Magnesium in PDB 6xrk: GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate

The structure of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate, PDB code: 6xrk was solved by C.A.Bingman, R.W.Smith, E.M.Glasgow, B.G.Fox, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.64 / 1.42
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.320, 84.990, 121.320, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 16.7

The structure of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate (pdb code 6xrk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate, PDB code: 6xrk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.0 occ:1.00 O A:HOH676 2.0 20.3 1.0 O A:HOH651 2.0 22.3 1.0 O A:HOH777 2.1 22.6 1.0 O A:HOH533 2.1 18.6 1.0 O A:HOH874 2.1 22.0 1.0 O A:HOH570 2.2 19.0 1.0 HA A:ASN12 3.5 24.1 1.0 HA A:ALA311 3.5 22.2 1.0 O A:HOH665 3.8 17.4 1.0 O A:PHE316 4.0 18.2 1.0 O A:SER310 4.0 22.4 1.0 O A:ALA311 4.0 26.8 1.0 OD1 A:ASN12 4.1 21.0 1.0 O A:HOH949 4.2 24.1 1.0 O A:HOH926 4.2 29.7 1.0 O A:HOH525 4.3 25.5 1.0 CA A:ASN12 4.3 20.0 1.0 HB3 A:ASN12 4.3 24.3 1.0 CA A:ALA311 4.4 18.5 1.0 O A:ASN12 4.4 21.8 1.0 O A:TYR313 4.5 20.5 1.0 O A:HOH880 4.5 39.4 1.0 O A:HOH998 4.5 39.1 1.0 CG A:ASN12 4.5 22.6 1.0 C A:ALA311 4.6 23.4 1.0 H A:PHE316 4.6 21.8 1.0 H A:GLY315 4.6 23.3 1.0 HA A:ASP314 4.6 26.1 1.0 CB A:ASN12 4.6 20.3 1.0 C A:ASN12 4.9 21.4 1.0

Magnesium binding site 2 out of 4 in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:18.1 occ:1.00 O B:HOH866 2.0 20.5 1.0 O B:HOH652 2.1 18.3 1.0 O B:HOH777 2.1 19.9 1.0 O B:HOH663 2.1 20.5 1.0 O B:HOH551 2.1 17.4 1.0 O B:HOH597 2.1 17.9 1.0 HA B:ALA311 3.5 23.2 1.0 HA B:ASN12 3.5 18.9 1.0 O B:HOH674 3.8 16.1 1.0 O B:ALA311 4.0 23.5 1.0 O B:SER310 4.0 18.1 1.0 O B:PHE316 4.0 16.7 1.0 OD1 B:ASN12 4.1 17.5 1.0 O B:HOH917 4.1 28.4 1.0 O B:HOH945 4.2 21.8 1.0 O B:HOH637 4.3 21.8 1.0 HB3 B:ASN12 4.4 21.0 1.0 CA B:ALA311 4.4 19.3 1.0 CA B:ASN12 4.4 15.7 1.0 O B:TYR313 4.5 18.8 1.0 O B:ASN12 4.5 19.0 1.0 C B:ALA311 4.5 21.0 1.0 CG B:ASN12 4.5 18.8 1.0 H B:GLY315 4.6 20.3 1.0 H B:PHE316 4.7 21.0 1.0 CB B:ASN12 4.7 17.5 1.0 HA B:ASP314 4.7 25.1 1.0 O B:HOH860 4.8 46.7 1.0 C B:ASN12 5.0 17.1 1.0 C B:SER310 5.0 19.9 1.0

Magnesium binding site 3 out of 4 in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:67.2 occ:1.00 O B:HOH758 2.3 48.0 1.0 O B:HOH819 2.3 40.6 1.0 O B:HOH995 2.5 52.3 1.0 O B:HOH658 4.2 30.2 1.0 HA B:TRP236 4.5 27.2 1.0 H B:THR237 4.6 27.1 1.0

Magnesium binding site 4 out of 4 in the GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of GH5-4 Broad Specificity Endoglucanase From An Uncultured Bovine Rumen Ciliate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:44.2 occ:1.00 O B:HOH536 2.2 44.0 1.0 O B:HOH606 2.2 45.9 1.0 O B:HOH570 2.2 31.4 1.0 OD1 B:ASN234 3.8 44.1 1.0 OE2 B:GLU292 3.9 24.6 1.0 HD3 B:LYS233 4.0 33.4 0.6 O B:HOH531 4.0 41.4 1.0 O B:HOH593 4.1 24.2 1.0 HD2 B:LYS233 4.2 42.8 0.4 HG B:SER231 4.5 24.8 1.0 HB2 B:LYS233 4.5 37.9 0.4 HB3 B:LYS233 4.5 36.7 0.6 O A:HOH710 4.8 47.7 1.0 CD B:LYS233 5.0 27.9 0.6

E.M.Glasgow, E.I.Kemna, C.A.Bingman, N.L.Ing, K.Deng, C.M.Bianchetti, T.E.Takasuka, T.R.Northen, B.G.Fox. A Structural and Kinetic Survey of GH5_4 Endoglucanases Reveals Determinants of Broad Substrate Specificity and Opportunities For Biomass Hydrolysis. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33067356
DOI: 10.1074/JBC.RA120.015328