Magnesium in PDB 5tkr: Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant

The structure of Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant, PDB code: 5tkr was solved by J.P.Bacik, J.R.Klesmith, R.Michalczyk, T.A.Whitehead, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.08 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.060, 70.060, 261.770, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.8

The structure of Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant (pdb code 5tkr). 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 Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant, PDB code: 5tkr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant


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 Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:19.5 occ:1.00 O2B A:ADP501 2.0 17.9 1.0 OD1 A:ASP26 2.1 20.6 1.0 O A:HOH658 2.1 16.6 1.0 O2A A:ADP501 2.1 19.5 1.0 O A:HOH646 2.1 17.4 1.0 O A:HOH735 2.2 17.5 1.0 CG A:ASP26 3.1 21.9 1.0 PB A:ADP501 3.2 18.2 1.0 PA A:ADP501 3.4 19.5 1.0 OD2 A:ASP26 3.4 22.9 1.0 O3A A:ADP501 3.5 20.2 1.0 O3B A:ADP501 3.7 17.9 1.0 O A:GLY27 4.1 19.9 1.0 N A:GLY27 4.1 19.4 1.0 N A:GLY22 4.1 18.1 1.0 K A:K506 4.2 24.3 1.0 C5' A:ADP501 4.2 19.9 1.0 OD1 A:ASP29 4.2 21.6 1.0 N A:ASP26 4.2 19.4 1.0 O5' A:ADP501 4.3 21.1 1.0 O A:HOH696 4.3 26.9 1.0 OD2 A:ASP29 4.4 22.8 1.0 O1A A:ADP501 4.4 19.5 1.0 O1B A:ADP501 4.4 18.9 1.0 CB A:ASP26 4.4 18.0 1.0 O A:HOH609 4.6 22.6 1.0 CB A:SER24 4.6 19.3 1.0 CA A:GLY22 4.7 18.1 1.0 CG A:ASP29 4.7 22.9 1.0 N A:MET25 4.7 17.4 1.0 CA A:ASP26 4.7 20.6 1.0 C A:GLY27 4.8 23.0 1.0 CA A:GLY27 4.9 22.6 1.0 C A:ASP26 4.9 21.0 1.0 O A:GLY22 4.9 18.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant


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 Lipomyces Starkeyi Levoglucosan Kinase G359R Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:19.2 occ:1.00 O3B A:ADP501 2.0 17.9 1.0 O2 A:SO4504 2.1 18.1 1.0 OE2 A:GLU362 2.1 18.6 1.0 O A:HOH725 2.1 17.4 1.0 O A:HOH622 2.1 15.5 1.0 OE1 A:GLU362 2.2 18.7 1.0 CD A:GLU362 2.4 16.4 1.0 S A:SO4504 3.2 18.4 1.0 PB A:ADP501 3.3 18.2 1.0 O3 A:SO4504 3.4 18.3 1.0 O1B A:ADP501 3.7 18.9 1.0 O3A A:ADP501 3.8 20.2 1.0 CG A:GLU362 4.0 16.4 1.0 O A:HOH700 4.0 20.6 1.0 O1A A:ADP501 4.1 19.5 1.0 ND2 A:ASN186 4.1 18.5 1.0 O1 A:SO4504 4.1 20.1 1.0 O A:HOH951 4.2 18.4 1.0 O A:HOH735 4.2 17.5 1.0 CA A:GLY188 4.2 17.6 1.0 OD1 A:ASN186 4.3 19.3 1.0 O4 A:SO4504 4.3 17.3 1.0 CA A:GLY22 4.3 18.1 1.0 O2B A:ADP501 4.4 17.9 1.0 ND2 A:ASN20 4.5 18.0 1.0 PA A:ADP501 4.5 19.5 1.0 CG A:ASN186 4.6 16.4 1.0 O A:HOH771 4.7 17.5 1.0 CB A:GLU362 4.8 17.3 1.0 N A:GLY188 4.8 18.7 1.0

J.R.Klesmith, J.P.Bacik, E.E.Wrenbeck, R.Michalczyk, T.A.Whitehead. Trade-Offs Between Enzyme Fitness and Solubility Illuminated By Deep Mutational Scanning. Proc. Natl. Acad. Sci. V. 114 2265 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28196882
DOI: 10.1073/PNAS.1614437114