Magnesium in PDB 6gfa: Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed

The structure of Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed, PDB code: 6gfa was solved by D.Gonzalez, G.Gotthard, G.J.Gozzi, R.Seigneuric, F.Neiers, L.Briand, C.Garrido, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.45 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.780, 109.780, 144.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.9

The binding sites of Magnesium atom in the Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed (pdb code 6gfa). 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 Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed, PDB code: 6gfa:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:23.9 occ:1.00 O A:HOH622 3.0 47.0 1.0 N A:ASN366 3.1 27.4 1.0 O A:HOH720 3.2 47.6 1.0 ND2 A:ASN179 3.3 23.8 1.0 CD A:ARG373 3.3 37.7 1.0 CB A:ASN366 3.6 25.1 1.0 CA A:ASN366 3.8 29.1 1.0 CA A:ALA370 3.8 23.0 1.0 CB A:LEU365 4.0 24.2 1.0 O A:ASN366 4.0 24.0 1.0 OD1 A:ASN179 4.0 31.1 1.0 CG A:ASN179 4.1 30.2 1.0 C A:LEU365 4.1 28.2 1.0 CA A:LEU365 4.1 25.0 1.0 NE A:ARG373 4.1 40.6 1.0 CB A:ALA370 4.1 22.5 1.0 N A:ALA370 4.2 22.9 1.0 CD2 A:LEU365 4.4 29.1 1.0 C A:ASN366 4.4 27.8 1.0 CG A:ARG373 4.5 33.1 1.0 C A:GLU369 4.6 26.8 1.0 O A:HOH694 4.6 52.1 1.0 CB A:ARG373 4.7 25.5 1.0 CG A:LEU365 4.8 26.9 1.0 O A:HOH698 4.8 49.0 1.0 O A:HOH681 4.9 53.0 1.0 O A:GLU369 4.9 27.6 1.0 CB A:GLU369 4.9 25.8 1.0 CG A:ASN366 4.9 31.1 1.0

Magnesium binding site 2 out of 2 in the Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Nucleotide Binding Domain of HSP110, Atp and MG2+ Complexed within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:15.0 occ:1.00 O2B A:ATP403 2.3 22.3 1.0 O A:HOH553 2.5 24.5 1.0 O3G A:ATP403 2.5 22.1 1.0 O A:HOH528 2.5 23.2 1.0 O A:HOH539 2.5 24.5 1.0 O A:HOH581 2.6 25.1 1.0 O A:HOH580 2.6 24.2 1.0 PG A:ATP403 3.4 24.0 1.0 PB A:ATP403 3.5 24.9 1.0 O1G A:ATP403 3.6 22.8 1.0 O3B A:ATP403 3.8 25.4 1.0 OD2 A:ASP172 4.2 25.8 1.0 O3A A:ATP403 4.2 23.5 1.0 O2A A:ATP403 4.2 24.6 1.0 O A:HOH565 4.3 28.1 1.0 O A:HOH658 4.3 27.8 1.0 NZ A:LYS67 4.4 24.4 1.0 O A:HOH521 4.5 28.0 1.0 OD2 A:ASP201 4.6 31.6 1.0 O A:HOH596 4.6 23.8 1.0 OD1 A:ASP6 4.6 22.6 1.0 CA A:GLY8 4.6 21.6 1.0 O A:HOH544 4.7 21.5 1.0 O A:HOH697 4.7 27.4 1.0 OD1 A:ASP201 4.7 29.6 1.0 O2G A:ATP403 4.8 28.2 1.0 O1B A:ATP403 4.8 25.0 1.0 PA A:ATP403 4.8 23.4 1.0 CA A:GLY203 4.8 23.8 1.0 CG A:ASP172 4.9 28.1 1.0 OD2 A:ASP6 4.9 25.9 1.0

G.J.Gozzi, D.Gonzalez, C.Boudesco, A.M.M.Dias, G.Gotthard, B.Uyanik, L.Dondaine, G.Marcion, F.Hermetet, C.Denis, L.Hardy, P.Suzanne, R.Douhard, G.Jego, L.Dubrez, O.N.Demidov, F.Neiers, L.Briand, J.Sopkova-De Oliveira Santos, A.S.Voisin-Chiret, C.Garrido. Selecting the First Chemical Molecule Inhibitor of HSP110 For Colorectal Cancer Therapy. Cell Death Differ. 2019.
ISSN: ISSN 1350-9047
PubMed: 31068676
DOI: 10.1038/S41418-019-0343-4