Magnesium in PDB 4dtf: Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Amp-Pnp and Mg++

The structure of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Amp-Pnp and Mg++, PDB code: 4dtf 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)	45.39 / 2.12
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.390, 128.390, 76.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 19.9

The binding sites of Magnesium atom in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Amp-Pnp and Mg++ (pdb code 4dtf). 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 Amp-Pnp and Mg++, PDB code: 4dtf:
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 Amp-Pnp 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 Amp-Pnp and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:48.8 occ:1.00 OE1 A:GLN162 2.5 43.4 1.0 OE2 A:GLU339 2.6 39.3 1.0 O A:HOH790 2.8 37.9 1.0 OE1 A:GLU16 3.0 29.7 1.0 CD A:GLU339 3.2 39.0 1.0 OE1 A:GLU339 3.4 37.6 1.0 OE2 A:GLU16 3.4 32.7 1.0 CD A:GLN162 3.4 44.5 1.0 CD A:GLU16 3.5 36.4 1.0 O A:HOH813 3.6 43.9 1.0 O A:HOH867 3.7 51.2 1.0 O4 A:SO4405 3.8 37.5 1.0 NH1 A:ARG341 3.8 15.2 1.0 CG A:GLN162 3.9 31.3 1.0 O A:HOH1004 3.9 47.3 1.0 O A:HOH788 4.1 29.7 1.0 CB A:GLN162 4.2 16.9 1.0 CG A:GLU339 4.3 24.8 1.0 NE2 A:GLN162 4.6 34.5 1.0 CG A:GLU16 4.7 26.0 1.0 OE2 A:GLU78 4.7 24.0 1.0 O A:HOH754 4.8 23.2 1.0 CB A:GLU16 4.9 17.3 1.0

Magnesium binding site 2 out of 2 in the Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Amp-Pnp 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 Amp-Pnp and Mg++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:59.5 occ:1.00 O2B A:ANP401 2.2 91.3 1.0 OE2 A:GLU16 2.7 32.7 1.0 N3B A:ANP401 2.9 94.6 1.0 PB A:ANP401 3.0 90.4 1.0 OE1 A:GLU78 3.1 21.2 1.0 O1G A:ANP401 3.2 97.4 1.0 O A:HOH623 3.5 24.6 1.0 PG A:ANP401 3.6 97.8 1.0 CG2 A:VAL80 3.7 17.6 1.0 O3A A:ANP401 3.8 81.4 1.0 CD A:GLU16 3.8 36.4 1.0 CD A:GLU78 3.9 30.3 1.0 O2A A:ANP401 4.0 70.4 1.0 O A:HOH1004 4.1 47.3 1.0 O5' A:ANP401 4.1 58.3 1.0 CG A:GLU16 4.1 26.0 1.0 O A:HOH867 4.1 51.2 1.0 PA A:ANP401 4.2 70.7 1.0 OE2 A:GLU78 4.2 24.0 1.0 O A:HOH925 4.3 54.8 1.0 O1B A:ANP401 4.3 90.6 1.0 O3G A:ANP401 4.3 98.0 1.0 O A:HOH905 4.4 55.1 1.0 CG1 A:VAL80 4.4 18.1 1.0 CB A:VAL80 4.7 18.1 1.0 O A:HOH790 4.7 37.9 1.0 OE1 A:GLU16 4.9 29.7 1.0 O2G A:ANP401 4.9 99.7 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 Amp-Pnp and Mg++ J.Biol.Chem. 2012.
ISSN: ESSN 1083-351X