Sodium in PDB 1o4z: The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Enzymatic activity of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
All present enzymatic activity of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans:
3.2.1.81;
Protein crystallography data
The structure of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans, PDB code: 1o4z
was solved by
J.Allouch,
M.Jam,
W.Helbert,
T.Barbeyron,
B.Kloareg,
B.Henrissat,
M.Czjzek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.448,
105.350,
97.369,
90.00,
94.13,
90.00
|
R / Rfree (%)
|
16.6 /
22.4
|
Other elements in 1o4z:
The structure of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
(pdb code 1o4z). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans, PDB code: 1o4z:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 1 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1004
b:23.9
occ:1.00
|
O
|
A:GLY127
|
2.2
|
26.4
|
1.0
|
O
|
A:HOH2119
|
2.3
|
28.5
|
1.0
|
O
|
A:ASN83
|
2.3
|
22.9
|
1.0
|
OD1
|
A:ASP343
|
2.3
|
25.1
|
1.0
|
O
|
A:ASP343
|
2.4
|
19.1
|
1.0
|
C
|
A:GLY127
|
3.3
|
26.0
|
1.0
|
C
|
A:ASN83
|
3.4
|
23.8
|
1.0
|
C
|
A:ASP343
|
3.4
|
19.1
|
1.0
|
CG
|
A:ASP343
|
3.5
|
21.3
|
1.0
|
OE2
|
A:GLU85
|
3.5
|
29.2
|
0.5
|
CA
|
A:ASP343
|
3.9
|
19.1
|
1.0
|
CA
|
A:GLY127
|
4.0
|
26.1
|
1.0
|
CA
|
A:ASN83
|
4.0
|
24.0
|
1.0
|
O
|
A:HOH2182
|
4.1
|
34.4
|
1.0
|
CB
|
A:ASN83
|
4.1
|
24.7
|
1.0
|
CD
|
A:GLU85
|
4.2
|
29.7
|
0.5
|
CB
|
A:ASP343
|
4.3
|
19.5
|
1.0
|
OD2
|
A:ASP343
|
4.3
|
22.4
|
1.0
|
N
|
A:GLU128
|
4.4
|
25.6
|
1.0
|
N
|
A:PHE84
|
4.4
|
24.2
|
1.0
|
CG
|
A:GLU85
|
4.4
|
29.3
|
1.0
|
O
|
A:PHE84
|
4.4
|
25.8
|
1.0
|
C
|
A:PHE84
|
4.5
|
25.8
|
1.0
|
N
|
A:TRP344
|
4.5
|
19.0
|
1.0
|
CB
|
A:PHE84
|
4.5
|
24.2
|
1.0
|
O
|
A:HOH2216
|
4.6
|
37.7
|
1.0
|
CA
|
A:GLU128
|
4.6
|
25.3
|
1.0
|
CB
|
A:TRP344
|
4.7
|
19.0
|
1.0
|
CA
|
A:PHE84
|
4.7
|
24.7
|
1.0
|
CD1
|
A:TRP344
|
4.7
|
17.8
|
1.0
|
N
|
A:GLU85
|
4.9
|
27.2
|
1.0
|
CG
|
A:ASN83
|
4.9
|
26.6
|
1.0
|
CA
|
A:TRP344
|
4.9
|
18.8
|
1.0
|
|
Sodium binding site 2 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 2 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na1007
b:38.5
occ:1.00
|
NH2
|
A:ARG246
|
3.4
|
27.6
|
1.0
|
O
|
A:HOH2117
|
3.6
|
23.2
|
1.0
|
CD
|
A:PRO64
|
4.4
|
25.2
|
1.0
|
CZ
|
A:ARG246
|
4.5
|
27.2
|
1.0
|
CG2
|
A:ILE63
|
4.6
|
27.7
|
1.0
|
O
|
A:HOH2070
|
4.6
|
35.0
|
1.0
|
CG
|
A:PRO64
|
4.7
|
25.2
|
1.0
|
|
Sodium binding site 3 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 3 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1005
b:25.4
occ:1.00
|
O
|
B:ASN83
|
2.2
|
22.9
|
1.0
|
O
|
B:GLY127
|
2.2
|
26.3
|
1.0
|
OD1
|
B:ASP343
|
2.3
|
20.8
|
1.0
|
O
|
B:ASP343
|
2.3
|
18.8
|
1.0
|
C
|
B:ASN83
|
3.3
|
23.8
|
1.0
|
C
|
B:ASP343
|
3.3
|
18.9
|
1.0
|
OE2
|
B:GLU85
|
3.3
|
30.3
|
0.5
|
C
|
B:GLY127
|
3.4
|
26.0
|
1.0
|
CG
|
B:ASP343
|
3.5
|
20.6
|
1.0
|
CA
|
B:ASP343
|
3.8
|
19.0
|
1.0
|
CA
|
B:ASN83
|
3.9
|
24.0
|
1.0
|
CB
|
B:ASN83
|
4.0
|
24.2
|
1.0
|
CA
|
B:GLY127
|
4.1
|
26.2
|
1.0
|
CD
|
B:GLU85
|
4.2
|
29.1
|
0.5
|
CB
|
B:ASP343
|
4.3
|
19.5
|
1.0
|
OD2
|
B:ASP343
|
4.3
|
22.2
|
1.0
|
N
|
B:PHE84
|
4.3
|
24.2
|
1.0
|
N
|
B:GLU128
|
4.4
|
25.6
|
1.0
|
N
|
B:TRP344
|
4.4
|
19.0
|
1.0
|
C
|
B:PHE84
|
4.4
|
25.7
|
1.0
|
O
|
B:PHE84
|
4.5
|
25.7
|
1.0
|
CB
|
B:PHE84
|
4.5
|
24.1
|
1.0
|
CG
|
B:GLU85
|
4.5
|
28.6
|
0.5
|
CA
|
B:PHE84
|
4.6
|
24.6
|
1.0
|
CB
|
B:TRP344
|
4.6
|
18.8
|
1.0
|
CD1
|
B:TRP344
|
4.7
|
16.9
|
1.0
|
CA
|
B:GLU128
|
4.7
|
25.4
|
1.0
|
CG
|
B:ASN83
|
4.8
|
26.7
|
1.0
|
O
|
B:HOH2159
|
4.8
|
29.8
|
1.0
|
CA
|
B:TRP344
|
4.8
|
18.9
|
1.0
|
N
|
B:GLU85
|
4.9
|
27.2
|
1.0
|
|
Sodium binding site 4 out
of 7 in 1o4z
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Sodium Binding Sites List in 1o4z
Sodium binding site 4 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na1008
b:45.3
occ:1.00
|
O
|
B:HOH2232
|
2.3
|
41.4
|
1.0
|
OE1
|
B:GLU128
|
3.2
|
30.0
|
1.0
|
NZ
|
B:LYS164
|
3.9
|
26.3
|
1.0
|
NZ
|
B:LYS130
|
4.0
|
27.3
|
1.0
|
O
|
B:HOH2062
|
4.1
|
26.6
|
1.0
|
CA
|
B:GLY341
|
4.3
|
18.7
|
1.0
|
CD
|
B:GLU128
|
4.3
|
29.4
|
1.0
|
OE1
|
B:GLU336
|
4.4
|
26.1
|
0.5
|
CG2
|
B:THR339
|
4.5
|
17.1
|
1.0
|
N
|
B:GLY341
|
4.5
|
18.6
|
1.0
|
O
|
B:THR339
|
4.6
|
18.3
|
1.0
|
OE2
|
B:GLU336
|
4.6
|
27.9
|
0.5
|
OE2
|
B:GLU128
|
4.6
|
33.2
|
1.0
|
CG
|
B:LYS130
|
4.7
|
24.5
|
1.0
|
CD
|
B:GLU336
|
4.7
|
25.4
|
0.5
|
CZ
|
B:PHE244
|
4.7
|
22.9
|
1.0
|
CE
|
B:LYS130
|
4.7
|
27.1
|
1.0
|
CD
|
B:LYS130
|
4.7
|
26.0
|
1.0
|
CE
|
B:LYS164
|
4.9
|
26.5
|
1.0
|
|
Sodium binding site 5 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 5 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1006
b:21.9
occ:1.00
|
O
|
C:ASP343
|
2.2
|
19.4
|
1.0
|
O
|
C:GLY127
|
2.3
|
26.1
|
1.0
|
OD1
|
C:ASP343
|
2.3
|
19.8
|
1.0
|
O
|
C:HOH2198
|
2.3
|
41.6
|
1.0
|
O
|
C:ASN83
|
2.4
|
23.1
|
1.0
|
C
|
C:ASP343
|
3.2
|
19.1
|
1.0
|
C
|
C:ASN83
|
3.4
|
23.8
|
1.0
|
CG
|
C:ASP343
|
3.4
|
20.2
|
1.0
|
C
|
C:GLY127
|
3.5
|
26.0
|
1.0
|
CA
|
C:ASP343
|
3.7
|
19.0
|
1.0
|
O
|
C:HOH2197
|
3.9
|
46.0
|
1.0
|
CA
|
C:ASN83
|
4.0
|
24.0
|
1.0
|
CB
|
C:ASN83
|
4.1
|
24.6
|
1.0
|
CA
|
C:GLY127
|
4.1
|
26.2
|
1.0
|
CB
|
C:ASP343
|
4.2
|
19.2
|
1.0
|
OD2
|
C:ASP343
|
4.2
|
20.0
|
1.0
|
O
|
C:HOH2063
|
4.3
|
31.1
|
1.0
|
N
|
C:TRP344
|
4.3
|
19.1
|
1.0
|
OE2
|
C:GLU85
|
4.4
|
29.2
|
0.5
|
N
|
C:PHE84
|
4.4
|
24.2
|
1.0
|
CD1
|
C:TRP344
|
4.5
|
20.3
|
1.0
|
N
|
C:GLU128
|
4.5
|
25.5
|
1.0
|
CB
|
C:TRP344
|
4.5
|
19.2
|
1.0
|
CB
|
C:PHE84
|
4.5
|
24.1
|
1.0
|
C
|
C:PHE84
|
4.6
|
25.8
|
1.0
|
O
|
C:PHE84
|
4.6
|
25.8
|
1.0
|
CG
|
C:GLU85
|
4.6
|
29.2
|
1.0
|
CA
|
C:GLU128
|
4.7
|
25.4
|
1.0
|
CA
|
C:PHE84
|
4.7
|
24.7
|
1.0
|
CA
|
C:TRP344
|
4.7
|
18.9
|
1.0
|
CG
|
C:TRP344
|
4.9
|
19.3
|
1.0
|
CG
|
C:ASN83
|
5.0
|
26.2
|
1.0
|
CD
|
C:GLU85
|
5.0
|
29.9
|
0.5
|
N
|
C:GLU85
|
5.0
|
27.3
|
1.0
|
|
Sodium binding site 6 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 6 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na1009
b:18.4
occ:1.00
|
N
|
C:ARG119
|
3.5
|
21.7
|
1.0
|
CD
|
C:LYS118
|
3.6
|
22.4
|
1.0
|
CG
|
C:ARG119
|
3.9
|
23.4
|
1.0
|
CA
|
C:LYS118
|
4.0
|
21.3
|
1.0
|
CB
|
C:ARG119
|
4.1
|
22.6
|
1.0
|
C
|
C:LYS118
|
4.2
|
21.6
|
1.0
|
NZ
|
C:LYS118
|
4.4
|
23.3
|
0.5
|
CA
|
C:ARG119
|
4.4
|
22.1
|
1.0
|
CD
|
C:ARG119
|
4.4
|
24.4
|
1.0
|
CB
|
C:LYS118
|
4.5
|
21.8
|
1.0
|
CG
|
C:LYS118
|
4.6
|
22.3
|
1.0
|
CE
|
C:LYS118
|
4.6
|
24.4
|
1.0
|
O
|
C:HOH2124
|
4.7
|
38.8
|
1.0
|
O
|
C:HOH2205
|
4.7
|
46.1
|
1.0
|
NE
|
C:ARG119
|
4.7
|
25.8
|
1.0
|
O
|
C:TRP117
|
4.7
|
20.4
|
1.0
|
CE1
|
C:PHE104
|
4.7
|
21.4
|
1.0
|
CD1
|
C:PHE104
|
4.9
|
21.4
|
1.0
|
|
Sodium binding site 7 out
of 7 in 1o4z
Go back to
Sodium Binding Sites List in 1o4z
Sodium binding site 7 out
of 7 in the The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of The Three-Dimensional Structure of Beta-Agarase B From Zobellia Galactanivorans within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na1003
b:21.9
occ:1.00
|
OD1
|
D:ASP343
|
2.3
|
18.8
|
1.0
|
O
|
D:GLY127
|
2.3
|
26.1
|
1.0
|
O
|
D:ASN83
|
2.3
|
22.5
|
1.0
|
O
|
D:ASP343
|
2.4
|
18.6
|
1.0
|
C
|
D:ASP343
|
3.3
|
18.9
|
1.0
|
C
|
D:ASN83
|
3.4
|
23.7
|
1.0
|
CG
|
D:ASP343
|
3.4
|
18.9
|
1.0
|
C
|
D:GLY127
|
3.5
|
26.0
|
1.0
|
OE2
|
D:GLU85
|
3.7
|
32.2
|
0.5
|
CA
|
D:ASP343
|
3.9
|
18.7
|
1.0
|
O
|
D:HOH2045
|
3.9
|
33.4
|
1.0
|
CA
|
D:ASN83
|
4.0
|
23.9
|
1.0
|
CB
|
D:ASN83
|
4.0
|
24.1
|
1.0
|
CA
|
D:GLY127
|
4.1
|
26.1
|
1.0
|
OD2
|
D:ASP343
|
4.2
|
19.2
|
1.0
|
CB
|
D:ASP343
|
4.2
|
18.5
|
1.0
|
N
|
D:TRP344
|
4.4
|
18.9
|
1.0
|
N
|
D:PHE84
|
4.5
|
24.2
|
1.0
|
N
|
D:GLU128
|
4.5
|
25.4
|
1.0
|
CD1
|
D:TRP344
|
4.6
|
15.1
|
1.0
|
CG
|
D:GLU85
|
4.6
|
30.1
|
1.0
|
CD
|
D:GLU85
|
4.6
|
31.9
|
1.0
|
CB
|
D:TRP344
|
4.6
|
18.5
|
1.0
|
CB
|
D:PHE84
|
4.6
|
24.5
|
1.0
|
C
|
D:PHE84
|
4.6
|
25.7
|
1.0
|
O
|
D:PHE84
|
4.7
|
25.9
|
1.0
|
CG
|
D:ASN83
|
4.7
|
26.3
|
1.0
|
CA
|
D:PHE84
|
4.8
|
24.8
|
1.0
|
CA
|
D:GLU128
|
4.8
|
25.2
|
1.0
|
CA
|
D:TRP344
|
4.8
|
18.8
|
1.0
|
OD1
|
D:ASN83
|
4.9
|
31.4
|
1.0
|
N
|
D:GLU85
|
5.0
|
27.1
|
1.0
|
|
Reference:
J.Allouch,
M.Jam,
W.Helbert,
T.Barbeyron,
B.Kloareg,
B.Henrissat,
M.Czjzek.
The Three-Dimensional Structures of Two {Beta}-Agarases. J.Biol.Chem. V. 278 47171 2003.
ISSN: ISSN 0021-9258
PubMed: 12970344
DOI: 10.1074/JBC.M308313200
Page generated: Sun Oct 6 21:08:35 2024
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