|
|
CE1
|
A:PHE47
|
4.2
|
15.7
|
1.0
|
|
O4
|
A:SO4203
|
4.2
|
41.1
|
1.0
|
|
HB1
|
A:ALA127
|
4.2
|
13.4
|
1.0
|
|
CG
|
A:LYS139
|
4.3
|
17.3
|
1.0
|
|
OH
|
A:TYR62
|
4.3
|
17.9
|
1.0
|
|
HZ3
|
A:TRP110
|
4.3
|
15.9
|
1.0
|
|
HZ2
|
A:LYS139
|
4.5
|
19.2
|
1.0
|
|
O
|
A:LYS139
|
4.5
|
15.9
|
1.0
|
|
NE
|
A:ARG60
|
4.6
|
16.0
|
1.0
|
|
CZ3
|
A:TRP110
|
4.6
|
16.0
|
1.0
|
|
O3
|
A:SO4203
|
4.7
|
81.4
|
1.0
|
|
HZ1
|
A:LYS139
|
4.8
|
19.2
|
1.0
|
|
HG3
|
A:LYS139
|
4.8
|
17.9
|
1.0
|
|
CD1
|
A:TYR125
|
4.8
|
14.5
|
1.0
|
|
HE1
|
A:PHE112
|
4.8
|
16.6
|
1.0
|
|
HE3
|
A:TRP110
|
4.8
|
15.9
|
1.0
|
|
CE
|
A:LYS139
|
4.8
|
20.4
|
1.0
|
|
CE3
|
A:TRP110
|
4.9
|
16.2
|
1.0
|
|
H
|
A:ALA127
|
4.9
|
12.6
|
1.0
|
|
HG2
|
A:ARG60
|
4.9
|
14.8
|
1.0
|
|
NZ
|
A:LYS139
|
4.9
|
18.7
|
1.0
|
|
CA
|
A:LYS139
|
4.9
|
14.9
|
1.0
|
|
HE
|
A:ARG60
|
4.9
|
16.2
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 7yax
Go back to
Chlorine Binding Sites List in 7yax
Chlorine binding site 2 out
of 4 in the Hydroxynitrile Lyase From the Millipede,
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Hydroxynitrile Lyase From the Millipede, within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl204
b:35.4
occ:1.00
|
HH
|
B:TYR125
|
2.2
|
20.0
|
0.0
|
|
HZ1
|
B:LYS139
|
2.5
|
15.3
|
0.2
|
|
O4
|
B:SO4201
|
2.5
|
47.2
|
0.8
|
|
HD2
|
B:LYS139
|
2.6
|
18.5
|
0.5
|
|
HD3
|
B:LYS139
|
2.8
|
20.9
|
0.2
|
|
HE1
|
B:TYR125
|
2.9
|
17.7
|
1.0
|
|
HD2
|
B:LYS139
|
2.9
|
20.9
|
0.2
|
|
HH21
|
B:ARG60
|
2.9
|
19.2
|
1.0
|
|
HB2
|
B:LYS139
|
2.9
|
21.1
|
0.2
|
|
HB2
|
B:LYS139
|
3.0
|
19.9
|
0.5
|
|
HH12
|
B:ARG60
|
3.0
|
18.2
|
0.0
|
|
HB2
|
B:LYS139
|
3.0
|
18.4
|
0.2
|
|
OH
|
B:TYR125
|
3.0
|
19.6
|
1.0
|
|
HB3
|
B:LYS139
|
3.1
|
19.9
|
0.5
|
|
HB3
|
B:LYS139
|
3.2
|
21.1
|
0.2
|
|
CD
|
B:LYS139
|
3.3
|
20.9
|
0.2
|
|
HB3
|
B:ALA127
|
3.3
|
18.4
|
1.0
|
|
NZ
|
B:LYS139
|
3.3
|
15.0
|
0.2
|
|
O
|
B:HOH358
|
3.3
|
24.8
|
1.0
|
|
HD3
|
B:LYS139
|
3.3
|
18.5
|
0.5
|
|
NH1
|
B:ARG60
|
3.4
|
18.1
|
1.0
|
|
CD
|
B:LYS139
|
3.4
|
18.3
|
0.5
|
|
HE1
|
B:PHE47
|
3.4
|
23.3
|
1.0
|
|
HD3
|
B:LYS139
|
3.4
|
16.8
|
0.2
|
|
NH2
|
B:ARG60
|
3.4
|
19.1
|
1.0
|
|
HZ
|
B:PHE47
|
3.5
|
23.4
|
1.0
|
|
CB
|
B:LYS139
|
3.5
|
21.4
|
0.2
|
|
CB
|
B:LYS139
|
3.5
|
20.4
|
0.5
|
|
CZ
|
B:ARG60
|
3.5
|
19.4
|
1.0
|
|
CE1
|
B:TYR125
|
3.6
|
17.5
|
1.0
|
|
HZ2
|
B:LYS139
|
3.6
|
15.3
|
0.2
|
|
CZ
|
B:TYR125
|
3.8
|
18.7
|
1.0
|
|
HE2
|
B:LYS139
|
3.9
|
15.9
|
0.2
|
|
CE1
|
B:PHE47
|
3.9
|
23.5
|
1.0
|
|
HZ3
|
B:LYS139
|
3.9
|
15.3
|
0.2
|
|
S
|
B:SO4201
|
3.9
|
61.2
|
0.8
|
|
CZ
|
B:PHE47
|
3.9
|
21.9
|
1.0
|
|
CB
|
B:LYS139
|
3.9
|
18.3
|
0.2
|
|
HH11
|
B:ARG60
|
3.9
|
18.2
|
0.0
|
|
CG
|
B:LYS139
|
3.9
|
21.1
|
0.2
|
|
CE
|
B:LYS139
|
4.0
|
15.8
|
0.2
|
|
HB3
|
B:LYS139
|
4.0
|
18.4
|
0.2
|
|
CG
|
B:LYS139
|
4.0
|
18.9
|
0.5
|
|
CD
|
B:LYS139
|
4.1
|
16.9
|
0.2
|
|
CB
|
B:ALA127
|
4.1
|
18.3
|
1.0
|
|
HH22
|
B:ARG60
|
4.1
|
19.2
|
1.0
|
|
HZ2
|
B:LYS139
|
4.2
|
17.3
|
0.5
|
|
HB2
|
B:ALA127
|
4.2
|
18.4
|
1.0
|
|
HH
|
B:TYR62
|
4.3
|
20.4
|
0.0
|
|
HB1
|
B:ALA127
|
4.4
|
18.4
|
1.0
|
|
HZ1
|
B:LYS139
|
4.4
|
20.6
|
0.2
|
|
HZ2
|
B:LYS139
|
4.4
|
20.6
|
0.2
|
|
HZ3
|
B:TRP110
|
4.4
|
18.4
|
1.0
|
|
O1
|
B:SO4201
|
4.4
|
42.3
|
0.8
|
|
O
|
B:LYS139
|
4.4
|
19.9
|
0.2
|
|
NE
|
B:ARG60
|
4.5
|
17.9
|
1.0
|
|
CE
|
B:LYS139
|
4.5
|
20.9
|
0.2
|
|
HG2
|
B:LYS139
|
4.5
|
21.1
|
0.2
|
|
CE
|
B:LYS139
|
4.6
|
18.6
|
0.5
|
|
CG
|
B:LYS139
|
4.6
|
17.7
|
0.2
|
|
O
|
B:LYS139
|
4.6
|
20.2
|
0.2
|
|
O2
|
B:SO4201
|
4.6
|
32.3
|
0.8
|
|
HG3
|
B:LYS139
|
4.6
|
19.1
|
0.5
|
|
HG3
|
B:LYS139
|
4.6
|
21.1
|
0.2
|
|
OH
|
B:TYR62
|
4.6
|
20.2
|
1.0
|
|
CZ3
|
B:TRP110
|
4.6
|
18.3
|
1.0
|
|
O
|
B:LYS139
|
4.7
|
19.3
|
0.5
|
|
NZ
|
B:LYS139
|
4.7
|
20.4
|
0.2
|
|
HG2
|
B:LYS139
|
4.7
|
19.1
|
0.5
|
|
NZ
|
B:LYS139
|
4.7
|
16.7
|
0.5
|
|
O3
|
B:SO4201
|
4.7
|
56.1
|
0.8
|
|
HZ1
|
B:LYS139
|
4.7
|
17.3
|
0.5
|
|
HE
|
B:ARG60
|
4.7
|
18.1
|
1.0
|
|
CA
|
B:LYS139
|
4.8
|
19.6
|
0.5
|
|
CA
|
B:LYS139
|
4.8
|
20.7
|
0.2
|
|
CD1
|
B:TYR125
|
4.9
|
17.4
|
1.0
|
|
HD2
|
B:LYS139
|
4.9
|
16.8
|
0.2
|
|
HE3
|
B:LYS139
|
4.9
|
15.9
|
0.2
|
|
HB2
|
B:ALA141
|
4.9
|
16.7
|
1.0
|
|
HG3
|
B:LYS139
|
4.9
|
17.6
|
0.2
|
|
CD1
|
B:PHE47
|
5.0
|
24.2
|
1.0
|
|
HG2
|
B:ARG60
|
5.0
|
17.8
|
1.0
|
|
HE3
|
B:TRP110
|
5.0
|
18.0
|
1.0
|
|
CE3
|
B:TRP110
|
5.0
|
17.7
|
1.0
|
|
CA
|
B:LYS139
|
5.0
|
19.3
|
0.2
|
|
HE3
|
B:LYS139
|
5.0
|
18.1
|
0.5
|
|
Chlorine binding site 3 out
of 4 in 7yax
Go back to
Chlorine Binding Sites List in 7yax
Chlorine binding site 3 out
of 4 in the Hydroxynitrile Lyase From the Millipede,
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Hydroxynitrile Lyase From the Millipede, within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl204
b:32.2
occ:1.00
|
HH
|
C:TYR125
|
2.1
|
19.5
|
0.0
|
|
HD2
|
C:LYS139
|
2.5
|
24.9
|
1.0
|
|
O2
|
C:SO4203
|
2.7
|
87.9
|
1.0
|
|
HH21
|
C:ARG60
|
2.8
|
16.7
|
1.0
|
|
HE1
|
C:TYR125
|
2.8
|
15.6
|
1.0
|
|
OH
|
C:TYR125
|
3.0
|
19.1
|
1.0
|
|
HB2
|
C:LYS139
|
3.0
|
20.0
|
1.0
|
|
HE1
|
C:PHE47
|
3.1
|
17.2
|
1.0
|
|
HH12
|
C:ARG60
|
3.1
|
16.6
|
0.0
|
|
HZ
|
C:PHE47
|
3.3
|
17.6
|
1.0
|
|
HB3
|
C:LYS139
|
3.3
|
20.0
|
1.0
|
|
NH1
|
C:ARG60
|
3.3
|
16.4
|
1.0
|
|
O
|
C:HOH345
|
3.3
|
17.3
|
1.0
|
|
CD
|
C:LYS139
|
3.4
|
24.0
|
1.0
|
|
HB3
|
C:ALA127
|
3.4
|
14.2
|
1.0
|
|
NH2
|
C:ARG60
|
3.4
|
16.5
|
1.0
|
|
HD3
|
C:LYS139
|
3.4
|
24.9
|
1.0
|
|
CZ
|
C:ARG60
|
3.5
|
17.1
|
1.0
|
|
CB
|
C:LYS139
|
3.6
|
20.3
|
1.0
|
|
CE1
|
C:TYR125
|
3.6
|
15.0
|
1.0
|
|
CE1
|
C:PHE47
|
3.6
|
17.7
|
1.0
|
|
CZ
|
C:TYR125
|
3.7
|
17.6
|
1.0
|
|
CZ
|
C:PHE47
|
3.7
|
16.1
|
1.0
|
|
O3
|
C:SO4203
|
3.7
|
55.4
|
1.0
|
|
S
|
C:SO4203
|
3.8
|
87.3
|
1.0
|
|
HH11
|
C:ARG60
|
3.8
|
16.6
|
0.0
|
|
CG
|
C:LYS139
|
4.1
|
21.6
|
1.0
|
|
HZ2
|
C:LYS139
|
4.1
|
26.2
|
1.0
|
|
CB
|
C:ALA127
|
4.2
|
14.0
|
1.0
|
|
HH22
|
C:ARG60
|
4.2
|
16.7
|
1.0
|
|
HB2
|
C:ALA127
|
4.3
|
14.2
|
1.0
|
|
NE
|
C:ARG60
|
4.4
|
16.1
|
1.0
|
|
HB1
|
C:ALA127
|
4.4
|
14.2
|
1.0
|
|
CE
|
C:LYS139
|
4.4
|
31.0
|
1.0
|
|
HZ1
|
C:LYS139
|
4.5
|
26.2
|
1.0
|
|
HH
|
C:TYR62
|
4.5
|
19.3
|
0.0
|
|
NZ
|
C:LYS139
|
4.5
|
24.3
|
1.0
|
|
HE
|
C:ARG60
|
4.5
|
16.2
|
1.0
|
|
HZ3
|
C:TRP110
|
4.5
|
16.3
|
1.0
|
|
HG3
|
C:LYS139
|
4.6
|
21.8
|
1.0
|
|
O1
|
C:SO4203
|
4.6
|
45.6
|
1.0
|
|
O
|
C:LYS139
|
4.6
|
16.6
|
1.0
|
|
OH
|
C:TYR62
|
4.7
|
19.1
|
1.0
|
|
HG2
|
C:ARG60
|
4.7
|
16.2
|
1.0
|
|
HB2
|
C:ALA141
|
4.8
|
14.8
|
1.0
|
|
CZ3
|
C:TRP110
|
4.8
|
16.0
|
1.0
|
|
CD1
|
C:PHE47
|
4.8
|
17.0
|
1.0
|
|
HG2
|
C:LYS139
|
4.8
|
21.8
|
1.0
|
|
CD1
|
C:TYR125
|
4.8
|
14.7
|
1.0
|
|
O4
|
C:SO4203
|
4.8
|
38.7
|
1.0
|
|
CA
|
C:LYS139
|
4.9
|
17.9
|
1.0
|
|
HE3
|
C:LYS139
|
4.9
|
27.5
|
1.0
|
|
CE2
|
C:PHE47
|
4.9
|
21.0
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 7yax
Go back to
Chlorine Binding Sites List in 7yax
Chlorine binding site 4 out
of 4 in the Hydroxynitrile Lyase From the Millipede,
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Hydroxynitrile Lyase From the Millipede, within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl204
b:31.8
occ:1.00
|
HH
|
D:TYR125
|
2.1
|
18.0
|
0.0
|
|
O2
|
D:SO4202
|
2.4
|
38.8
|
0.6
|
|
HD2
|
D:LYS139
|
2.7
|
24.9
|
1.0
|
|
HH21
|
D:ARG60
|
2.7
|
17.4
|
1.0
|
|
HE1
|
D:TYR125
|
2.9
|
17.0
|
1.0
|
|
HB2
|
D:LYS139
|
2.9
|
21.2
|
1.0
|
|
OH
|
D:TYR125
|
2.9
|
17.6
|
1.0
|
|
HH12
|
D:ARG60
|
3.1
|
18.6
|
0.0
|
|
HE1
|
D:PHE47
|
3.3
|
19.4
|
1.0
|
|
HB3
|
D:ALA127
|
3.3
|
16.1
|
1.0
|
|
O
|
D:HOH369
|
3.3
|
22.5
|
1.0
|
|
NH1
|
D:ARG60
|
3.4
|
18.5
|
1.0
|
|
HD3
|
D:LYS139
|
3.4
|
24.9
|
1.0
|
|
NH2
|
D:ARG60
|
3.4
|
17.2
|
1.0
|
|
HZ
|
D:PHE47
|
3.4
|
20.2
|
1.0
|
|
HB3
|
D:LYS139
|
3.5
|
21.2
|
1.0
|
|
CD
|
D:LYS139
|
3.5
|
23.9
|
1.0
|
|
CZ
|
D:ARG60
|
3.5
|
17.7
|
1.0
|
|
CE1
|
D:TYR125
|
3.6
|
17.2
|
1.0
|
|
CB
|
D:LYS139
|
3.6
|
21.8
|
1.0
|
|
CZ
|
D:TYR125
|
3.7
|
17.8
|
1.0
|
|
CE1
|
D:PHE47
|
3.8
|
20.0
|
1.0
|
|
S
|
D:SO4202
|
3.8
|
48.7
|
0.6
|
|
CZ
|
D:PHE47
|
3.9
|
19.0
|
1.0
|
|
HH11
|
D:ARG60
|
3.9
|
18.6
|
0.0
|
|
CG
|
D:LYS139
|
4.1
|
23.2
|
1.0
|
|
CB
|
D:ALA127
|
4.1
|
16.2
|
1.0
|
|
HH22
|
D:ARG60
|
4.2
|
17.4
|
1.0
|
|
HB2
|
D:ALA127
|
4.2
|
16.1
|
1.0
|
|
HZ2
|
D:LYS139
|
4.3
|
26.9
|
1.0
|
|
HB1
|
D:ALA127
|
4.4
|
16.1
|
1.0
|
|
HZ3
|
D:TRP110
|
4.4
|
16.8
|
1.0
|
|
NE
|
D:ARG60
|
4.4
|
16.6
|
1.0
|
|
O1
|
D:SO4202
|
4.5
|
45.2
|
0.6
|
|
HZ1
|
D:LYS139
|
4.5
|
26.9
|
1.0
|
|
HH
|
D:TYR62
|
4.5
|
20.1
|
0.0
|
|
O4
|
D:SO4202
|
4.5
|
25.4
|
0.6
|
|
O3
|
D:SO4202
|
4.6
|
32.0
|
0.6
|
|
O
|
D:LYS139
|
4.6
|
16.4
|
1.0
|
|
HG3
|
D:LYS139
|
4.6
|
23.0
|
1.0
|
|
OH
|
D:TYR62
|
4.6
|
20.0
|
1.0
|
|
CE
|
D:LYS139
|
4.6
|
29.4
|
1.0
|
|
CZ3
|
D:TRP110
|
4.7
|
16.8
|
1.0
|
|
NZ
|
D:LYS139
|
4.7
|
25.8
|
1.0
|
|
HE
|
D:ARG60
|
4.7
|
16.4
|
1.0
|
|
HB2
|
D:ALA141
|
4.8
|
16.6
|
1.0
|
|
CA
|
D:LYS139
|
4.9
|
18.3
|
1.0
|
|
CD1
|
D:TYR125
|
4.9
|
16.0
|
1.0
|
|
HG2
|
D:ARG60
|
4.9
|
16.4
|
1.0
|
|
HG2
|
D:LYS139
|
4.9
|
23.0
|
1.0
|
|
CD1
|
D:PHE47
|
4.9
|
18.3
|
1.0
|
|
C
|
D:LYS139
|
5.0
|
16.6
|
1.0
|
|
CE2
|
D:PHE47
|
5.0
|
24.0
|
1.0
|
|
Reference:
S.Chaikaew,
Y.Watanabe,
D.Zheng,
F.Motojima,
Y.Asano.
Structure-Based Site-Directed Mutagenesis of Hydroxynitrile Lyase From Cyanogenic Millipede, Oxidus Gracilis For Enhancing Catalytic Efficiency and Enantioselectivity To Be Published.
Page generated: Sun Jul 13 08:33:20 2025
|
