Chlorine in PDB 4toq: Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Enzymatic activity of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
All present enzymatic activity of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity:
3.2.1.14;
Protein crystallography data
The structure of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity, PDB code: 4toq
was solved by
T.Masuda,
G.Zhao,
B.Mikami,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.60 /
1.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.462,
79.969,
97.532,
90.00,
102.97,
90.00
|
R / Rfree (%)
|
15.5 /
19.2
|
Other elements in 4toq:
The structure of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
(pdb code 4toq). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity, PDB code: 4toq:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 1 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl306
b:21.4
occ:1.00
|
N
|
A:ALA41
|
3.3
|
9.8
|
1.0
|
CA
|
A:ARG40
|
3.7
|
6.8
|
1.0
|
CB
|
A:ARG40
|
3.9
|
10.2
|
1.0
|
NE
|
A:ARG40
|
4.0
|
35.8
|
1.0
|
C
|
A:ARG40
|
4.0
|
8.9
|
1.0
|
CB
|
A:ALA41
|
4.0
|
9.5
|
1.0
|
O
|
A:HOH553
|
4.2
|
26.8
|
1.0
|
CA
|
A:ALA41
|
4.3
|
10.7
|
1.0
|
CG
|
A:ARG40
|
4.4
|
16.4
|
1.0
|
NH2
|
A:ARG40
|
4.5
|
32.2
|
1.0
|
CZ
|
A:ARG40
|
4.7
|
37.5
|
1.0
|
CD
|
A:ARG40
|
4.8
|
36.5
|
1.0
|
O
|
A:PHE39
|
5.0
|
11.9
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 2 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl307
b:17.7
occ:1.00
|
O
|
A:HOH436
|
2.8
|
23.2
|
1.0
|
N
|
A:LEU187
|
3.1
|
7.2
|
1.0
|
C
|
A:ASN185
|
3.4
|
7.0
|
1.0
|
N
|
A:PRO186
|
3.5
|
8.0
|
1.0
|
CA
|
A:ASN185
|
3.5
|
9.7
|
1.0
|
CD
|
A:PRO186
|
3.6
|
9.0
|
1.0
|
N
|
A:ALA188
|
3.7
|
9.7
|
1.0
|
CB
|
A:LEU187
|
3.7
|
9.4
|
1.0
|
CA
|
A:LEU187
|
3.7
|
9.9
|
1.0
|
O
|
A:ASN185
|
3.8
|
8.8
|
1.0
|
C
|
A:LEU187
|
3.9
|
14.1
|
1.0
|
CB
|
A:ALA188
|
4.0
|
10.3
|
1.0
|
CB
|
A:ASN185
|
4.1
|
7.7
|
1.0
|
C
|
A:PRO186
|
4.2
|
9.6
|
1.0
|
CG
|
A:LEU187
|
4.3
|
12.7
|
1.0
|
CA
|
A:PRO186
|
4.4
|
8.7
|
1.0
|
CG
|
A:PRO186
|
4.4
|
8.3
|
1.0
|
CA
|
A:ALA188
|
4.4
|
7.8
|
1.0
|
OD1
|
A:ASN185
|
4.5
|
14.2
|
1.0
|
CG
|
A:ASN185
|
4.7
|
12.9
|
1.0
|
N
|
A:ASN185
|
4.8
|
6.2
|
1.0
|
O
|
A:ASN184
|
4.8
|
11.5
|
1.0
|
O
|
A:LEU187
|
4.8
|
14.4
|
1.0
|
CD1
|
A:LEU187
|
4.9
|
12.7
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 3 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl303
b:28.8
occ:1.00
|
ND1
|
B:HIS49
|
3.0
|
12.0
|
1.0
|
O
|
B:HOH441
|
3.2
|
25.0
|
1.0
|
O
|
B:HOH419
|
3.4
|
24.0
|
1.0
|
CE1
|
B:HIS49
|
3.8
|
12.3
|
1.0
|
CG2
|
B:THR15
|
3.8
|
11.1
|
1.0
|
O
|
B:HOH609
|
3.9
|
20.0
|
1.0
|
CA
|
B:THR15
|
3.9
|
12.4
|
1.0
|
CG
|
B:HIS49
|
4.0
|
11.4
|
1.0
|
O
|
B:GLY14
|
4.1
|
10.7
|
1.0
|
N
|
B:THR15
|
4.2
|
11.8
|
1.0
|
C
|
B:GLY14
|
4.2
|
15.9
|
1.0
|
CB
|
B:HIS49
|
4.3
|
13.5
|
1.0
|
CB
|
B:THR15
|
4.3
|
14.6
|
1.0
|
CA
|
B:HIS49
|
4.5
|
14.2
|
1.0
|
O
|
B:HOH411
|
4.6
|
20.5
|
1.0
|
CZ2
|
B:TRP7
|
4.7
|
10.8
|
1.0
|
O
|
B:HIS49
|
4.7
|
13.6
|
1.0
|
O
|
B:GLY11
|
4.9
|
13.2
|
1.0
|
NE2
|
B:HIS49
|
5.0
|
9.9
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 4 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl304
b:18.4
occ:1.00
|
N
|
B:GLY11
|
3.1
|
11.4
|
1.0
|
N
|
B:GLY48
|
3.4
|
11.9
|
1.0
|
CB
|
B:ALA47
|
3.6
|
13.2
|
1.0
|
CA
|
B:GLY48
|
3.9
|
9.4
|
1.0
|
CA
|
B:ASN10
|
3.9
|
8.9
|
1.0
|
CA
|
B:GLY11
|
4.0
|
13.3
|
1.0
|
C
|
B:ASN10
|
4.0
|
9.8
|
1.0
|
C
|
B:ALA47
|
4.3
|
16.9
|
1.0
|
OD1
|
B:ASN10
|
4.3
|
15.7
|
1.0
|
CA
|
B:ALA47
|
4.5
|
8.3
|
1.0
|
O
|
B:GLN9
|
4.5
|
10.8
|
1.0
|
CG
|
B:ASN10
|
4.5
|
14.4
|
1.0
|
N
|
B:ASN10
|
4.8
|
8.7
|
1.0
|
CB
|
B:ASN10
|
4.8
|
9.8
|
1.0
|
C
|
B:GLY48
|
5.0
|
14.8
|
1.0
|
C
|
B:GLN9
|
5.0
|
10.7
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 5 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl305
b:23.1
occ:1.00
|
O
|
B:HOH444
|
3.1
|
25.4
|
1.0
|
N
|
B:LEU187
|
3.1
|
13.1
|
1.0
|
C
|
B:ASN185
|
3.4
|
9.8
|
1.0
|
N
|
B:PRO186
|
3.4
|
11.5
|
1.0
|
CD
|
B:PRO186
|
3.5
|
15.7
|
1.0
|
CA
|
B:ASN185
|
3.5
|
10.0
|
1.0
|
CB
|
B:LEU187
|
3.7
|
16.4
|
1.0
|
CA
|
B:LEU187
|
3.7
|
13.9
|
1.0
|
N
|
B:ALA188
|
3.8
|
14.5
|
1.0
|
O
|
B:ASN185
|
3.9
|
10.0
|
1.0
|
C
|
B:LEU187
|
4.0
|
16.5
|
1.0
|
C
|
B:PRO186
|
4.2
|
11.6
|
1.0
|
CG
|
B:PRO186
|
4.2
|
12.2
|
1.0
|
CB
|
B:ASN185
|
4.2
|
9.6
|
1.0
|
CB
|
B:ALA188
|
4.3
|
15.3
|
1.0
|
CA
|
B:PRO186
|
4.3
|
13.7
|
1.0
|
CG
|
B:LEU187
|
4.4
|
19.4
|
1.0
|
OD1
|
B:ASN185
|
4.6
|
12.3
|
1.0
|
CA
|
B:ALA188
|
4.6
|
13.4
|
1.0
|
O
|
B:ASN184
|
4.7
|
12.3
|
1.0
|
N
|
B:ASN185
|
4.8
|
7.7
|
1.0
|
CG
|
B:ASN185
|
4.8
|
10.6
|
1.0
|
O
|
B:LEU187
|
4.9
|
18.2
|
1.0
|
CD1
|
B:LEU187
|
4.9
|
24.6
|
1.0
|
CB
|
B:PRO186
|
4.9
|
15.1
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 4toq
Go back to
Chlorine Binding Sites List in 4toq
Chlorine binding site 6 out
of 6 in the Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl305
b:19.0
occ:1.00
|
O
|
D:HOH613
|
3.1
|
22.1
|
1.0
|
O
|
C:HOH548
|
3.1
|
14.6
|
1.0
|
NH1
|
C:ARG144
|
3.1
|
23.0
|
1.0
|
O
|
C:HOH623
|
3.2
|
25.9
|
1.0
|
ND2
|
D:ASN102
|
3.3
|
14.8
|
1.0
|
CZ2
|
C:TRP101
|
3.8
|
15.1
|
1.0
|
CD
|
C:ARG144
|
3.9
|
18.4
|
1.0
|
CG
|
C:ARG144
|
3.9
|
18.3
|
1.0
|
CB
|
D:ASP98
|
4.1
|
10.6
|
1.0
|
CE2
|
C:TRP101
|
4.2
|
12.9
|
1.0
|
CB
|
C:ARG144
|
4.2
|
19.1
|
1.0
|
CG
|
D:ASN102
|
4.2
|
14.5
|
1.0
|
CG
|
D:ASP98
|
4.2
|
17.6
|
1.0
|
CZ
|
C:ARG144
|
4.2
|
27.8
|
1.0
|
OD2
|
D:ASP98
|
4.3
|
17.7
|
1.0
|
OD1
|
D:ASN102
|
4.3
|
14.0
|
1.0
|
CH2
|
C:TRP101
|
4.4
|
13.0
|
1.0
|
NE1
|
C:TRP101
|
4.4
|
14.2
|
1.0
|
NE
|
C:ARG144
|
4.5
|
21.0
|
1.0
|
CA
|
C:ARG144
|
4.5
|
12.4
|
1.0
|
O
|
C:HOH600
|
4.8
|
20.0
|
1.0
|
OD1
|
D:ASP98
|
4.8
|
20.0
|
1.0
|
O
|
D:HOH556
|
4.9
|
18.4
|
1.0
|
O
|
C:ARG144
|
4.9
|
13.1
|
1.0
|
|
Reference:
T.Masuda,
G.Zhao,
B.Mikami.
Crystal Structure of Class III Chitinase From Pomegranate Provides the Insight Into Its Metal Storage Capacity. Biosci.Biotechnol.Biochem. 1 2014.
ISSN: ISSN 0916-8451
PubMed: 25252615
DOI: 10.1080/09168451.2014.962475
Page generated: Fri Jul 26 01:49:56 2024
|