Magnesium in PDB 7kzi: Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide

The structure of Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide, PDB code: 7kzi was solved by W.Wang, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 2.82
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.518, 121.518, 457.878, 90, 90, 120
R / Rfree (%)	25.5 / 27.3

The structure of Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide (pdb code 7kzi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide, PDB code: 7kzi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg704 b:60.7 occ:1.00 O A:HOH801 1.9 38.4 1.0 O A:HOH804 2.0 66.8 1.0 O1G A:ATP701 2.0 53.7 1.0 O1B A:ATP701 2.0 56.6 1.0 O A:HOH803 2.0 49.7 1.0 O A:HOH802 2.1 44.7 1.0 PG A:ATP701 3.1 51.6 1.0 PB A:ATP701 3.2 51.8 1.0 O3B A:ATP701 3.5 57.3 1.0 O3G A:ATP701 3.6 43.4 1.0 O2A A:ATP701 4.0 50.4 1.0 O3A A:ATP701 4.1 58.5 1.0 OD2 A:ASP194 4.1 54.4 1.0 OE1 A:GLU171 4.1 48.8 1.0 OD1 A:ASP194 4.1 58.5 1.0 OD2 A:ASP8 4.3 51.5 1.0 OD1 A:ASP8 4.4 50.3 1.0 O2G A:ATP701 4.4 42.9 1.0 O2B A:ATP701 4.4 49.8 1.0 CD A:GLU171 4.5 48.9 1.0 OE2 A:GLU171 4.5 48.1 1.0 CG A:ASP194 4.6 55.6 1.0 PA A:ATP701 4.6 57.3 1.0 CA A:GLY196 4.6 51.5 1.0 CG A:ASP8 4.8 50.5 1.0 CA A:GLY10 4.9 50.0 1.0

Magnesium binding site 2 out of 2 in the Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Intermediate State (Qqq) of Near Full-Length Dnak Alternatively Fused with A Substrate Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg704 b:43.9 occ:1.00 O1G B:ATP702 1.9 39.8 1.0 O1B B:ATP702 1.9 37.5 1.0 O B:HOH801 2.0 41.3 1.0 O B:HOH804 2.0 35.9 1.0 O B:HOH802 2.0 28.1 1.0 O B:HOH803 2.1 46.4 1.0 PG B:ATP702 3.1 66.8 1.0 PB B:ATP702 3.2 45.1 1.0 O3B B:ATP702 3.5 44.1 1.0 O3G B:ATP702 3.5 27.9 1.0 OD2 B:ASP194 4.0 40.4 1.0 OE1 B:GLU171 4.0 38.9 1.0 OD1 B:ASP8 4.1 35.5 1.0 O3A B:ATP702 4.1 40.3 1.0 O2A B:ATP702 4.2 39.9 1.0 OD2 B:ASP8 4.3 40.3 1.0 O2B B:ATP702 4.3 33.1 1.0 O2G B:ATP702 4.3 32.1 1.0 CD B:GLU171 4.4 40.4 1.0 OD1 B:ASP194 4.5 45.5 1.0 OE2 B:GLU171 4.6 41.5 1.0 CG B:ASP8 4.6 36.4 1.0 PA B:ATP702 4.7 78.6 1.0 CG B:ASP194 4.8 37.7 1.0 CA B:GLY10 4.8 36.4 1.0 CA B:GLY196 4.9 36.7 1.0

W.Wang, W.A.Hendrickson. Intermediates in Allosteric Equilibria of Dnak-Atp Interactions with Substrate Peptides Acta Crystallogr.,Sect.D V. 77 606 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321002436