Magnesium in PDB 5dj3: Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound

The structure of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound, PDB code: 5dj3 was solved by N.R.Silvaggi, L.Han, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.53 / 2.23
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.718, 108.277, 195.412, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.9

The binding sites of Magnesium atom in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound (pdb code 5dj3). 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 the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound, PDB code: 5dj3:

Magnesium binding site 1 out of 1 in the Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Plp-Dependent L-Arginine Hydroxylase Mppp with D- Arginine Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:67.7 occ:1.00 O B:HOH532 2.3 25.5 1.0 OD2 B:ASP116 2.4 41.2 1.0 O B:HOH653 2.4 32.5 1.0 O C:HOH702 2.4 39.7 1.0 O B:HOH521 2.9 31.7 1.0 OD2 B:ASP120 3.3 26.5 1.0 CG B:ASP116 3.5 39.3 1.0 O C:HOH735 3.5 35.1 1.0 OD1 B:ASP120 3.7 27.3 1.0 HB2 B:ASP116 3.8 38.6 1.0 CG B:ASP120 3.9 33.1 1.0 O B:HOH552 3.9 40.0 1.0 HG2 C:GLU180 3.9 47.6 1.0 HG3 C:GLU180 4.1 47.6 1.0 CB B:ASP116 4.2 32.2 1.0 OD1 B:ASP116 4.3 66.4 1.0 HB2 B:GLN338 4.3 33.9 1.0 O B:HOH525 4.4 33.7 1.0 CG C:GLU180 4.5 39.7 1.0 O C:HOH621 4.6 25.4 1.0 HB3 B:ASP116 4.8 38.6 1.0 O B:GLN338 4.9 24.0 1.0 HA B:GLN338 4.9 33.6 1.0 OE2 C:GLU180 5.0 62.5 1.0

L.Han, A.W.Schwabacher, G.R.Moran, N.R.Silvaggi. Streptomyces Wadayamensis Mppp Is A Pyridoxal 5'-Phosphate-Dependent L-Arginine Alpha-Deaminase, Gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry V. 54 7029 2015.
ISSN: ISSN 0006-2960
PubMed: 26551990
DOI: 10.1021/ACS.BIOCHEM.5B01016