Magnesium in PDB 4b9q: Open Conformation of Atp-Bound HSP70 Homolog Dnak

The structure of Open Conformation of Atp-Bound HSP70 Homolog Dnak, PDB code: 4b9q was solved by J.Kopp, M.P.Mayer, I.Sinning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.72 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	202.331, 77.470, 182.960, 90.00, 101.71, 90.00
R / Rfree (%)	19.6 / 23.9

The binding sites of Magnesium atom in the Open Conformation of Atp-Bound HSP70 Homolog Dnak (pdb code 4b9q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Open Conformation of Atp-Bound HSP70 Homolog Dnak, PDB code: 4b9q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Open Conformation of Atp-Bound HSP70 Homolog Dnak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Open Conformation of Atp-Bound HSP70 Homolog Dnak within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:35.7 occ:1.00 O1B A:ATP700 1.9 26.9 1.0 O A:HOH2084 2.1 33.4 1.0 O A:HOH2079 2.1 27.5 1.0 O2G A:ATP700 2.1 28.1 1.0 O A:HOH2006 2.1 23.6 1.0 O A:HOH2008 2.2 27.5 1.0 PB A:ATP700 3.2 29.9 1.0 PG A:ATP700 3.4 38.5 1.0 O3B A:ATP700 3.6 27.5 1.0 O A:HOH2009 3.8 49.0 1.0 O A:HOH2114 3.9 33.5 1.0 O A:HOH2083 4.0 27.9 1.0 O3A A:ATP700 4.0 29.9 1.0 OD1 A:ASP8 4.0 43.0 1.0 OD2 A:ASP8 4.0 35.5 1.0 O1A A:ATP700 4.1 37.6 1.0 O1G A:ATP700 4.1 39.4 1.0 OE1 A:GLU171 4.2 44.5 1.0 OD1 A:ASP194 4.4 41.4 1.0 O2B A:ATP700 4.4 21.6 1.0 CD A:GLU171 4.4 55.7 1.0 CG A:ASP8 4.5 48.7 1.0 OD2 A:ASP194 4.5 66.2 1.0 O3G A:ATP700 4.6 36.8 1.0 PA A:ATP700 4.6 36.9 1.0 OE2 A:GLU171 4.7 47.2 1.0 CA A:GLY10 4.8 32.5 1.0 CG A:ASP194 4.9 63.0 1.0 NZ A:LYS70 4.9 38.4 1.0 CA A:GLY196 5.0 28.6 1.0

Magnesium binding site 2 out of 4 in the Open Conformation of Atp-Bound HSP70 Homolog Dnak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Open Conformation of Atp-Bound HSP70 Homolog Dnak within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:33.2 occ:1.00 O B:HOH2005 2.0 33.6 1.0 O1B B:ATP700 2.0 29.4 1.0 O B:HOH2078 2.1 33.4 1.0 O B:HOH2082 2.1 49.4 1.0 O B:HOH2004 2.1 30.7 1.0 O2G B:ATP700 2.3 22.6 1.0 PB B:ATP700 3.4 30.7 1.0 PG B:ATP700 3.5 33.8 1.0 O B:HOH2006 3.7 50.8 1.0 O3B B:ATP700 3.8 61.1 1.0 O B:HOH2119 3.9 44.0 1.0 OD2 B:ASP8 3.9 37.0 1.0 OD1 B:ASP8 3.9 45.4 1.0 O1G B:ATP700 4.1 35.1 1.0 OE1 B:GLU171 4.1 49.1 1.0 O3A B:ATP700 4.2 52.5 1.0 CD B:GLU171 4.3 55.0 1.0 O1A B:ATP700 4.3 32.7 1.0 CG B:ASP8 4.4 43.2 1.0 OE2 B:GLU171 4.4 51.0 1.0 OD1 B:ASP194 4.5 49.5 1.0 O B:HOH2081 4.5 34.4 1.0 OD2 B:ASP194 4.6 65.1 1.0 O2B B:ATP700 4.6 36.1 1.0 CA B:GLY10 4.7 39.3 1.0 O3G B:ATP700 4.7 47.7 1.0 PA B:ATP700 4.8 37.1 1.0 NZ B:LYS70 4.8 43.2 1.0 CG B:ASP194 5.0 66.4 1.0 CG B:GLU171 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in the Open Conformation of Atp-Bound HSP70 Homolog Dnak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Open Conformation of Atp-Bound HSP70 Homolog Dnak within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg701 b:33.8 occ:1.00 O2G C:ATP700 1.9 26.7 1.0 O C:HOH2072 2.0 30.9 1.0 O C:HOH2075 2.1 33.6 1.0 O1B C:ATP700 2.1 25.6 1.0 O C:HOH2002 2.1 30.3 1.0 O C:HOH2003 2.2 29.6 1.0 PG C:ATP700 3.3 40.6 1.0 PB C:ATP700 3.4 34.5 1.0 O3B C:ATP700 3.7 31.7 1.0 OE1 C:GLU171 3.9 49.3 1.0 OD1 C:ASP194 4.1 52.6 1.0 O1G C:ATP700 4.1 48.8 1.0 O C:HOH2004 4.2 48.0 1.0 O3A C:ATP700 4.2 45.2 1.0 CD C:GLU171 4.2 53.2 1.0 OD2 C:ASP194 4.2 67.5 1.0 O1A C:ATP700 4.2 32.1 1.0 OD1 C:ASP8 4.3 46.6 1.0 O C:HOH2094 4.3 51.0 1.0 OD2 C:ASP8 4.3 43.6 1.0 O3G C:ATP700 4.4 38.1 1.0 OE2 C:GLU171 4.5 51.7 1.0 CG C:ASP194 4.6 64.3 1.0 O C:HOH2071 4.6 54.5 1.0 O2B C:ATP700 4.6 22.3 1.0 CG C:ASP8 4.7 41.9 1.0 CA C:GLY196 4.9 33.5 1.0 PA C:ATP700 4.9 42.8 1.0 NZ C:LYS70 4.9 36.3 1.0 CG C:GLU171 5.0 43.9 1.0

Magnesium binding site 4 out of 4 in the Open Conformation of Atp-Bound HSP70 Homolog Dnak


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Open Conformation of Atp-Bound HSP70 Homolog Dnak within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg701 b:43.8 occ:1.00 O D:HOH2003 2.0 45.0 1.0 O D:HOH2049 2.0 43.9 1.0 O D:HOH2002 2.1 47.5 1.0 O D:HOH2053 2.1 67.2 1.0 O2G D:ATP700 2.2 39.7 1.0 O1B D:ATP700 2.2 30.9 1.0 PB D:ATP700 3.6 37.7 1.0 PG D:ATP700 3.6 49.9 1.0 O D:HOH2052 3.8 49.7 1.0 O3B D:ATP700 4.0 56.0 1.0 OD1 D:ASP194 4.1 59.9 1.0 OD2 D:ASP8 4.1 55.7 1.0 OE1 D:GLU171 4.2 53.9 1.0 O D:HOH2065 4.2 53.5 1.0 O1A D:ATP700 4.2 42.4 1.0 OD2 D:ASP194 4.2 68.8 1.0 O3A D:ATP700 4.2 59.2 1.0 OD1 D:ASP8 4.3 47.3 1.0 CD D:GLU171 4.4 58.4 1.0 O1G D:ATP700 4.5 42.7 1.0 CG D:ASP194 4.6 67.8 1.0 CG D:ASP8 4.6 50.5 1.0 OE2 D:GLU171 4.7 59.5 1.0 O3G D:ATP700 4.7 59.6 1.0 O2B D:ATP700 4.8 44.0 1.0 PA D:ATP700 4.8 48.2 1.0 CG2 D:VAL371 4.9 44.0 1.0 CA D:GLY196 5.0 37.0 1.0

R.Kityk, J.Kopp, I.Sinning, M.P.Mayer. Structure and Dynamics of the Atp-Bound Open Conformation of HSP70 Chaperones Mol.Cell V. 48 863 2012.
ISSN: ISSN 1097-2765
PubMed: 23123194
DOI: 10.1016/J.MOLCEL.2012.09.023