Magnesium in PDB 6nhk: Mortalin Nucleotide Binding Domain in the Adp-Bound State

The structure of Mortalin Nucleotide Binding Domain in the Adp-Bound State, PDB code: 6nhk was solved by R.C.Page, M.A.Moseng, J.C.Nix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.87 / 2.78
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.263, 60.102, 91.699, 90.00, 97.56, 90.00
R / Rfree (%)	25.6 / 29.6

The binding sites of Magnesium atom in the Mortalin Nucleotide Binding Domain in the Adp-Bound State (pdb code 6nhk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mortalin Nucleotide Binding Domain in the Adp-Bound State, PDB code: 6nhk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mortalin Nucleotide Binding Domain in the Adp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mortalin Nucleotide Binding Domain in the Adp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:68.9 occ:1.00 O1 A:PO4502 1.8 59.1 1.0 O1B A:ADP501 2.3 72.7 1.0 P A:PO4502 3.3 48.1 1.0 PB A:ADP501 3.4 65.1 1.0 O3A A:ADP501 3.6 67.3 1.0 O2B A:ADP501 3.6 47.8 1.0 OD2 A:ASP244 3.6 62.9 1.0 OD1 A:ASP244 3.9 65.7 1.0 O4 A:PO4502 3.9 73.1 1.0 O2 A:PO4502 3.9 63.5 1.0 CG A:ASP244 4.2 66.9 1.0 O3 A:PO4502 4.2 54.0 1.0 OD2 A:ASP59 4.3 66.3 1.0 OE1 A:GLU222 4.4 69.4 1.0 OD1 A:ASP59 4.6 71.6 1.0 CG2 A:VAL417 4.6 69.2 1.0 O3B A:ADP501 4.7 60.3 1.0 CD A:GLU222 4.9 63.9 1.0 CG A:ASP59 4.9 64.7 1.0

Magnesium binding site 2 out of 2 in the Mortalin Nucleotide Binding Domain in the Adp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mortalin Nucleotide Binding Domain in the Adp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:85.6 occ:1.00 O1 B:PO4601 2.1 71.8 1.0 O1B B:ADP600 2.4 80.1 1.0 OD2 B:ASP244 2.9 74.3 1.0 O2B B:ADP600 3.1 90.0 1.0 PB B:ADP600 3.1 77.7 1.0 OD1 B:ASP244 3.3 80.5 1.0 O3A B:ADP600 3.4 73.9 1.0 P B:PO4601 3.5 65.5 1.0 CG B:ASP244 3.5 80.5 1.0 O2 B:PO4601 4.1 73.0 1.0 O4 B:PO4601 4.2 75.8 1.0 CG2 B:VAL417 4.4 77.2 1.0 O3 B:PO4601 4.5 59.5 1.0 CA B:GLY387 4.5 73.1 1.0 O1A B:ADP600 4.5 63.5 1.0 O3B B:ADP600 4.5 60.3 1.0 PA B:ADP600 4.6 74.8 1.0 N B:GLY387 4.7 73.9 1.0 CA B:GLY246 4.8 71.6 1.0

M.A.Moseng, J.C.Nix, R.C.Page. Biophysical Consequences of Even-Plus Syndrome Mutations For the Function of Mortalin. J.Phys.Chem.B V. 123 3383 2019.
ISSN: ISSN 1089-5647
PubMed: 30933555
DOI: 10.1021/ACS.JPCB.9B00071