Magnesium in PDB 6p58: Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K

The structure of Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K, PDB code: 6p58 was solved by J.A.Clinger, M.D.Miller, E.S.Buirgie, R.D.Vierstra, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.83 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.618, 61.052, 116.148, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.6

The binding sites of Magnesium atom in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K (pdb code 6p58). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K, PDB code: 6p58:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:21.3 occ:1.00 O A:HIS584 2.0 19.2 1.0 O A:HOH717 2.0 19.9 1.0 O A:GLU581 2.0 18.0 1.0 O A:HOH757 2.0 15.6 0.7 O A:HOH723 2.2 21.2 1.0 C A:HIS584 3.1 20.7 1.0 C A:GLU581 3.2 17.0 1.0 O A:HOH757 3.3 16.0 0.3 OXT A:HIS584 3.4 20.4 1.0 HA A:GLU581 3.5 19.5 1.0 HG3 A:GLU581 3.9 22.5 1.0 CA A:GLU581 3.9 16.3 1.0 HG2 A:GLU581 4.0 22.5 1.0 HA A:ARG582 4.0 21.1 0.5 HA A:ARG582 4.0 21.1 0.5 H A:HIS584 4.0 20.5 1.0 OD1 A:ASP543 4.1 24.9 1.0 OD2 A:ASP543 4.2 22.2 1.0 O A:HOH744 4.2 38.2 1.0 N A:ARG582 4.3 16.7 0.5 N A:ARG582 4.3 16.7 0.5 CG A:GLU581 4.3 18.9 1.0 CA A:HIS584 4.4 18.7 1.0 N A:HIS584 4.5 17.1 1.0 O A:LEU580 4.5 15.3 1.0 CA A:ARG582 4.5 17.7 0.5 CA A:ARG582 4.5 17.7 0.5 CG A:ASP543 4.6 22.3 1.0 CB A:GLU581 4.7 16.9 1.0 C A:ARG582 4.8 17.4 0.5 C A:ARG582 4.8 17.4 0.5 HA A:HIS584 4.9 22.5 1.0

Magnesium binding site 2 out of 4 in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:29.4 occ:1.00 O B:HOH729 2.0 40.4 1.0 O A:HOH707 2.0 35.5 1.0 O A:HOH821 2.1 34.4 1.0 O A:HOH701 2.2 27.1 1.0 O A:HOH735 2.2 39.2 1.0 HD12 B:LEU454 3.4 96.9 1.0 OE2 A:GLU571 3.8 40.2 1.0 OD2 A:ASP567 3.9 23.1 0.7 HE22 B:GLN568 4.0 77.4 1.0 O A:HOH730 4.2 43.4 1.0 HA B:LEU454 4.2 25.4 1.0 OD1 A:ASP567 4.2 21.2 0.7 OE1 B:GLN568 4.3 56.9 1.0 CD1 B:LEU454 4.3 80.7 1.0 O B:LEU454 4.4 24.6 1.0 CG A:ASP567 4.5 18.2 0.7 HD11 B:LEU454 4.5 96.9 1.0 HD13 B:LEU454 4.6 96.9 1.0 NE2 B:GLN568 4.7 64.5 1.0 HG3 A:GLU571 4.9 28.7 1.0 CD B:GLN568 4.9 83.5 1.0 CD A:GLU571 5.0 39.0 1.0

Magnesium binding site 3 out of 4 in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:29.9 occ:1.00 O B:HOH797 2.0 39.3 1.0 O A:HOH832 2.0 30.3 1.0 O B:HOH739 2.1 41.8 1.0 O B:HOH766 2.1 48.1 1.0 HE1 A:HIS584 3.7 27.7 1.0 O A:HOH785 3.9 48.7 1.0 OD2 B:ASP439 3.9 33.1 1.0 HE1 B:HIS584 3.9 49.1 1.0 OD2 A:ASP439 3.9 23.4 1.0 N A:SER435 4.3 32.0 1.0 OD1 B:ASP439 4.3 27.4 1.0 N B:SER435 4.5 30.9 1.0 OD1 A:ASP439 4.6 22.7 1.0 CG B:ASP439 4.6 26.8 1.0 CE1 A:HIS584 4.6 23.0 1.0 CE1 B:HIS584 4.7 40.9 1.0 CG A:ASP439 4.7 21.9 1.0 HA B:SER435 4.9 32.2 1.0 NE2 B:HIS584 5.0 35.0 1.0

Magnesium binding site 4 out of 4 in the Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor Pixj at 150K within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:31.2 occ:1.00 O B:HOH749 2.0 29.6 1.0 O B:HOH759 2.0 38.9 1.0 O B:HIS584 2.0 39.9 1.0 O B:GLU581 2.0 27.0 1.0 O B:HOH709 2.2 33.6 1.0 O B:HOH783 2.3 36.3 1.0 C B:GLU581 3.2 25.4 1.0 C B:HIS584 3.2 45.2 1.0 HA B:GLU581 3.4 28.2 1.0 OXT B:HIS584 3.6 51.6 1.0 CA B:GLU581 3.8 23.5 1.0 H B:HIS584 3.9 35.7 1.0 HB3 B:GLU581 4.0 30.6 1.0 HA B:ARG582 4.1 31.4 1.0 OD2 B:ASP543 4.1 36.3 1.0 OD1 B:ASP543 4.1 32.2 1.0 N B:ARG582 4.3 23.6 1.0 CA B:HIS584 4.4 38.6 1.0 CB B:GLU581 4.5 25.5 1.0 N B:HIS584 4.5 29.7 1.0 CG B:ASP543 4.6 34.1 1.0 CA B:ARG582 4.6 26.1 1.0 O B:LEU580 4.7 25.1 1.0 C B:ARG582 4.9 25.3 1.0

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