Magnesium in PDB 8c10: Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont

The structure of Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont, PDB code: 8c10 was solved by I.Leiros, G.Vaaje-Kolstad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.83 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.041, 68.426, 87.188, 90, 90, 90
R / Rfree (%)	11.2 / 13.3

The structure of Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont (pdb code 8c10). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont, PDB code: 8c10:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:7.3 occ:1.00 OD1 A:ASP182 2.0 8.0 1.0 OD1 A:ASP184 2.1 7.9 1.0 ND2 A:ASN185 2.1 5.1 1.0 O A:GLY145 2.1 8.9 1.0 O A:HOH573 2.1 9.0 1.0 O A:HOH697 2.1 9.8 1.0 CG A:ASP182 3.0 6.5 1.0 CG A:ASP184 3.1 8.7 1.0 CG A:ASN185 3.2 6.0 1.0 C A:GLY145 3.2 7.5 1.0 OD2 A:ASP182 3.5 6.6 1.0 OD2 A:ASP184 3.5 10.7 1.0 N A:ASN185 3.9 6.3 1.0 OD1 A:ASN185 4.0 8.9 1.0 O A:HOH675 4.1 9.4 1.0 CA A:GLY145 4.1 7.8 1.0 CB A:ASN185 4.2 6.0 1.0 N A:ASN146 4.2 8.4 1.0 CB A:ASP182 4.3 7.2 1.0 CA A:ASN146 4.3 9.2 1.0 O A:HOH749 4.4 31.9 1.0 O A:HOH593 4.4 13.2 1.0 N A:ASP184 4.4 7.3 1.0 CB A:ASP184 4.4 8.3 1.0 OD1 A:ASN146 4.5 23.2 1.0 CA A:ASP182 4.5 7.3 1.0 CA A:ASN185 4.6 5.7 1.0 O A:HOH589 4.6 25.7 1.0 CA A:ASP184 4.7 7.6 1.0 C A:ASP182 4.7 7.3 1.0 C A:ASP184 4.7 6.7 1.0 CD A:PRO183 4.8 9.4 1.0 N A:PRO183 4.8 8.0 1.0 C A:ASN146 5.0 9.5 1.0

Magnesium binding site 2 out of 2 in the Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Biochemical and Structural Characterisation of An Alkaline Family GH5 Cellulase From A Shipworm Symbiont within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.6 occ:1.00 O A:HOH585 1.9 18.8 1.0 O A:HOH716 2.0 18.5 1.0 O A:HOH754 2.0 34.3 1.0 O A:HOH805 2.0 26.7 1.0 O A:GLY221 2.1 11.5 1.0 O A:HOH740 2.2 22.4 1.0 C A:GLY221 3.3 9.4 1.0 O A:HOH770 3.5 29.6 1.0 CA A:GLY221 3.9 9.4 1.0 OD1 A:ASP250 4.2 13.7 1.0 N A:THR222 4.3 8.9 1.0 NE2 A:GLN224 4.5 12.9 1.0 CA A:THR222 4.7 9.2 1.0

M.Junghare, T.Manavalan, L.Fredriksen, I.Leiros, B.Altermark, V.G.H.Eijsink, G.Vaaje-Kolstad. Biochemical and Structural Characterisation of A Family GH5 Cellulase From Endosymbiont of Shipworm P. Megotara. Biotechnol Biofuels Bioprod V. 16 61 2023.
ISSN: ISSN 2731-3654
PubMed: 37016457
DOI: 10.1186/S13068-023-02307-1