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Magnesium in PDB 5a8m: Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans

Enzymatic activity of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans

All present enzymatic activity of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans, PDB code: 5a8m 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) 47.33 / 1.86
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 142.605, 142.605, 136.277, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.5

Other elements in 5a8m:

The structure of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans (pdb code 5a8m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans, PDB code: 5a8m:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5a8m

Go back to Magnesium Binding Sites List in 5a8m
Magnesium binding site 1 out of 3 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1368

b:16.1
occ:1.00
 O A:VAL178 2.3 13.1 1.0
O A:HOH2260 2.3 13.0 1.0
O A:HOH2267 2.3 17.9 1.0
O A:VAL181 2.3 13.1 1.0
O A:HOH2264 2.4 14.4 1.0
C A:VAL178 3.4 13.5 1.0
C A:VAL181 3.5 12.8 1.0
CG1 A:VAL223 3.8 14.8 0.5
N A:VAL178 4.1 14.0 1.0
CB A:VAL181 4.1 14.3 1.0
CA A:VAL181 4.2 13.2 1.0
CA A:VAL178 4.2 13.8 1.0
O A:TYR175 4.2 11.5 1.0
N A:VAL181 4.3 12.7 1.0
N A:PRO179 4.3 13.2 1.0
CA A:PRO179 4.4 13.0 1.0
CG2 A:VAL223 4.4 15.6 0.5
CB A:VAL178 4.5 14.5 1.0
C A:PRO179 4.5 12.5 1.0
N A:ALA182 4.5 13.2 1.0
OD2 A:ASP220 4.6 15.6 1.0
O A:PRO179 4.6 13.0 1.0
OG1 A:THR222 4.6 20.8 1.0
CG1 A:VAL181 4.6 15.7 1.0
O A:HOH2074 4.6 15.9 1.0
CB A:VAL223 4.6 15.3 0.5
CE2 A:PHE50 4.7 15.3 1.0
CA A:ALA182 4.7 12.6 1.0
O A:HOH2072 4.7 12.0 1.0
CB A:VAL223 4.8 14.8 0.5
CA A:VAL223 4.8 15.0 0.5
CA A:VAL223 4.8 14.8 0.5
OH A:TYR184 4.9 12.3 1.0

Magnesium binding site 2 out of 3 in 5a8m

Go back to Magnesium Binding Sites List in 5a8m
Magnesium binding site 2 out of 3 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1369

b:15.8
occ:1.00
 O B:HOH2236 2.2 13.9 1.0
O B:VAL178 2.3 12.9 1.0
O B:HOH2240 2.3 16.7 1.0
O B:HOH2243 2.3 16.1 1.0
O B:VAL181 2.3 13.0 1.0
C B:VAL178 3.4 13.5 1.0
C B:VAL181 3.5 13.0 1.0
CG1 B:VAL223 3.7 18.0 0.6
N B:VAL178 4.1 14.3 1.0
CB B:VAL181 4.1 13.4 1.0
CA B:VAL181 4.2 13.2 1.0
CA B:VAL178 4.2 13.7 1.0
O B:TYR175 4.2 11.8 1.0
N B:PRO179 4.3 13.6 1.0
N B:VAL181 4.3 13.5 1.0
CA B:PRO179 4.4 13.9 1.0
CB B:VAL178 4.5 13.8 1.0
CG2 B:VAL223 4.5 15.9 0.4
CB B:VAL223 4.5 16.0 0.4
C B:PRO179 4.5 14.1 1.0
N B:ALA182 4.5 12.9 1.0
OG1 B:THR222 4.6 21.1 1.0
CG1 B:VAL181 4.6 15.0 1.0
OD2 B:ASP220 4.6 15.1 1.0
O B:PRO179 4.6 13.9 1.0
CE2 B:PHE50 4.7 17.0 1.0
O B:HOH2055 4.7 16.1 1.0
CA B:ALA182 4.7 12.7 1.0
CB B:VAL223 4.8 17.1 0.6
CA B:VAL223 4.8 16.0 0.4
O B:HOH2054 4.8 16.3 1.0
CA B:VAL223 4.8 16.4 0.6
OH B:TYR184 4.9 13.8 1.0
CD2 B:PHE50 5.0 16.7 1.0

Magnesium binding site 3 out of 3 in 5a8m

Go back to Magnesium Binding Sites List in 5a8m
Magnesium binding site 3 out of 3 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1368

b:18.2
occ:1.00
 O C:VAL178 2.2 11.0 1.0
O C:VAL181 2.3 10.7 1.0
O C:HOH2223 2.4 11.0 1.0
O C:HOH2231 2.4 17.1 1.0
O C:HOH2226 2.5 14.6 1.0
C C:VAL178 3.3 12.0 1.0
C C:VAL181 3.5 11.2 1.0
CG1 C:VAL223 3.8 20.4 1.0
CB C:VAL181 4.0 11.8 1.0
N C:VAL178 4.1 13.6 1.0
CA C:VAL181 4.2 11.4 1.0
CA C:VAL178 4.2 12.6 1.0
N C:VAL181 4.2 11.7 1.0
O C:TYR175 4.3 11.9 1.0
N C:PRO179 4.3 11.7 1.0
CA C:PRO179 4.3 11.9 1.0
CB C:VAL178 4.5 12.5 1.0
C C:PRO179 4.5 11.7 1.0
N C:ALA182 4.5 11.4 1.0
OG1 C:THR222 4.5 19.8 1.0
CG1 C:VAL181 4.6 12.3 1.0
O C:PRO179 4.6 11.2 1.0
OD2 C:ASP220 4.6 15.2 1.0
O C:HOH2056 4.6 14.6 1.0
CE2 C:PHE50 4.7 14.6 1.0
CA C:ALA182 4.7 11.5 1.0
CB C:VAL223 4.8 17.8 1.0
O C:HOH2055 4.8 13.8 1.0
CA C:VAL223 4.9 16.1 1.0
OH C:TYR184 4.9 14.3 1.0
CD2 C:PHE50 5.0 14.3 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 00:20:29 2024

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