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Sodium in PDB 5a95: Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2

Enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2

All present enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2, PDB code: 5a95 was solved by G.Sulzenbacher, M.Lafond, T.Freyd, B.Henrissat, R.M.Coutinho, J.G.Berrin, M.L.Garron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.44 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.048, 60.384, 130.326, 90.00, 104.75, 90.00
R / Rfree (%) 12.9 / 15.6

Other elements in 5a95:

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2 also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2 (pdb code 5a95). 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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2, PDB code: 5a95:

Sodium binding site 1 out of 1 in 5a95

Go back to Sodium Binding Sites List in 5a95
Sodium binding site 1 out of 1 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:13.3
occ:1.00
O A:HOH664 2.7 7.3 1.0
O A:MET215 2.8 6.8 1.0
O B:THR196 2.8 6.7 1.0
C A:MET215 3.5 6.4 1.0
CB B:THR196 3.6 6.3 1.0
C B:THR196 3.7 6.0 1.0
CA A:ARG169 3.7 6.0 1.0
CB A:SER219 3.7 7.3 1.0
CA B:THR196 3.8 6.5 1.0
CG A:ARG169 3.9 6.7 1.0
CB A:MET215 3.9 11.5 1.0
CB A:ARG169 4.0 6.7 1.0
CA A:MET215 4.2 7.8 1.0
N A:ILE216 4.3 6.2 1.0
CE A:MET215 4.3 9.3 1.0
CG2 B:THR196 4.3 7.0 1.0
OG A:SER219 4.3 8.5 1.0
O A:ARG169 4.5 7.5 1.0
CA A:ILE216 4.5 6.5 1.0
N A:ARG169 4.6 5.9 1.0
C A:ARG169 4.6 6.1 1.0
OG1 B:THR196 4.7 6.8 1.0
O A:HOH957 4.7 9.7 1.0
CB A:THR172 4.8 6.7 1.0
O A:TRP168 4.9 6.4 1.0
CG A:MET215 4.9 13.5 1.0
N B:LEU197 4.9 5.8 1.0
N A:SER219 4.9 7.9 1.0
CA A:SER219 5.0 7.4 1.0

Reference:

M.Lafond, G.Sulzenbacher, T.Freyd, B.Henrissat, J.G.Berrin, M.L.Garron. The Quaternary Structure of A Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans J.Biol.Chem. V. 291 7183 2016.
ISSN: ISSN 0021-9258
PubMed: 26755730
DOI: 10.1074/JBC.M115.695999
Page generated: Tue Dec 15 10:18:42 2020

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