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Sodium in PDB 4be3: Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans

Enzymatic activity of Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans

All present enzymatic activity of Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans:
4.2.2.11; 4.2.2.3;

Protein crystallography data

The structure of Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans, PDB code: 4be3 was solved by F.Thomas, A.Jeudy, G.Michel, M.Czjzek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.95 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.420, 93.910, 130.150, 90.00, 90.00, 90.00
R / Rfree (%) 15.634 / 17.802

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans (pdb code 4be3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans, PDB code: 4be3:

Sodium binding site 1 out of 1 in 4be3

Go back to Sodium Binding Sites List in 4be3
Sodium binding site 1 out of 1 in the Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 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 Crystal Structure of the Exolytic PL7 Alginate Lyase ALYA5 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na399

b:20.4
occ:1.00
 OG1 B:THR116 3.1 25.6 1.0
OG1 A:THR116 3.2 26.0 1.0
N B:ILE113 3.4 25.2 1.0
N A:ILE113 3.4 25.4 1.0
CA B:TRP112 3.6 22.7 1.0
CA A:TRP112 3.6 22.1 1.0
CG1 B:ILE113 3.8 24.5 1.0
CG1 A:ILE113 3.8 22.5 1.0
CG2 B:THR116 3.9 24.9 1.0
CG2 A:THR116 4.0 25.1 1.0
C B:TRP112 4.0 23.4 1.0
C A:TRP112 4.0 24.5 1.0
CB B:THR116 4.0 25.0 1.0
CB A:THR116 4.1 26.9 1.0
CB A:TRP112 4.2 22.8 1.0
CB B:TRP112 4.2 22.8 1.0
O A:HOH2092 4.4 40.4 1.0
CG2 A:ILE113 4.4 25.6 1.0
CB B:ILE113 4.4 23.3 1.0
CG2 B:ILE113 4.5 23.9 1.0
O A:HIS111 4.5 24.1 1.0
CA B:ILE113 4.5 23.0 1.0
CB A:ILE113 4.5 23.5 1.0
O B:HIS111 4.5 23.2 1.0
CA A:ILE113 4.5 24.1 1.0
O A:HOH2095 4.7 37.6 1.0
N A:TRP112 4.7 22.9 1.0
N B:TRP112 4.7 20.3 1.0
O A:HOH2091 4.8 34.0 1.0
CD1 A:ILE113 4.8 24.4 1.0
O A:HOH2103 4.8 31.0 1.0
CD1 B:ILE113 4.9 24.0 1.0
O B:ILE113 5.0 24.0 1.0

Reference:

F.Thomas, L.C.E.Lundqvist, M.Jam, A.Jeudy, T.Barbeyron, C.Sandstrom, G.Michel, M.Czjzek. Comparative Characterization of Two Marine Alginate Lyases From Zobellia Galactanivorans Reveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate. J.Biol.Chem. V. 288 23021 2013.
ISSN: ISSN 0021-9258
PubMed: 23782694
DOI: 10.1074/JBC.M113.467217
Page generated: Sun Aug 17 18:37:30 2025

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