Magnesium in PDB 4tyq: Crystal Structure of An Adenylate Kinase Mutant--AKM2

All present enzymatic activity of Crystal Structure of An Adenylate Kinase Mutant--AKM2:
2.7.4.3;

The structure of Crystal Structure of An Adenylate Kinase Mutant--AKM2, PDB code: 4tyq 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 / 1.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.003, 48.790, 54.832, 90.98, 97.34, 95.83
R / Rfree (%)	17.5 / 21.9

The structure of Crystal Structure of An Adenylate Kinase Mutant--AKM2 also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Magnesium atom in the Crystal Structure of An Adenylate Kinase Mutant--AKM2 (pdb code 4tyq). 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 An Adenylate Kinase Mutant--AKM2, PDB code: 4tyq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of An Adenylate Kinase Mutant--AKM2


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 An Adenylate Kinase Mutant--AKM2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:19.3 occ:1.00 O A:HOH503 2.2 27.2 1.0 O2G A:AP5301 2.3 10.2 1.0 O2B A:AP5301 2.3 8.1 1.0 O A:HOH507 2.4 24.2 1.0 O A:HOH519 2.5 34.7 1.0 O A:HOH518 2.5 31.7 1.0 PG A:AP5301 3.5 9.7 1.0 PB A:AP5301 3.6 7.4 1.0 O3B A:AP5301 3.8 9.5 1.0 O2E A:AP5301 4.1 14.7 1.0 N A:GLY14 4.1 11.4 1.0 O1E A:AP5301 4.2 11.4 1.0 O3G A:AP5301 4.2 15.4 1.0 CA A:GLY14 4.2 11.6 1.0 O2A A:AP5301 4.2 11.6 1.0 PE A:AP5301 4.3 12.3 1.0 OD2 A:ASP84 4.5 18.0 1.0 OD1 A:ASP33 4.5 17.8 1.0 O3D A:AP5301 4.5 14.0 1.0 OD1 A:ASP84 4.5 19.4 1.0 O3A A:AP5301 4.6 8.1 1.0 NH2 A:ARG160 4.6 29.3 1.0 NH1 A:ARG160 4.7 21.7 1.0 O1B A:AP5301 4.7 10.4 1.0 O1G A:AP5301 4.8 17.4 1.0 PA A:AP5301 4.8 8.9 1.0 PD A:AP5301 4.9 14.4 1.0 OG A:SER30 4.9 16.2 1.0 CG A:ASP84 4.9 17.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of An Adenylate Kinase Mutant--AKM2


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 An Adenylate Kinase Mutant--AKM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:18.1 occ:1.00 O B:HOH532 2.1 27.2 1.0 O B:HOH503 2.1 29.4 1.0 O2G B:AP5301 2.3 9.3 1.0 O B:HOH509 2.3 26.4 1.0 O2B B:AP5301 2.4 7.4 1.0 O B:HOH497 2.4 25.2 1.0 PG B:AP5301 3.6 8.8 1.0 PB B:AP5301 3.6 7.3 1.0 O3B B:AP5301 3.9 7.9 1.0 O B:HOH547 3.9 43.7 1.0 O2E B:AP5301 4.0 13.0 1.0 N B:GLY14 4.1 10.9 1.0 O B:HOH531 4.1 31.1 1.0 CA B:GLY14 4.2 11.5 1.0 O3G B:AP5301 4.2 12.6 1.0 O2A B:AP5301 4.3 10.5 1.0 O1E B:AP5301 4.3 9.8 1.0 PE B:AP5301 4.4 11.1 1.0 OD1 B:ASP33 4.5 16.3 1.0 NH2 B:ARG160 4.5 27.3 1.0 OD2 B:ASP84 4.5 19.5 1.0 O1B B:AP5301 4.6 8.3 1.0 OD1 B:ASP84 4.6 19.0 1.0 O3A B:AP5301 4.6 8.3 1.0 NH1 B:ARG160 4.6 19.2 1.0 O3D B:AP5301 4.7 12.4 1.0 O1G B:AP5301 4.8 13.7 1.0 PA B:AP5301 4.9 7.6 1.0 PD B:AP5301 4.9 12.3 1.0 OG B:SER30 4.9 14.8 1.0

S.Moon, E.Bae. Crystal Structures of Thermally Stable Adenylate Kinase Mutants Designed By Local Structural Entropy Optimization and Structure-Guided Mutagenesis J Korean Soc Appl Biol Chem V. 57 661 2014.
ISSN: ISSN 1738-2203
DOI: 10.1007/S13765-014-4228-4