Magnesium in PDB 3dnt: Structures of Mdt Proteins

The structure of Structures of Mdt Proteins, PDB code: 3dnt was solved by M.A.Schumacher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.58 / 1.66
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.540, 84.090, 69.250, 90.00, 91.56, 90.00
R / Rfree (%)	18.4 / 21.7

The binding sites of Magnesium atom in the Structures of Mdt Proteins (pdb code 3dnt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structures of Mdt Proteins, PDB code: 3dnt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structures of Mdt Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Mdt Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg441 b:30.6 occ:1.00 OD1 A:ASN314 2.2 16.3 1.0 O A:HOH860 2.2 20.0 1.0 OD2 A:ASP332 2.3 25.7 1.0 O3B A:ATP500 2.3 40.4 1.0 O2A A:ATP500 2.3 20.7 1.0 O1G A:ATP500 2.6 43.3 1.0 PG A:ATP500 3.0 49.8 1.0 CG A:ASN314 3.1 15.2 1.0 CG A:ASP332 3.2 25.0 1.0 ND2 A:ASN314 3.4 18.9 1.0 O3A A:ATP500 3.4 32.9 1.0 PA A:ATP500 3.4 26.3 1.0 PB A:ATP500 3.5 35.1 1.0 CB A:ASP332 3.6 18.4 1.0 O2B A:ATP500 3.7 39.9 1.0 O2G A:ATP500 3.9 44.7 1.0 MG A:MG442 4.0 42.0 1.0 CE1 A:HIS311 4.1 12.9 1.0 O A:HOH932 4.1 21.8 1.0 O3G A:ATP500 4.2 46.8 1.0 OD1 A:ASP332 4.2 29.4 1.0 NE2 A:HIS311 4.2 15.5 1.0 O3' A:ATP500 4.3 30.3 1.0 O1A A:ATP500 4.4 18.5 1.0 O5' A:ATP500 4.5 27.3 1.0 CB A:ASN314 4.5 12.2 1.0 O1B A:ATP500 4.6 38.6 1.0 C3' A:ATP500 4.7 28.3 1.0 C5' A:ATP500 4.7 26.7 1.0 CA A:GLY153 4.8 26.6 1.0 CA A:ASN314 4.9 11.3 1.0 O A:LYS313 4.9 12.5 1.0 CE1 A:TYR331 5.0 15.5 1.0

Magnesium binding site 2 out of 4 in the Structures of Mdt Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Mdt Proteins within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg442 b:42.0 occ:1.00 OD2 A:ASP332 2.5 25.7 1.0 OD1 A:ASP332 2.5 29.4 1.0 O2B A:ATP500 2.8 39.9 1.0 O3G A:ATP500 2.8 46.8 1.0 CG A:ASP332 2.8 25.0 1.0 O1G A:ATP500 3.2 43.3 1.0 PG A:ATP500 3.4 49.8 1.0 O A:HOH1000 3.4 44.6 1.0 O3B A:ATP500 3.6 40.4 1.0 PB A:ATP500 3.6 35.1 1.0 OE1 A:GLN309 3.6 33.8 1.0 MG A:MG441 4.0 30.6 1.0 CD A:GLN309 4.1 31.1 1.0 CD1 A:ILE334 4.1 37.3 1.0 NE2 A:GLN309 4.3 33.7 1.0 CB A:ASP332 4.3 18.4 1.0 ND2 A:ASN314 4.5 18.9 1.0 OE1 A:GLN155 4.6 45.7 1.0 O A:ASP332 4.6 20.4 1.0 O3A A:ATP500 4.7 32.9 1.0 CB A:GLN309 4.8 21.7 1.0 O2G A:ATP500 4.8 44.7 1.0 NZ A:LYS181 4.8 28.5 1.0 CG1 A:ILE334 4.8 31.9 1.0 O1B A:ATP500 4.9 38.6 1.0

Magnesium binding site 3 out of 4 in the Structures of Mdt Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structures of Mdt Proteins within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg441 b:18.0 occ:1.00 O B:HOH1058 2.1 17.8 1.0 OD2 B:ASP332 2.2 13.4 1.0 O B:HOH1165 2.2 19.2 1.0 OD1 B:ASP332 2.3 13.5 1.0 O2B B:ATP501 2.4 29.7 1.0 O3G B:ATP501 2.5 47.2 1.0 CG B:ASP332 2.5 14.6 1.0 PG B:ATP501 3.1 47.2 1.0 PB B:ATP501 3.1 21.9 1.0 O3B B:ATP501 3.1 29.3 1.0 O1G B:ATP501 3.2 36.7 1.0 MG B:MG442 3.7 15.7 1.0 O B:HOH1011 4.0 27.3 1.0 CB B:ASP332 4.0 10.9 1.0 NZ B:LYS181 4.1 16.2 1.0 O B:HOH868 4.2 20.3 1.0 O3A B:ATP501 4.2 18.4 1.0 OE1 B:GLN155 4.3 27.2 1.0 OE1 B:GLN309 4.3 20.4 1.0 O1B B:ATP501 4.5 23.6 1.0 O2G B:ATP501 4.5 40.2 1.0 CD1 B:ILE334 4.5 28.5 1.0 ND2 B:ASN314 4.6 16.0 1.0 O2A B:ATP501 4.7 11.0 1.0 PA B:ATP501 4.8 14.6 1.0 CA B:ASP332 4.9 11.6 1.0 O B:ASP332 5.0 13.9 1.0

Magnesium binding site 4 out of 4 in the Structures of Mdt Proteins


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structures of Mdt Proteins within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg442 b:15.7 occ:1.00 O B:HOH835 2.1 13.4 1.0 OD1 B:ASN314 2.1 13.3 1.0 OD2 B:ASP332 2.1 13.4 1.0 O2A B:ATP501 2.2 11.0 1.0 O3B B:ATP501 2.3 29.3 1.0 O1G B:ATP501 2.7 36.7 1.0 PG B:ATP501 3.0 47.2 1.0 CG B:ASN314 3.1 13.0 1.0 CG B:ASP332 3.1 14.6 1.0 PA B:ATP501 3.3 14.6 1.0 ND2 B:ASN314 3.4 16.0 1.0 O3A B:ATP501 3.4 18.4 1.0 PB B:ATP501 3.5 21.9 1.0 CB B:ASP332 3.6 10.9 1.0 MG B:MG441 3.7 18.0 1.0 O2B B:ATP501 3.8 29.7 1.0 O2G B:ATP501 3.9 40.2 1.0 O B:HOH842 4.0 15.2 1.0 CE1 B:HIS311 4.1 12.2 1.0 NE2 B:HIS311 4.1 12.6 1.0 O3G B:ATP501 4.2 47.2 1.0 OD1 B:ASP332 4.2 13.5 1.0 O3' B:ATP501 4.2 15.4 1.0 O1A B:ATP501 4.3 13.9 1.0 O5' B:ATP501 4.5 13.8 1.0 CB B:ASN314 4.5 8.4 1.0 O1B B:ATP501 4.6 23.6 1.0 C5' B:ATP501 4.7 14.7 1.0 C3' B:ATP501 4.7 12.6 1.0 CA B:ASN314 4.8 9.1 1.0 CE1 B:TYR331 4.8 12.4 1.0 O B:HOH1165 4.9 19.2 1.0 CA B:GLY153 4.9 15.3 1.0 O B:LYS313 5.0 12.6 1.0

M.A.Schumacher, K.M.Piro, W.Xu, S.Hansen, K.Lewis, R.G.Brennan. Molecular Mechanisms of Hipa-Mediated Multidrug Tolerance and Its Neutralization By Hipb. Science V. 323 396 2009.
ISSN: ISSN 0036-8075
PubMed: 19150849
DOI: 10.1126/SCIENCE.1163806