Magnesium in PDB 4dth: Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++

The structure of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++, PDB code: 4dth was solved by E.Durand, G.Audoly, E.Derrez, S.Spinelli, M.Ortiz-Lombardia, E.Cascales, D.Raoult, C.Cambillau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.06 / 1.78
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.680, 128.680, 76.820, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 19.2

The binding sites of Magnesium atom in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++ (pdb code 4dth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++, PDB code: 4dth:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:45.0 occ:1.00 OE1 A:GLN162 2.5 41.1 1.0 OE2 A:GLU339 2.6 30.2 1.0 OE1 A:GLU16 2.9 30.3 1.0 O A:HOH1044 2.9 42.2 1.0 CD A:GLU339 3.3 36.0 1.0 O A:HOH717 3.3 40.6 1.0 CD A:GLU16 3.4 36.9 1.0 CD A:GLN162 3.4 43.8 1.0 OE2 A:GLU16 3.4 34.1 1.0 OE1 A:GLU339 3.5 36.5 1.0 O A:HOH823 3.7 49.5 1.0 CG A:GLN162 3.7 28.8 1.0 O4 A:SO4405 3.8 37.1 1.0 NH1 A:ARG341 3.9 22.1 1.0 O A:HOH1068 4.0 55.5 1.0 CB A:GLN162 4.1 19.7 1.0 CG A:GLU339 4.3 23.9 1.0 NE2 A:GLN162 4.5 35.0 1.0 CG A:GLU16 4.6 24.3 1.0 CB A:GLU16 4.7 19.6 1.0 OE2 A:GLU78 4.8 26.9 1.0 O1G A:ATP401 4.8 93.3 0.5 O A:HOH551 4.8 31.6 1.0

Magnesium binding site 2 out of 2 in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:51.1 occ:1.00 OE2 A:GLU16 2.6 34.1 1.0 OE1 A:GLU78 2.9 29.4 1.0 O A:HOH985 3.0 49.9 1.0 O A:HOH993 3.3 52.7 1.0 O A:HOH544 3.5 30.8 1.0 CD A:GLU16 3.6 36.9 1.0 O2B A:ATP401 3.7 86.3 0.5 CG2 A:VAL80 3.7 20.1 1.0 CD A:GLU78 3.8 36.0 1.0 O A:HOH1068 3.8 55.5 1.0 CG A:GLU16 3.9 24.3 1.0 O3A A:ATP401 4.0 79.3 0.6 OE2 A:GLU78 4.1 26.9 1.0 O A:HOH823 4.1 49.5 1.0 PB A:ATP401 4.3 85.6 0.5 CG1 A:VAL80 4.5 20.6 1.0 O3B A:ATP401 4.6 89.3 0.5 C5' A:ATP401 4.7 49.5 1.0 OE1 A:GLU16 4.7 30.3 1.0 O A:HOH1044 4.7 42.2 1.0 O A:HOH1053 4.7 53.3 1.0 CB A:VAL80 4.8 20.5 1.0 O A:HOH998 4.8 64.8 1.0 CB A:GLU16 4.8 19.6 1.0 CG A:GLU78 4.9 25.2 1.0

E.Durand, G.Audoly, E.Derrez, S.Spinelli, M.Ortiz-Lombardia, E.Cascales, D.Raoult, C.Cambillau. Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mg++ J.Biol.Chem. 2012.
ISSN: ESSN 1083-351X