Magnesium in PDB 6mgl: Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan

The structure of Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan, PDB code: 6mgl was solved by P.J.Stogios, T.Skarina, G.Arnal, N.Watanabe, H.Brumer, A.Savchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.170, 100.840, 118.689, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.7

The structure of Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan (pdb code 6mgl). 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 Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan, PDB code: 6mgl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan


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 Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg822 b:15.1 occ:0.74 OD2 A:ASP356 2.0 16.7 1.0 O A:HOH1480 2.1 21.0 1.0 O A:HOH1110 2.1 18.9 1.0 O A:HOH1788 2.1 20.3 1.0 O A:HOH1298 2.2 18.3 1.0 CG A:ASP356 3.1 15.1 1.0 CB A:ASP356 3.6 13.6 1.0 O A:HOH912 3.9 56.6 1.0 O A:HOH1408 3.9 31.3 1.0 OD1 A:ASP356 4.1 15.5 1.0 O A:PRO353 4.2 12.8 1.0 O A:HOH958 4.2 22.6 1.0 O A:HOH997 4.3 21.4 1.0 O A:HOH2231 4.5 22.3 1.0 O A:HOH1982 4.5 19.6 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan


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 Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg823 b:29.9 occ:0.80 O A:HOH1714 2.0 32.0 1.0 O A:HOH1678 2.0 32.5 1.0 O A:HOH1709 2.1 31.4 1.0 O A:HOH2178 2.2 38.5 1.0 NE2 A:HIS711 2.3 19.9 1.0 O A:HOH1405 2.3 27.5 1.0 CE1 A:HIS711 3.2 22.3 1.0 CD2 A:HIS711 3.3 17.5 1.0 O A:HOH1468 4.1 22.3 1.0 O A:HOH2187 4.3 40.1 1.0 O A:HOH1143 4.3 21.3 1.0 O A:HOH1108 4.3 33.9 1.0 ND1 A:HIS711 4.3 19.3 1.0 CG A:HIS711 4.4 17.4 1.0 O A:HOH1224 4.4 15.5 1.0 O A:HOH2093 4.4 55.4 1.0 O A:HOH2220 4.5 36.9 1.0 O A:TRP6 4.6 17.1 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan


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 Catalytic Domain From GH74 Enzyme POGH74 From Paenibacillus Odorifer, D60A Mutant in Complex with Xxlg and Xgxxlg Xyloglucan within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg824 b:10.8 occ:1.00 OE2 A:GLU378 2.1 19.1 1.0 OD2 A:ASP376 2.2 12.9 1.0 O A:HOH993 2.3 16.3 1.0 O A:HOH1679 2.3 16.2 1.0 O A:HOH1724 2.5 17.1 1.0 O A:ILE21 2.6 10.8 1.0 OD1 A:ASP376 2.6 12.4 1.0 CG A:ASP376 2.8 11.6 1.0 CD A:GLU378 3.1 17.3 1.0 C A:ILE21 3.7 10.2 1.0 CG A:GLU378 3.8 12.4 1.0 N A:ILE21 4.0 9.2 1.0 OE1 A:GLU378 4.0 22.8 1.0 O A:HOH1286 4.2 35.5 1.0 CB A:ASP376 4.3 9.1 1.0 O A:HOH1533 4.3 18.3 1.0 O A:HOH1090 4.4 11.2 1.0 CA A:ILE21 4.5 9.2 1.0 O A:HOH1154 4.6 9.6 1.0 O A:HOH1601 4.7 35.5 1.0 O A:HOH1372 4.7 16.5 1.0 OE1 A:GLU127 4.7 12.7 1.0 N A:ILE22 4.7 9.4 1.0 O A:HOH1366 4.8 29.9 1.0 CA A:ILE22 4.8 9.3 1.0 CA A:GLY20 4.8 8.4 1.0 CG1 A:ILE22 4.8 13.4 1.0 C A:GLY20 4.9 9.7 1.0 CE1 A:HIS240 4.9 10.9 1.0

G.Arnal, P.J.Stogios, J.Asohan, T.Skarina, A.Savchenko, H.Brumer. Structural Enzymology Reveals the Molecular Basis of Substrate Regiospecificity and Processivity of An Exemplar Bacterial Glycoside Hydrolase Family 74ENDO-Xyloglucanase. Biochem. J. V. 475 3963 2018.
ISSN: ESSN 1470-8728
PubMed: 30463871
DOI: 10.1042/BCJ20180763