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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:

Magnesium (Mg) 2 atoms

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

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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

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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

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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 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

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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

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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

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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: Tue Dec 15 05:32:04 2020

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