Magnesium in PDB 6pru: Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus

The structure of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus, PDB code: 6pru was solved by E.S.Burgie, J.A.Clinger, M.D.Miller, G.N.Phillips Jr., R.D.Vierstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.12 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.590, 61.085, 116.297, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.7

The structure of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

The binding sites of Magnesium atom in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus (pdb code 6pru). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus, PDB code: 6pru:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:33.3 occ:1.00 O A:HOH737 2.0 28.4 0.6 O A:GLU581 2.1 31.8 1.0 O A:HOH794 2.1 40.9 1.0 O A:HOH728 2.1 40.6 1.0 OXT A:HIS584 2.1 43.1 1.0 O A:HOH711 2.1 42.0 1.0 C A:HIS584 3.1 36.7 1.0 C A:GLU581 3.3 23.1 1.0 O A:HIS584 3.5 31.8 1.0 O A:HOH737 3.7 32.2 0.4 HA A:GLU581 3.8 26.9 1.0 HA A:ARG582 3.8 29.8 1.0 HG3 A:GLU581 4.1 35.2 1.0 H A:HIS584 4.1 37.4 1.0 CA A:GLU581 4.1 22.5 1.0 HG2 A:GLU581 4.1 35.2 1.0 O A:HOH823 4.1 63.3 1.0 OD2 A:ASP543 4.2 37.2 1.0 N A:ARG582 4.2 23.1 1.0 O A:HOH789 4.3 40.4 0.5 OD1 A:ASP543 4.3 45.4 1.0 CA A:ARG582 4.4 24.8 1.0 CA A:HIS584 4.4 37.9 1.0 CG A:GLU581 4.5 29.3 1.0 N A:HIS584 4.5 31.1 1.0 C A:ARG582 4.6 27.9 1.0 CG A:ASP543 4.7 34.9 1.0 O A:LEU580 4.7 24.9 1.0 O A:ARG582 4.9 27.5 1.0 CB A:GLU581 4.9 20.9 1.0 HA A:HIS584 5.0 45.4 1.0

Magnesium binding site 2 out of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:35.8 occ:1.00 O B:HOH709 2.1 41.9 1.0 CL B:CL612 2.8 81.1 1.0 HE21 B:GLN505 3.7 60.6 1.0 OD2 B:ASP544 4.0 29.7 0.6 OD1 B:ASP544 4.0 33.6 0.4 OD2 B:ASP544 4.1 30.1 0.4 O B:HOH814 4.1 45.8 1.0 OD1 B:ASP544 4.2 30.8 0.6 CG B:ASP544 4.5 35.8 0.4 NE2 B:GLN505 4.5 50.5 1.0 CG B:ASP544 4.6 38.0 0.6 HG2 B:GLN505 4.7 41.8 1.0 HE22 B:GLN505 4.8 60.6 1.0

Magnesium binding site 3 out of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg609 b:66.3 occ:1.00 O B:HOH708 2.0 65.2 1.0 O B:HOH702 2.2 46.6 1.0 O B:GLU581 2.3 35.3 1.0 O B:HOH764 2.5 49.5 1.0 O B:HOH841 2.7 74.6 1.0 OXT B:HIS584 2.7 80.5 0.5 OXT B:HIS584 2.8 80.3 0.5 O B:HIS584 3.3 84.7 0.5 C B:HIS584 3.4 82.5 0.5 C B:GLU581 3.4 34.6 1.0 C B:HIS584 3.5 82.8 0.5 OD2 B:ASP543 3.5 35.0 0.4 HG2 B:GLU581 3.5 57.7 1.0 OD1 B:ASP543 3.5 37.1 0.6 O B:HIS584 3.6 84.9 0.5 HA B:GLU581 3.6 35.8 1.0 OD1 B:ASP543 3.6 25.7 0.4 HG3 B:GLU581 3.8 57.7 1.0 CG B:ASP543 4.0 35.4 0.4 CA B:GLU581 4.0 29.8 1.0 CG B:GLU581 4.1 48.1 1.0 HA B:ARG582 4.3 41.7 1.0 OD2 B:ASP543 4.3 41.5 0.6 CG B:ASP543 4.3 31.5 0.6 H B:HIS584 4.4 93.5 0.5 H B:HIS584 4.4 93.5 0.5 N B:ARG582 4.5 32.6 1.0 CB B:GLU581 4.6 39.1 1.0 CA B:HIS584 4.7 83.5 0.5 CA B:HIS584 4.8 83.4 0.5 CA B:ARG582 4.8 34.7 1.0 N B:HIS584 4.9 77.9 0.5 N B:HIS584 4.9 77.9 0.5

Magnesium binding site 4 out of 4 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg610 b:43.6 occ:1.00 O B:HOH701 1.9 30.2 0.5 O A:HOH829 2.0 29.8 0.5 O A:HOH829 2.1 31.0 0.5 O B:HOH723 2.1 29.9 0.5 O B:HOH701 2.2 35.4 0.5 OD2 B:ASP439 2.5 50.5 0.5 N B:SER435 3.3 69.0 0.5 N B:SER435 3.4 65.5 0.5 CG B:ASP439 3.6 35.6 0.5 HE1 A:HIS584 3.6 51.4 1.0 HE2 B:HIS584 3.8 0.8 0.5 N A:SER435 3.8 48.3 0.3 OD2 B:ASP439 3.9 32.3 0.5 HE1 B:HIS584 3.9 0.7 0.5 OD1 B:ASP439 4.0 35.2 0.5 OD2 A:ASP439 4.0 28.1 0.7 OD2 A:ASP439 4.0 29.3 0.3 O A:SER435 4.0 42.7 0.3 O B:HOH723 4.1 37.5 0.5 OD1 B:ASP439 4.2 31.2 0.5 O B:SER435 4.2 63.2 0.5 HE2 A:HIS584 4.4 44.5 1.0 CE1 A:HIS584 4.4 42.8 1.0 CG B:ASP439 4.4 36.6 0.5 CA B:SER435 4.5 66.5 0.5 C B:SER435 4.5 65.3 0.5 OD1 A:ASP439 4.5 28.2 0.7 N A:SER435 4.6 39.5 0.7 HA A:SER435 4.6 50.9 0.3 NE2 B:HIS584 4.6 91.5 0.5 CA A:SER435 4.6 42.4 0.3 CA B:SER435 4.7 65.5 0.5 C A:SER435 4.7 40.1 0.3 CG A:ASP439 4.7 27.8 0.7 CE1 B:HIS584 4.7 90.6 0.5 NE2 A:HIS584 4.8 37.1 1.0 HE2 B:HIS584 4.9 0.2 0.5 CB B:ASP439 4.9 37.5 0.5 HB2 B:ASP439 4.9 44.9 0.5 HA B:SER435 5.0 79.8 0.5 HA B:SER435 5.0 78.6 0.5 O B:SER435 5.0 60.6 0.5

E.S.Burgie, J.A.Clinger, M.D.Miller, A.S.Brewster, P.Aller, A.Butryn, F.D.Fuller, S.Gul, I.D.Young, C.C.Pham, I.S.Kim, A.Bhowmick, L.J.O'riordan, K.D.Sutherlin, J.V.Heinemann, A.Batyuk, R.Alonso-Mori, M.S.Hunter, J.E.Koglin, J.Yano, V.K.Yachandra, N.K.Sauter, A.E.Cohen, J.Kern, A.M.Orville, G.N.Phillips Jr., R.D.Vierstra. Photoreversible Interconversion of A Phytochrome Photosensory Module in the Crystalline State. Proc.Natl.Acad.Sci.Usa 2019.
ISSN: ESSN 1091-6490
PubMed: 31852825
DOI: 10.1073/PNAS.1912041116