Manganese in PDB 4dtl: Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mn++

The structure of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mn++, PDB code: 4dtl 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)	45.88 / 2.39
Space group	P 43 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.480, 128.480, 76.190, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 20.9

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mn++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:33.5 occ:0.60 OE1 A:GLU16 2.3 35.5 1.0 O2G A:ATP401 2.4 55.2 0.5 OE2 A:GLU16 2.5 47.7 1.0 O3B A:ATP401 2.6 37.4 0.5 OE1 A:GLN162 2.6 43.2 1.0 CD A:GLU16 2.7 45.7 1.0 OE2 A:GLU339 2.9 43.9 1.0 CD A:GLU339 3.1 41.5 1.0 O3B A:ATP401 3.1 58.9 0.5 PG A:ATP401 3.2 56.2 0.5 OE1 A:GLU339 3.2 39.0 1.0 O1G A:ATP401 3.6 55.8 0.5 CD A:GLN162 3.7 55.1 1.0 PB A:ATP401 3.9 36.7 0.5 MN A:MN404 4.0 54.4 1.0 CG A:GLU339 4.0 25.7 1.0 O A:HOH601 4.1 22.7 1.0 PB A:ATP401 4.1 60.9 0.5 CG A:GLU16 4.2 30.8 1.0 CG A:GLN162 4.3 40.5 1.0 O A:HOH554 4.3 15.7 1.0 O2B A:ATP401 4.3 62.1 0.5 O2B A:ATP401 4.3 34.5 0.5 CB A:GLN162 4.3 23.5 1.0 O4 A:SO4405 4.4 74.3 1.0 NH1 A:ARG341 4.5 19.5 1.0 O3A A:ATP401 4.5 34.5 0.5 O3G A:ATP401 4.5 55.9 0.5 O3A A:ATP401 4.6 57.7 0.5 NE2 A:GLN162 4.7 59.0 1.0 CB A:GLU16 4.7 24.0 1.0 O A:HOH513 4.8 20.1 1.0 O1B A:ATP401 5.0 39.1 0.5

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Vgrg Vibrio Cholerae Toxin Acd Domain in Complex with Atp and Mn++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:54.4 occ:1.00 O2B A:ATP401 1.6 62.1 0.5 O1G A:ATP401 1.9 55.8 0.5 OE2 A:GLU16 2.2 47.7 1.0 OE1 A:GLU78 2.3 37.7 1.0 O2A A:ATP401 2.7 33.6 0.5 PB A:ATP401 2.9 60.9 0.5 O3B A:ATP401 3.0 37.4 0.5 CD A:GLU78 3.1 41.9 1.0 PG A:ATP401 3.1 56.2 0.5 OE2 A:GLU78 3.2 39.6 1.0 O3B A:ATP401 3.2 58.9 0.5 CD A:GLU16 3.4 45.7 1.0 O2A A:ATP401 3.5 53.1 0.5 O A:HOH559 3.6 44.2 1.0 O1B A:ATP401 3.7 39.1 0.5 PB A:ATP401 3.8 36.7 0.5 O1B A:ATP401 3.9 61.8 0.5 PA A:ATP401 3.9 36.7 0.5 O3A A:ATP401 3.9 57.7 0.5 O2G A:ATP401 4.0 55.2 0.5 CG A:GLU16 4.0 30.8 1.0 MN A:MN403 4.0 33.5 0.6 O3A A:ATP401 4.0 34.5 0.5 O3G A:ATP401 4.2 55.9 0.5 PA A:ATP401 4.2 53.7 0.5 OE1 A:GLU16 4.4 35.5 1.0 CG2 A:VAL80 4.5 20.2 1.0 CG A:GLU78 4.5 30.3 1.0 OD1 A:ASP51 4.5 38.0 1.0 O5' A:ATP401 4.6 36.1 0.5 CB A:GLU16 4.6 24.0 1.0 O5' A:ATP401 4.7 47.1 0.5 O A:HOH811 4.8 45.0 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 Mn++ J.Biol.Chem. 2012.
ISSN: ESSN 1083-351X