Magnesium in PDB 3dl0: Crystal Structure of Adenylate Kinase Variant AKLSE3

All present enzymatic activity of Crystal Structure of Adenylate Kinase Variant AKLSE3:
2.7.4.3;

The structure of Crystal Structure of Adenylate Kinase Variant AKLSE3, PDB code: 3dl0 was solved by R.M.Bannen, C.M.Bianchetti, C.A.Bingman, J.G.Mccoy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.84 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.003, 76.688, 77.993, 90.00, 95.30, 90.00
R / Rfree (%)	20 / 23.9

The structure of Crystal Structure of Adenylate Kinase Variant AKLSE3 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Adenylate Kinase Variant AKLSE3 (pdb code 3dl0). 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 Adenylate Kinase Variant AKLSE3, PDB code: 3dl0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Adenylate Kinase Variant AKLSE3


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 Adenylate Kinase Variant AKLSE3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg220 b:10.2 occ:1.00 O A:HOH460 2.2 25.2 1.0 O A:HOH231 2.2 15.8 1.0 O2B A:AP5218 2.4 13.2 1.0 O2G A:AP5218 2.4 9.5 1.0 O A:HOH241 2.4 14.6 1.0 O A:HOH225 2.6 14.5 1.0 O A:HOH284 3.5 25.4 1.0 PG A:AP5218 3.6 12.1 1.0 PB A:AP5218 3.7 13.1 1.0 O3B A:AP5218 4.0 13.5 1.0 N A:GLY14 4.0 11.2 1.0 CA A:GLY14 4.0 12.4 1.0 O A:HOH349 4.2 24.2 1.0 O1E A:AP5218 4.2 14.4 1.0 O3G A:AP5218 4.2 17.6 1.0 O2E A:AP5218 4.3 17.6 1.0 O2A A:AP5218 4.4 18.0 1.0 OD2 A:ASP84 4.4 12.7 1.0 PE A:AP5218 4.6 15.4 1.0 NH1 A:ARG160 4.6 13.4 1.0 OD1 A:ASP84 4.6 13.1 1.0 OD1 A:ASP33 4.6 14.9 1.0 O A:HOH373 4.6 30.3 1.0 O3A A:AP5218 4.7 14.1 1.0 NH1 A:ARG127 4.7 17.1 1.0 O1B A:AP5218 4.7 14.5 1.0 OG A:SER30 4.7 12.4 1.0 NH2 A:ARG36 4.8 21.0 1.0 O A:HOH369 4.8 25.6 1.0 O1G A:AP5218 4.8 13.8 1.0 PA A:AP5218 4.9 15.3 1.0 O A:HOH263 4.9 18.3 1.0 CG A:ASP84 5.0 12.6 1.0 O3D A:AP5218 5.0 17.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Adenylate Kinase Variant AKLSE3


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 Adenylate Kinase Variant AKLSE3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg220 b:14.2 occ:1.00 O B:HOH254 2.3 15.0 1.0 O B:HOH499 2.3 27.0 1.0 O2G B:AP5218 2.3 10.1 1.0 O B:HOH226 2.3 13.5 1.0 O2B B:AP5218 2.4 12.2 1.0 O B:HOH231 2.6 16.9 1.0 PG B:AP5218 3.5 11.8 1.0 PB B:AP5218 3.6 12.4 1.0 O2E B:AP5218 3.7 16.4 1.0 O3B B:AP5218 3.9 14.8 1.0 O B:HOH437 4.0 30.1 1.0 O3G B:AP5218 4.0 17.9 1.0 O1E B:AP5218 4.0 14.2 1.0 N B:GLY14 4.1 11.1 1.0 CA B:GLY14 4.2 12.5 1.0 PE B:AP5218 4.3 16.4 1.0 O B:HOH333 4.3 21.3 1.0 OD2 B:ASP84 4.4 13.8 1.0 O2A B:AP5218 4.4 17.8 1.0 OD1 B:ASP84 4.5 14.8 1.0 OG B:SER30 4.6 12.7 1.0 O3A B:AP5218 4.6 12.4 1.0 OD1 B:ASP33 4.7 14.7 1.0 NH1 B:ARG160 4.7 15.6 1.0 O1B B:AP5218 4.7 14.0 1.0 O3D B:AP5218 4.7 16.9 1.0 NH1 B:ARG127 4.8 14.2 1.0 O1G B:AP5218 4.8 14.6 1.0 NH2 B:ARG36 4.8 27.6 1.0 CG B:ASP84 4.9 12.9 1.0 O B:HOH387 4.9 27.6 1.0 PD B:AP5218 4.9 18.8 1.0 PA B:AP5218 5.0 13.7 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 2631 2014.
ISSN: ISSN 0887-3585
PubMed: 24931334
DOI: 10.1002/PROT.24627