Magnesium in PDB 5dzq: C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form

All present enzymatic activity of C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form:
2.4.2.30;

The structure of C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form, PDB code: 5dzq was solved by D.Dutta, R.Ravulapalli, A.R.Merrill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.073, 76.002, 89.367, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23

The binding sites of Magnesium atom in the C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form (pdb code 5dzq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form, PDB code: 5dzq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:37.9 occ:1.00 OG A:SER180 3.1 35.2 1.0 N A:GLY179 3.4 36.4 1.0 C A:GLY179 3.5 43.6 1.0 CA A:GLY179 3.6 42.7 1.0 N A:SER180 3.6 31.4 1.0 CB A:SER180 3.7 38.2 1.0 O A:GLY179 4.0 36.1 1.0 CB A:ASN177 4.1 32.7 1.0 CA A:SER180 4.2 30.5 1.0 O A:HOH334 4.5 32.9 1.0 C A:LYS178 4.6 39.4 1.0 N A:LYS178 4.7 34.2 1.0 ND2 A:ASN177 5.0 30.3 1.0 CG A:ASN177 5.0 36.8 1.0

Magnesium binding site 2 out of 2 in the C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C3LARVIN Toxin, An Adp-Ribosyltransferase From Paenibacillus Larvae, Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg201 b:34.5 occ:1.00 OG O:SER180 2.6 37.8 1.0 CB O:SER180 3.6 41.3 1.0 N O:GLY179 3.6 33.2 1.0 N O:SER180 3.7 33.6 1.0 CB O:ASN177 3.7 32.1 1.0 C O:GLY179 3.8 42.2 1.0 CA O:GLY179 4.0 39.1 1.0 CA O:SER180 4.2 32.5 1.0 O O:GLY179 4.3 42.2 1.0 ND2 O:ASN177 4.4 34.5 1.0 CG O:ASN177 4.5 32.1 1.0 N O:LYS178 4.5 31.5 1.0 C O:LYS178 4.8 36.0 1.0 C O:ASN177 4.9 35.8 1.0 CA O:ASN177 4.9 29.8 1.0 C O:SER180 5.0 34.6 1.0 O O:SER180 5.0 33.6 1.0

M.R.Lugo, R.Ravulapalli, D.Dutta, A.R.Merrill. Structural Variability of C3LARVIN Toxin. Intrinsic Dynamics of the Alpha / Beta Fold of the C3-Like Group of Mono-Adp-Ribosyltransferase Toxins. J. Biomol. Struct. Dyn. V. 34 2537 2016.
ISSN: ESSN 1538-0254
PubMed: 26610041
DOI: 10.1080/07391102.2015.1123189