Magnesium in PDB 4x8o: Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A

All present enzymatic activity of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A:
2.7.4.3;

The structure of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A, PDB code: 4x8o was solved by A.E.Sauer-Eriksson, M.Kovermann, J.Aden, C.Grundstrom, M.Wolf-Watz, U.H.Sauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.13 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.257, 72.654, 79.480, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 24

The structure of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A (pdb code 4x8o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A, PDB code: 4x8o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:25.8 occ:1.00 O2B A:AP5301 2.7 6.3 1.0 O1G A:AP5301 2.8 24.6 1.0 OD1 A:ASP84 2.9 12.7 1.0 OD2 A:ASP84 2.9 18.6 1.0 O A:HOH579 3.1 22.4 1.0 CG A:ASP84 3.2 11.9 1.0 O A:HOH557 3.3 14.7 1.0 N A:GLY14 3.6 7.5 1.0 O2G A:AP5301 3.6 13.0 1.0 PG A:AP5301 3.7 13.8 1.0 CA A:GLY14 3.9 7.0 1.0 PB A:AP5301 3.9 6.7 1.0 O A:HOH558 4.0 12.6 1.0 CB A:LYS13 4.0 6.7 1.0 O A:HOH483 4.2 21.2 1.0 O3B A:AP5301 4.3 9.0 1.0 CE A:LYS13 4.3 9.0 1.0 C A:LYS13 4.4 11.0 1.0 O1B A:AP5301 4.4 5.0 1.0 OG A:SER30 4.4 10.9 1.0 O1E A:AP5301 4.5 27.1 1.0 O A:ASP84 4.6 7.6 1.0 CB A:ASP84 4.6 10.7 1.0 C A:ASP84 4.7 5.8 1.0 CA A:LYS13 4.8 8.1 1.0 NZ A:LYS13 4.8 4.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of E. Coli Adenylate Kinase Y171W Mutant in Complex with Inhibitor AP5A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:40.2 occ:1.00 OD1 B:ASP84 2.6 21.0 1.0 O B:HOH534 2.8 33.9 1.0 OD2 B:ASP84 2.8 18.1 1.0 O1G B:AP5301 2.8 37.5 1.0 O2B B:AP5301 2.8 14.2 1.0 CG B:ASP84 3.0 18.5 1.0 O B:HOH531 3.5 15.3 1.0 N B:GLY14 3.7 7.7 1.0 PG B:AP5301 3.8 20.6 1.0 O2G B:AP5301 3.8 27.0 1.0 O B:HOH530 3.9 21.7 1.0 O B:HOH532 3.9 13.1 1.0 CA B:GLY14 4.0 10.0 1.0 PB B:AP5301 4.0 8.7 1.0 CB B:LYS13 4.2 5.4 1.0 CE B:LYS13 4.3 14.7 1.0 O B:ASP84 4.3 11.6 1.0 O3B B:AP5301 4.3 19.5 1.0 O1E B:AP5301 4.4 16.6 1.0 CB B:ASP84 4.4 14.3 1.0 O1B B:AP5301 4.4 9.4 1.0 OG B:SER30 4.4 17.8 1.0 C B:ASP84 4.5 12.5 1.0 C B:LYS13 4.6 9.6 1.0 NZ B:LYS13 4.7 11.5 1.0 N B:GLY85 4.9 12.3 1.0 CA B:ASP84 5.0 13.5 1.0 CA B:LYS13 5.0 10.2 1.0

M.Kovermann, J.Aden, C.Grundstrom, A.Elisabeth Sauer-Eriksson, U.H.Sauer, M.Wolf-Watz. Structural Basis For Catalytically Restrictive Dynamics of A High-Energy Enzyme State. Nat Commun V. 6 7644 2015.
ISSN: ESSN 2041-1723
PubMed: 26138143
DOI: 10.1038/NCOMMS8644