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Magnesium 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:

Chlorine (Cl) 12 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 2, PDB code: 5a95:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5a95

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Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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
A:Mg401

b:10.0
occ:1.00
 O A:VAL181 2.3 9.0 1.0
O A:VAL178 2.3 9.2 1.0
O A:HOH704 2.3 8.9 1.0
O A:HOH872 2.4 10.8 1.0
O A:HOH662 2.5 9.9 1.0
C A:VAL178 3.4 9.3 1.0
C A:VAL181 3.4 7.7 1.0
CG1 A:VAL223 4.0 12.3 1.0
N A:VAL178 4.1 9.1 1.0
CB A:VAL181 4.1 9.4 1.0
CA A:VAL181 4.1 8.2 1.0
CA A:VAL178 4.2 9.4 1.0
O A:TYR175 4.2 8.4 1.0
N A:VAL181 4.2 8.1 1.0
N A:PRO179 4.3 9.7 1.0
CA A:PRO179 4.3 8.8 1.0
OG1 A:THR222 4.4 11.8 1.0
CE1 A:PHE50 4.4 10.9 1.0
C A:PRO179 4.5 8.6 1.0
N A:ALA182 4.5 7.2 1.0
CB A:VAL178 4.5 9.8 1.0
O A:HOH715 4.5 9.4 1.0
O A:PRO179 4.5 9.1 1.0
OD2 A:ASP220 4.6 9.8 1.0
O A:HOH661 4.7 9.7 1.0
CG1 A:VAL181 4.7 13.0 1.0
CA A:ALA182 4.7 7.6 1.0
CD1 A:PHE50 4.7 10.6 1.0
OH A:TYR184 4.9 8.5 1.0
CB A:VAL223 5.0 10.6 1.0

Magnesium binding site 2 out of 5 in 5a95

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Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg402

b:10.6
occ:1.00
 O B:VAL181 2.3 9.9 1.0
O B:HOH679 2.3 10.0 1.0
O B:VAL178 2.3 10.3 1.0
O B:HOH838 2.3 12.5 1.0
O B:HOH622 2.4 12.3 1.0
C B:VAL178 3.4 9.6 1.0
C B:VAL181 3.4 9.4 1.0
CG1 B:VAL223 3.7 22.9 1.0
N B:VAL178 4.1 10.8 1.0
CB B:VAL181 4.1 11.1 1.0
CA B:VAL181 4.1 8.9 1.0
CA B:VAL178 4.2 10.5 1.0
N B:VAL181 4.2 8.7 1.0
O B:TYR175 4.3 9.6 1.0
N B:PRO179 4.3 9.2 1.0
CA B:PRO179 4.4 10.3 1.0
OG1 B:THR222 4.4 15.0 1.0
CB B:VAL178 4.5 9.8 1.0
N B:ALA182 4.5 9.1 1.0
CE1 B:PHE50 4.5 12.1 1.0
C B:PRO179 4.5 9.6 1.0
O B:PRO179 4.6 10.3 1.0
OD2 B:ASP220 4.6 11.4 1.0
O B:HOH658 4.7 11.8 1.0
CA B:ALA182 4.7 9.0 1.0
CB B:VAL223 4.7 17.7 1.0
CG1 B:VAL181 4.7 15.2 1.0
O B:HOH607 4.8 11.0 1.0
OH B:TYR184 4.9 10.2 1.0
CA B:VAL223 4.9 11.7 1.0
CD1 B:PHE50 4.9 11.9 1.0

Magnesium binding site 3 out of 5 in 5a95

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Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg binding site number 3 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:Mg407

b:10.6
occ:1.00
 O A:HOH931 2.1 11.3 1.0
O B:HOH699 2.1 10.6 1.0
O A:HOH1033 4.2 21.8 1.0
O A:HOH1070 4.2 15.5 1.0
O A:HOH925 4.3 10.9 1.0
O A:HOH576 4.3 13.1 1.0
O B:HOH1020 4.3 18.6 1.0
O B:HOH856 4.4 14.7 1.0
O A:ALA218 4.4 8.5 1.0
O B:HOH921 4.4 13.7 1.0
CG2 B:THR196 4.5 7.0 1.0
O B:MET193 4.5 7.0 1.0
O A:HOH1117 4.9 38.4 1.0
O A:HOH785 5.0 20.1 1.0
O B:HOH953 5.0 19.6 1.0

Magnesium binding site 4 out of 5 in 5a95

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Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg binding site number 4 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
C:Mg401

b:8.9
occ:1.00
 O C:HOH529 2.0 13.7 1.0
O C:HOH564 2.1 9.7 1.0
O C:HOH660 2.2 14.4 1.0
O C:HOH896 2.2 13.7 1.0
O C:HOH726 4.0 15.9 1.0
OE2 C:GLU92 4.2 9.9 1.0
OE1 C:GLU92 4.2 8.6 1.0
O C:HOH641 4.3 12.4 1.0
CD C:GLU92 4.6 7.6 1.0
O C:ASP345 4.7 10.9 1.0
ND2 C:ASN96 4.9 10.8 1.0

Magnesium binding site 5 out of 5 in 5a95

Go back to Magnesium Binding Sites List in 5a95
Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg binding site number 5 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
C:Mg403

b:10.4
occ:1.00
 O C:HOH855 2.3 13.6 1.0
O C:VAL181 2.3 10.3 1.0
O C:VAL178 2.3 9.6 1.0
O C:HOH644 2.3 9.4 1.0
O C:HOH610 2.4 11.8 1.0
C C:VAL178 3.4 9.7 1.0
C C:VAL181 3.4 8.5 1.0
CG1 C:VAL223 3.8 24.0 1.0
CB C:VAL181 4.1 10.5 1.0
N C:VAL178 4.1 9.6 1.0
CA C:VAL181 4.1 8.9 1.0
CA C:VAL178 4.2 8.8 1.0
N C:VAL181 4.2 9.0 1.0
O C:TYR175 4.2 8.5 1.0
N C:PRO179 4.3 10.1 1.0
OG1 C:THR222 4.4 14.5 1.0
CA C:PRO179 4.4 10.1 0.5
CA C:PRO179 4.4 9.7 0.5
CB C:VAL178 4.5 9.6 1.0
CE1 C:PHE50 4.5 12.2 1.0
N C:ALA182 4.5 9.2 1.0
C C:PRO179 4.5 8.4 1.0
O C:PRO179 4.6 10.2 1.0
OD2 C:ASP220 4.7 11.3 1.0
O C:HOH681 4.7 12.7 1.0
CA C:ALA182 4.7 8.8 1.0
CB C:VAL223 4.8 19.9 1.0
O C:HOH598 4.8 11.4 1.0
CG1 C:VAL181 4.8 13.2 1.0
CA C:VAL223 4.8 12.9 1.0
OH C:TYR184 4.9 9.9 1.0
CD1 C:PHE50 4.9 10.9 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: Sun Sep 29 00:21:22 2024

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