Magnesium in PDB 5lcd: Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp

The structure of Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp, PDB code: 5lcd was solved by S.Gerhardt, O.Einsle, F.Kemper, N.Schwarzer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	116.28 / 2.66
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	164.441, 164.441, 95.044, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.3

The binding sites of Magnesium atom in the Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp (pdb code 5lcd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp, PDB code: 5lcd:

Magnesium binding site 1 out of 1 in the Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Polyphosphate Kinase From Meiothermus Ruber Bound to Amp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:57.3 occ:1.00 O1P C:AMP301 2.2 80.8 1.0 NE C:ARG122 3.0 52.8 1.0 P C:AMP301 3.6 81.0 1.0 NH1 C:ARG122 3.9 53.0 1.0 CD C:ARG122 3.9 44.6 1.0 CZ C:ARG122 3.9 62.0 1.0 O5' C:AMP301 3.9 73.8 1.0 CE C:LYS70 4.1 39.0 1.0 O2P C:AMP301 4.5 81.1 1.0 OD1 C:ASN121 4.5 37.9 1.0 CG C:ARG122 4.5 36.4 1.0 O3P C:AMP301 4.5 82.8 1.0 C5' C:AMP301 4.5 63.2 1.0 NZ C:LYS70 4.6 40.5 1.0 OD1 C:ASP66 5.0 70.7 1.0

A.E.Parnell, S.Mordhorst, F.Kemper, M.Giurrandino, J.P.Prince, N.J.Schwarzer, A.Hofer, D.Wohlwend, H.J.Jessen, S.Gerhardt, O.Einsle, P.C.F.Oyston, J.N.Andexer, P.L.Roach. Substrate Recognition and Mechanism Revealed By Ligand-Bound Polyphosphate Kinase 2 Structures. Proc. Natl. Acad. Sci. V. 115 3350 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29531036
DOI: 10.1073/PNAS.1710741115