Magnesium in PDB 6yq4: Crystal Structure of Fusobacterium Nucleatum Tannase

The structure of Crystal Structure of Fusobacterium Nucleatum Tannase, PDB code: 6yq4 was solved by J.M.Mancheno, J.Anguita, H.Rodriguez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.79 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.84, 91.067, 124.068, 90, 101.7, 90
R / Rfree (%)	17.1 / 25.1

The binding sites of Magnesium atom in the Crystal Structure of Fusobacterium Nucleatum Tannase (pdb code 6yq4). 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 Fusobacterium Nucleatum Tannase, PDB code: 6yq4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Fusobacterium Nucleatum Tannase


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 Fusobacterium Nucleatum Tannase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:41.1 occ:1.00 O A:GLY155 2.1 53.5 1.0 O A:MET153 2.3 49.7 1.0 OD2 A:ASP150 2.4 59.7 1.0 O A:ASP150 2.5 42.9 1.0 O A:HOH676 2.7 31.0 1.0 O A:HOH759 2.8 37.2 1.0 C A:GLY155 3.1 42.6 1.0 O A:HOH748 3.2 29.8 1.0 C A:MET153 3.5 49.0 1.0 C A:ASP150 3.5 43.7 1.0 CG A:ASP150 3.6 58.4 1.0 N A:GLY155 3.6 46.9 1.0 C A:PRO154 3.7 43.0 1.0 O A:PRO154 3.9 36.5 1.0 CA A:GLY155 3.9 47.2 1.0 CA A:ASP150 3.9 46.7 1.0 N A:ASP156 4.0 44.7 1.0 CA A:PRO154 4.2 46.5 1.0 CA A:ASP156 4.3 43.1 1.0 N A:PRO154 4.3 48.1 1.0 CB A:ASP150 4.4 53.4 1.0 OD1 A:ASP150 4.4 57.3 1.0 CA A:MET153 4.5 48.7 1.0 O A:HOH680 4.5 28.4 1.0 N A:MET153 4.6 47.0 1.0 N A:GLU151 4.7 40.2 1.0 N A:ALA157 4.8 39.9 1.0 CB A:MET153 4.8 43.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Fusobacterium Nucleatum Tannase


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 Fusobacterium Nucleatum Tannase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:32.0 occ:1.00 OD2 B:ASP150 2.2 64.9 1.0 O B:GLY155 2.2 57.4 1.0 O B:MET153 2.4 46.0 1.0 O B:ASP150 2.5 43.0 1.0 O B:HOH680 2.7 43.7 1.0 O B:HOH685 2.9 44.2 1.0 C B:GLY155 3.3 49.4 1.0 CG B:ASP150 3.3 60.5 1.0 C B:ASP150 3.4 42.5 1.0 C B:MET153 3.6 47.2 1.0 CA B:ASP150 3.7 42.3 1.0 C B:PRO154 4.0 54.4 1.0 N B:ASP156 4.1 40.8 1.0 N B:GLY155 4.1 58.2 1.0 O B:PRO154 4.1 48.0 1.0 OD1 B:ASP150 4.1 61.8 1.0 CB B:ASP150 4.1 39.2 1.0 CA B:ASP156 4.2 41.5 1.0 CA B:GLY155 4.2 51.4 1.0 CA B:MET153 4.5 45.3 1.0 N B:ALA157 4.5 38.6 1.0 CA B:PRO154 4.5 50.4 1.0 N B:MET153 4.5 44.7 1.0 N B:PRO154 4.5 50.1 1.0 CB B:MET153 4.6 45.5 1.0 N B:GLU151 4.7 44.3 1.0 O B:HOH612 4.7 36.9 1.0 C B:ASP156 4.8 35.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Fusobacterium Nucleatum Tannase


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 Fusobacterium Nucleatum Tannase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:48.3 occ:1.00 O C:MET153 2.4 53.4 1.0 O C:GLY155 2.4 56.9 1.0 O C:ASP150 2.5 57.6 1.0 OD2 C:ASP150 2.6 45.1 1.0 CA C:ASP150 3.1 43.4 1.0 C C:ASP150 3.2 52.4 1.0 CG C:ASP150 3.4 44.4 1.0 C C:GLY155 3.5 48.7 1.0 C C:MET153 3.6 51.9 1.0 CB C:ASP150 3.9 41.0 1.0 C C:PRO154 4.0 56.7 1.0 N C:GLY155 4.0 59.2 1.0 O C:PRO154 4.1 56.1 1.0 O C:HOH646 4.2 36.3 1.0 CA C:GLY155 4.3 51.3 1.0 O C:ASN149 4.3 58.8 1.0 N C:ASP150 4.3 46.2 1.0 N C:MET153 4.4 51.0 1.0 N C:ASP156 4.4 45.8 1.0 OD1 C:ASP150 4.4 46.2 1.0 CA C:PRO154 4.5 51.2 1.0 N C:GLU151 4.5 55.2 1.0 CA C:MET153 4.5 52.3 1.0 N C:PRO154 4.5 51.0 1.0 CA C:ASP156 4.7 47.8 1.0 C C:ASN149 4.8 49.4 1.0 N C:ALA157 4.8 34.5 1.0 CB C:MET153 4.8 52.5 1.0 O C:SER68 4.9 49.4 1.0

J.M.Mancheno, E.Atondo, J.Tomas-Cortazar, J.Luis Lavin, L.Plaza-Vinuesa, I.Martin-Ruiz, D.Barriales, A.Palacios, C.Daniel Navo, L.Sampedro, A.Pena-Cearra, M.Angel Pascual-Itoiz, J.Castelo, A.Carreras-Gonzalez, D.Castellana, A.Pellon, S.Delgado, P.Ruas-Madiedo, B.De Las Rivas, L.Abecia, R.Munoz, G.Jimenez-Oses, J.Anguita, H.Rodriguez. A Structurally Unique Fusobacterium Nucleatum Tannase Provides Detoxicant Activity Against Gallotannins and Pathogen Resistance. Microb Biotechnol 2020.
ISSN: ISSN 1751-7915
PubMed: 33336898
DOI: 10.1111/1751-7915.13732