Atomistry » Sodium » PDB 1nnh-1oan » 1o4z
Atomistry »
  Sodium »
    PDB 1nnh-1oan »
      1o4z »

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

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

Go back to 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy