Magnesium in PDB 4qbi: Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6

All present enzymatic activity of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6:
2.7.4.3;

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6, PDB code: 4qbi was solved by S.Moon, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.814, 76.512, 85.130, 90.00, 90.20, 90.00
R / Rfree (%)	16.8 / 20.8

The structure of Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6 (pdb code 4qbi). 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 A Stable Adenylate Kinase Variant AKLSE6, PDB code: 4qbi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6


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 A Stable Adenylate Kinase Variant AKLSE6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.7 occ:1.00 O A:HOH677 2.0 30.3 1.0 O A:HOH675 2.1 34.8 1.0 O A:HOH674 2.2 37.9 1.0 O A:HOH678 2.2 34.5 1.0 O A:HOH676 2.2 27.3 1.0 O2G A:AP5303 2.5 20.8 0.5 O2B A:AP5303 3.6 16.0 1.0 O1E A:AP5303 3.9 28.9 1.0 PG A:AP5303 4.0 30.3 0.5 O A:HOH512 4.1 36.4 1.0 OG A:SER30 4.1 25.5 1.0 OD2 A:ASP84 4.2 19.8 1.0 O2E A:AP5303 4.2 26.4 1.0 OD1 A:ASP33 4.3 31.2 1.0 OD1 A:ASP84 4.4 22.2 1.0 NH1 A:ARG160 4.5 21.0 1.0 O3G A:AP5303 4.6 30.9 0.5 PE A:AP5303 4.6 29.3 1.0 CG A:ASP84 4.6 20.8 1.0 CA A:GLY14 4.7 16.7 1.0 O3B A:AP5303 4.7 18.1 1.0 PB A:AP5303 4.8 16.6 1.0 O3D A:AP5303 4.8 32.5 0.5 O A:HOH440 4.8 33.7 1.0 N A:GLY14 4.8 16.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Stable Adenylate Kinase Variant AKLSE6


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 A Stable Adenylate Kinase Variant AKLSE6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:31.4 occ:1.00 O B:HOH653 2.1 29.9 1.0 O B:HOH654 2.1 31.2 1.0 O B:HOH655 2.2 27.1 1.0 O B:HOH652 2.2 28.2 1.0 O2B B:AP5303 2.3 14.9 1.0 O2G B:AP5303 2.3 15.6 0.5 PG B:AP5303 3.4 28.7 0.5 PB B:AP5303 3.4 16.0 1.0 O3B B:AP5303 3.6 17.5 1.0 N B:GLY14 4.1 16.7 1.0 O B:HOH479 4.2 32.7 1.0 O1E B:AP5303 4.3 17.6 1.0 O3G B:AP5303 4.3 27.8 0.5 O2A B:AP5303 4.3 16.3 1.0 NH1 B:ARG160 4.3 17.0 1.0 CA B:GLY14 4.3 17.2 1.0 O B:HOH441 4.4 29.0 1.0 O2E B:AP5303 4.4 19.0 1.0 OD1 B:ASP84 4.4 18.9 1.0 OD2 B:ASP84 4.4 20.0 1.0 O1B B:AP5303 4.4 16.7 1.0 O3A B:AP5303 4.5 15.7 1.0 NH1 B:ARG127 4.6 19.8 1.0 PE B:AP5303 4.6 19.6 1.0 O3D B:AP5303 4.7 16.6 0.5 O1G B:AP5303 4.7 17.7 0.5 PA B:AP5303 4.8 16.5 1.0 CG B:ASP84 4.8 19.0 1.0

S.Moon, R.M.Bannen, T.J.Rutkoski, G.N.Phillips, E.Bae. Effectiveness and Limitations of Local Structural Entropy Optimization in the Thermal Stabilization of Mesophilic and Thermophilic Adenylate Kinases Proteins V. 82 2014.
ISSN: ESSN 1097-0134
DOI: 10.1002/PROT.24627