Magnesium in PDB 8w1m: T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp

The structure of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp, PDB code: 8w1m was solved by D.J.Miller, C.Kalodimos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.10 / 2.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	90.761, 179.939, 66.587, 90, 90, 90
R / Rfree (%)	22.5 / 25.9

The structure of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp (pdb code 8w1m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp, PDB code: 8w1m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:60.8 occ:1.00 O A:HOH509 2.2 58.2 1.0 O2A A:ADP401 2.5 63.0 1.0 O A:HOH510 2.6 53.1 1.0 O1B A:ADP401 2.6 69.5 1.0 O A:HOH501 2.8 55.1 1.0 OD2 A:ASP8 3.3 61.1 1.0 PA A:ADP401 3.6 75.6 1.0 PB A:ADP401 3.8 71.2 1.0 O3A A:ADP401 3.9 71.8 1.0 O1A A:ADP401 4.1 72.1 1.0 O2B A:ADP401 4.3 64.7 1.0 CG A:ASP8 4.3 59.6 1.0 CA A:GLY335 4.5 60.6 1.0 OD1 A:ASP8 4.5 58.6 1.0 O A:HOH514 4.6 48.7 1.0 OD1 A:ASP190 4.8 63.1 1.0 O5' A:ADP401 4.9 67.6 1.0 N A:GLY335 4.9 54.6 1.0

Magnesium binding site 2 out of 2 in the T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:62.9 occ:1.00 O1B B:ADP401 2.1 71.4 1.0 O B:HOH506 2.5 47.7 1.0 O1A B:ADP401 3.0 70.4 1.0 OD2 B:ASP8 3.5 55.8 1.0 PB B:ADP401 3.6 63.0 1.0 O3A B:ADP401 4.1 53.2 1.0 PA B:ADP401 4.1 63.9 1.0 O2B B:ADP401 4.4 54.0 1.0 CG B:ASP8 4.4 53.6 1.0 CA B:GLY335 4.5 59.0 1.0 O3B B:ADP401 4.5 49.5 1.0 OD1 B:ASP190 4.5 63.6 1.0 OD1 B:ASP8 4.6 55.6 1.0 OD2 B:ASP190 4.8 65.5 1.0 O2A B:ADP401 4.9 60.6 1.0 CG1 B:VAL334 4.9 53.0 1.0 N B:GLY335 5.0 47.1 1.0

D.J.Miller, C.Kalodimos. T.Thermophilus Dnak Nucleotide Binding Domain in Complex with Adp To Be Published.