Magnesium in PDB 5l43: Structure of K26-Dcp

The structure of Structure of K26-Dcp, PDB code: 5l43 was solved by G.Masuyer, K.R.Acharya, G.J.Kramer, B.O.Bachmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.81 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.470, 66.936, 101.786, 97.34, 90.86, 117.31
R / Rfree (%)	17.7 / 20

The structure of Structure of K26-Dcp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Structure of K26-Dcp (pdb code 5l43). 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 K26-Dcp, PDB code: 5l43:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of K26-Dcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of K26-Dcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:22.1 occ:1.00 OD2 A:ASP527 2.1 17.6 1.0 O A:HOH1429 2.1 20.7 1.0 OD1 A:ASP524 2.1 17.0 1.0 O B:HOH1122 2.2 17.4 1.0 O B:HOH1131 2.2 20.9 1.0 O B:HOH1109 2.3 21.2 1.0 CG A:ASP527 3.1 17.9 1.0 CG A:ASP524 3.3 17.1 1.0 CB A:ASP527 3.5 17.4 1.0 OE2 B:GLU354 3.9 21.4 1.0 CB A:ASP524 4.0 16.6 1.0 CA A:ASP524 4.0 16.2 1.0 OD2 B:ASP356 4.1 18.8 1.0 OD2 A:ASP524 4.2 17.7 1.0 OG1 B:THR451 4.2 13.4 1.0 NZ A:LYS523 4.2 15.8 1.0 OD1 A:ASP527 4.2 18.4 1.0 OD1 B:ASP356 4.2 16.9 1.0 CE A:LYS523 4.4 16.2 1.0 O B:GLU449 4.4 17.6 1.0 O A:ASP524 4.4 17.5 1.0 CD A:LYS523 4.5 16.0 1.0 O B:HOH1300 4.5 33.8 1.0 CG B:ASP356 4.5 17.4 1.0 OH B:TYR409 4.6 12.3 1.0 C A:ASP524 4.7 16.7 1.0 N B:THR451 4.8 13.8 1.0 NH2 B:ARG389 4.9 21.6 1.0 N A:ASP524 4.9 15.3 1.0 CD B:GLU354 5.0 19.8 1.0

Magnesium binding site 2 out of 2 in the Structure of K26-Dcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of K26-Dcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:18.3 occ:1.00 OD2 B:ASP527 2.1 17.2 1.0 O B:HOH1391 2.1 17.0 1.0 OD1 B:ASP524 2.1 16.4 1.0 CG B:ASP527 3.1 17.3 1.0 CG B:ASP524 3.3 16.7 1.0 CB B:ASP527 3.5 17.1 1.0 CB B:ASP524 4.0 16.5 1.0 CA B:ASP524 4.0 15.7 1.0 OD2 B:ASP524 4.2 17.4 1.0 OD1 B:ASP527 4.2 17.7 1.0 NZ B:LYS523 4.3 16.6 1.0 CE B:LYS523 4.4 16.9 1.0 O B:ASP524 4.5 16.6 1.0 CD B:LYS523 4.5 16.4 1.0 C B:ASP524 4.7 16.1 1.0 N B:ASP524 4.9 15.1 1.0

G.Masuyer, G.E.Cozier, G.J.Kramer, B.O.Bachmann, K.R.Acharya. Crystal Structure of A Peptidyl-Dipeptidase K-26-Dcp From Actinomycete in Complex with Its Natural Inhibitor. Febs J. V. 283 4357 2016.
ISSN: ISSN 1742-4658
PubMed: 27754586
DOI: 10.1111/FEBS.13928