Magnesium in PDB 1rky: Pplo + Xe

All present enzymatic activity of Pplo + Xe:
1.4.3.13;

The structure of Pplo + Xe, PDB code: 1rky was solved by J.M.Guss, A.P.Duff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.47 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.144, 66.702, 108.620, 90.00, 119.24, 90.00
R / Rfree (%)	15.1 / 18.2

The structure of Pplo + Xe also contains other interesting chemical elements:

Xenon	(Xe)	8 atoms
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	6 atoms
Copper	(Cu)	1 atom

The binding sites of Magnesium atom in the Pplo + Xe (pdb code 1rky). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pplo + Xe, PDB code: 1rky:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:31.6 occ:1.00 O A:HOH2611 2.0 29.5 1.0 O A:HOH2534 2.0 33.2 1.0 O A:HOH2306 2.0 30.8 1.0 O A:HOH2589 2.1 32.5 1.0 O A:HOH2614 2.1 27.0 1.0 O A:HOH2609 2.1 35.0 1.0 O A:SER63 3.9 25.3 1.0 OD2 A:ASP425 4.0 39.1 1.0 OG A:SER63 4.1 30.0 1.0 OG1 A:THR62 4.3 27.6 1.0 O A:HOH2607 4.3 57.3 1.0 O A:HOH2222 4.3 42.6 1.0 O A:HOH2127 4.4 33.2 1.0 O A:HOH2155 4.4 34.8 1.0 O A:HOH2527 4.4 45.8 1.0 CA A:ALA65 4.5 31.2 1.0 O A:LEU64 4.5 28.4 1.0 N A:ALA65 4.6 31.7 1.0 C A:LEU64 4.7 28.0 1.0 C A:SER63 4.7 26.9 1.0 CB A:ALA65 4.9 33.3 1.0 CG2 A:THR62 4.9 30.0 1.0 CG A:ASP425 5.0 36.9 1.0

Magnesium binding site 2 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:37.4 occ:0.50 O A:HOH2362 2.1 47.1 1.0 OD2 A:ASP117 4.0 62.0 1.0 OD1 A:ASP117 4.4 47.8 1.0 CG A:ASP117 4.6 52.8 1.0

Magnesium binding site 3 out of 3 in the Pplo + Xe


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pplo + Xe within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg806 b:59.0 occ:0.60 O A:HOH2617 2.0 49.5 1.0 O A:HOH2313 2.1 45.7 1.0 O A:HOH2440 2.3 43.8 1.0 O A:HOH2380 2.3 47.0 1.0 OD2 A:ASP336 3.9 28.0 1.0 OD1 A:ASP336 4.2 30.6 1.0 CB A:ASP338 4.5 38.2 1.0 OE2 A:GLU339 4.5 37.6 1.0 OD2 A:ASP338 4.5 78.7 1.0 CG A:ASP336 4.6 31.1 1.0 OE2 A:GLU54 4.6 41.2 0.5 CG A:GLU339 4.6 30.6 1.0 O A:HOH2531 4.6 56.2 1.0 CG A:GLU54 4.8 24.3 0.5 CG A:ASP338 5.0 81.7 1.0 CG A:GLU54 5.0 40.5 0.5

A.P.Duff, D.M.Trambaiolo, A.E.Cohen, P.J.Ellis, G.A.Juda, E.M.Shepard, D.B.Langley, D.M.Dooley, H.C.Freeman, J.M.Guss. Using Xenon As A Probe For Dioxygen-Binding Sites in Copper Amine Oxidases J.Mol.Biol. V. 344 599 2004.
ISSN: ISSN 0022-2836
PubMed: 15533431
DOI: 10.1016/J.JMB.2004.09.075