Magnesium in PDB 6upp: Radiation Damage Test of Pixj Pb State Crystals

The structure of Radiation Damage Test of Pixj Pb State Crystals, PDB code: 6upp was solved by J.A.Clinger, M.D.Miller, E.S.Burgie, 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)	34.58 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.910, 61.179, 116.643, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.2

The binding sites of Magnesium atom in the Radiation Damage Test of Pixj Pb State Crystals (pdb code 6upp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Radiation Damage Test of Pixj Pb State Crystals, PDB code: 6upp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Radiation Damage Test of Pixj Pb State Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Radiation Damage Test of Pixj Pb State Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:20.9 occ:1.00 O A:HOH743 2.0 21.7 1.0 O A:HOH720 2.0 23.7 1.0 O A:HIS584 2.1 24.2 1.0 O A:HOH722 2.1 24.6 1.0 O A:GLU581 2.1 16.9 1.0 C A:HIS584 3.1 22.3 1.0 C A:GLU581 3.3 15.8 1.0 OXT A:HIS584 3.4 20.9 1.0 HA A:GLU581 3.6 18.0 1.0 HG3 A:GLU581 4.0 23.5 1.0 HA A:ARG582 4.0 21.1 0.4 HG2 A:GLU581 4.0 23.5 1.0 CA A:GLU581 4.0 15.0 1.0 H A:HIS584 4.0 19.3 1.0 HA A:ARG582 4.1 22.3 0.6 OD1 A:ASP543 4.1 24.2 1.0 OD2 A:ASP543 4.2 26.6 1.0 N A:ARG582 4.3 15.4 0.4 N A:ARG582 4.3 15.4 0.6 O A:HOH752 4.4 48.7 1.0 CG A:GLU581 4.4 19.6 1.0 CA A:HIS584 4.4 19.1 1.0 N A:HIS584 4.5 16.1 1.0 CA A:ARG582 4.6 17.6 0.4 CA A:ARG582 4.6 18.6 0.6 CG A:ASP543 4.6 24.7 1.0 O A:LEU580 4.6 14.1 1.0 O A:HOH844 4.6 60.7 1.0 C A:ARG582 4.7 16.3 0.6 CB A:GLU581 4.8 15.4 1.0 C A:ARG582 4.9 16.3 0.4 O A:ARG582 4.9 17.4 0.6 O A:HOH802 4.9 45.5 1.0 HA A:HIS584 5.0 22.9 1.0

Magnesium binding site 2 out of 4 in the Radiation Damage Test of Pixj Pb State Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Radiation Damage Test of Pixj Pb State Crystals within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:23.4 occ:1.00 O B:HOH753 1.9 35.5 1.0 O A:HOH710 1.9 25.6 1.0 O B:HOH747 2.0 35.3 1.0 O B:HOH797 2.0 30.7 1.0 O A:HOH841 2.1 27.0 1.0 HE1 A:HIS584 3.6 25.9 1.0 OD2 A:ASP439 3.8 22.3 1.0 OD2 B:ASP439 3.9 31.2 1.0 O A:HOH788 4.0 44.2 1.0 HE1 B:HIS584 4.0 95.2 1.0 N A:SER435 4.1 40.1 1.0 O B:HOH711 4.2 62.5 1.0 OD1 B:ASP439 4.3 28.5 1.0 O B:HOH800 4.3 47.7 1.0 N B:SER435 4.4 54.1 1.0 OD1 A:ASP439 4.4 23.1 1.0 CE1 A:HIS584 4.5 21.6 1.0 CG B:ASP439 4.5 28.8 1.0 CG A:ASP439 4.6 20.9 1.0 CE1 B:HIS584 4.8 79.4 1.0 NE2 A:HIS584 4.9 18.4 1.0

Magnesium binding site 3 out of 4 in the Radiation Damage Test of Pixj Pb State Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Radiation Damage Test of Pixj Pb State Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:23.4 occ:1.00 O A:HOH837 2.0 28.6 1.0 O B:HOH760 2.0 33.6 1.0 O A:HOH721 2.0 24.7 1.0 O A:HOH732 2.0 31.4 1.0 O A:HOH773 2.4 39.9 1.0 HE22 B:GLN568 3.5 48.5 1.0 HD23 B:LEU454 3.9 0.4 1.0 OE2 A:GLU571 4.0 42.3 1.0 OD2 A:ASP567 4.0 21.2 0.7 O B:HOH719 4.2 31.9 1.0 HA B:LEU454 4.2 27.0 1.0 OD1 A:ASP567 4.2 18.9 0.7 OE1 B:GLN568 4.3 74.8 1.0 NE2 B:GLN568 4.3 40.4 1.0 O B:LEU454 4.4 23.5 1.0 HD22 B:LEU454 4.5 0.4 1.0 CG A:ASP567 4.6 17.2 0.7 CD2 B:LEU454 4.6 87.9 1.0 CD B:GLN568 4.7 55.5 1.0 HE21 B:GLN568 5.0 48.5 1.0 HG3 A:GLU571 5.0 34.0 1.0

Magnesium binding site 4 out of 4 in the Radiation Damage Test of Pixj Pb State Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Radiation Damage Test of Pixj Pb State Crystals within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:30.0 occ:1.00 O B:HOH709 1.8 30.3 1.0 O B:HOH751 2.0 27.8 1.0 O B:GLU581 2.1 31.4 1.0 O B:HIS584 2.2 57.5 1.0 O B:HOH774 2.3 33.0 1.0 O B:HOH781 2.3 35.2 1.0 C B:HIS584 3.1 52.2 1.0 C B:GLU581 3.2 27.6 1.0 HA B:GLU581 3.4 32.7 1.0 OXT B:HIS584 3.4 56.9 1.0 CA B:GLU581 3.8 27.3 1.0 H B:HIS584 3.9 46.1 1.0 HB3 B:GLU581 4.0 41.0 1.0 OD2 B:ASP543 4.0 35.2 1.0 OD1 B:ASP543 4.1 36.2 1.0 HA B:ARG582 4.2 27.9 1.0 N B:ARG582 4.3 22.0 1.0 CA B:HIS584 4.4 56.8 1.0 CB B:GLU581 4.4 34.1 1.0 N B:HIS584 4.5 38.4 1.0 CG B:ASP543 4.5 30.9 1.0 HG2 B:GLU581 4.6 47.9 1.0 O B:LEU580 4.7 23.0 1.0 CA B:ARG582 4.7 23.2 1.0 C B:ARG582 4.9 29.1 1.0 HB2 B:HIS584 5.0 87.1 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