Magnesium in PDB 6pry: X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis

The structure of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis, PDB code: 6pry was solved by E.S.Burgie, J.A.Clinger, M.D.Miller, G.N.Phillips Jr., R.D.Vierstra, A.M.Orville, J.F.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.09 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.788, 61.417, 116.484, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.5

The structure of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis (pdb code 6pry). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis, PDB code: 6pry:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:69.4 occ:0.61 MG A:MG602 0.0 69.4 0.6 O B:HOH714 2.0 87.4 1.0 OD2 A:ASP439 2.3 32.0 0.3 MG A:MG602 2.4 43.1 0.4 HG A:SER435 2.6 0.9 0.4 HG A:SER435 2.6 0.7 0.7 OD2 A:ASP439 2.6 37.5 0.7 OG A:SER435 3.1 92.4 0.3 OG A:SER435 3.2 94.8 0.7 OD1 A:ASP439 3.3 38.5 0.7 CG A:ASP439 3.4 28.9 0.7 OD2 B:ASP439 3.5 77.0 1.0 CG A:ASP439 3.5 39.4 0.3 O A:SER435 3.8 84.5 0.3 O B:HOH754 3.9 27.2 0.3 O A:SER435 4.0 83.1 0.7 OD1 A:ASP439 4.1 29.5 0.3 HG B:SER435 4.2 0.3 1.0 C A:SER435 4.4 76.2 0.3 CB A:SER435 4.4 85.5 0.3 C A:SER435 4.4 75.9 0.7 CB A:SER435 4.4 83.5 0.7 OG B:SER435 4.6 0.1 1.0 HE A:ARG438 4.6 99.4 0.7 HB2 A:ASP439 4.6 32.4 0.3 OE2 B:GLU436 4.6 0.1 1.0 HE A:ARG438 4.6 90.9 0.3 HA A:GLU436 4.6 67.9 0.7 CB A:ASP439 4.6 27.0 0.3 HG B:LEU583 4.6 0.1 1.0 HA A:GLU436 4.7 67.8 0.3 CG B:ASP439 4.7 68.5 1.0 HB2 A:SER435 4.7 0.2 0.7 HB2 A:SER435 4.7 0.5 0.4 HH21 A:ARG438 4.7 89.7 0.3 HB2 B:SER435 4.8 0.9 1.0 CA A:SER435 4.8 90.8 0.3 CB A:ASP439 4.8 34.5 0.7 HH21 A:ARG438 4.8 92.6 0.7 CA A:SER435 4.9 94.5 0.7 HB3 A:ASP439 4.9 32.4 0.3 N A:SER435 4.9 96.3 0.3 HA B:GLU436 4.9 0.8 1.0 O B:LEU583 5.0 0.4 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:43.1 occ:0.39 MG A:MG602 0.0 43.1 0.4 MG A:MG602 2.4 69.4 0.6 HG A:SER435 2.5 0.9 0.4 HG A:SER435 2.6 0.7 0.7 OG A:SER435 2.8 92.4 0.3 HE A:ARG438 2.8 90.9 0.3 HE A:ARG438 2.8 99.4 0.7 HH21 A:ARG438 2.8 89.7 0.3 OD2 A:ASP439 2.9 32.0 0.3 OG A:SER435 2.9 94.8 0.7 HH21 A:ARG438 3.0 92.6 0.7 OD1 A:ASP439 3.2 38.5 0.7 OD1 A:ASP439 3.3 29.5 0.3 O B:HIS584 3.4 0.7 1.0 NE A:ARG438 3.5 75.7 0.3 NH2 A:ARG438 3.5 74.7 0.3 NE A:ARG438 3.5 82.8 0.7 CG A:ASP439 3.5 39.4 0.3 NH2 A:ARG438 3.6 77.2 0.7 O B:HOH714 3.8 87.4 1.0 CZ A:ARG438 3.9 79.2 0.3 HB2 A:SER435 3.9 0.5 0.4 HB2 A:SER435 3.9 0.2 0.7 CB A:SER435 3.9 85.5 0.3 CZ A:ARG438 4.0 85.6 0.7 CB A:SER435 4.0 83.5 0.7 OD2 A:ASP439 4.1 37.5 0.7 CG A:ASP439 4.1 28.9 0.7 HH22 A:ARG438 4.1 89.7 0.3 O A:SER435 4.2 84.5 0.3 HG3 A:ARG438 4.2 55.2 0.3 HG3 A:ARG438 4.2 46.8 0.7 O A:SER435 4.2 83.1 0.7 HH22 A:ARG438 4.3 92.6 0.7 O B:LEU583 4.3 0.4 1.0 HB3 A:SER435 4.4 0.5 0.4 C B:HIS584 4.5 0.6 1.0 HG2 A:ARG438 4.5 46.8 0.7 CD A:ARG438 4.5 46.1 0.7 CD A:ARG438 4.6 47.0 0.3 HB3 A:SER435 4.6 0.2 0.7 O B:HOH754 4.6 40.0 0.7 HG2 A:ARG438 4.6 55.2 0.3 CG A:ARG438 4.6 39.0 0.7 CG A:ARG438 4.7 46.0 0.3 HD2 A:ARG438 4.8 55.3 0.7 OXT B:HIS584 4.8 0.1 1.0 HD2 A:ARG438 4.8 56.4 0.3 C B:LEU583 4.9 92.7 1.0 OE2 B:GLU436 4.9 0.1 1.0 HA B:LEU583 4.9 73.5 1.0 C A:SER435 4.9 76.2 0.3 C A:SER435 5.0 75.9 0.7

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:42.8 occ:1.00 O B:HOH777 2.2 35.8 0.5 NE2 B:HIS498 2.3 25.0 1.0 O B:HOH779 2.6 67.6 1.0 O B:HOH777 2.9 47.9 0.6 OE1 B:GLU497 3.0 38.9 1.0 CE1 B:HIS498 3.1 25.6 1.0 HE1 B:HIS498 3.1 30.7 1.0 O B:HOH745 3.3 32.5 0.5 CD2 B:HIS498 3.3 23.6 1.0 O B:HOH719 3.6 60.4 1.0 HD2 B:HIS498 3.6 28.3 1.0 HB3 B:GLU497 3.8 35.7 1.0 CD B:GLU497 4.2 50.5 1.0 ND1 B:HIS498 4.2 21.7 1.0 O B:HOH745 4.3 24.3 0.5 HB2 B:GLU497 4.3 35.7 1.0 CG B:HIS498 4.4 22.4 1.0 CB B:GLU497 4.5 29.7 1.0 CG B:GLU497 4.9 33.4 1.0 HD1 B:HIS498 5.0 26.1 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of the Blue-Light Absorbing State of Pixj From Thermosynechococcus Elongatus By Serial Femtosecond Crystallographic Analysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:71.0 occ:1.00 O A:HOH724 2.2 76.3 1.0 HD23 B:LEU454 3.3 71.9 1.0 HE22 B:GLN568 3.7 80.6 1.0 HD22 B:LEU454 4.0 71.9 1.0 CD2 B:LEU454 4.0 59.9 1.0 HA B:LEU454 4.0 40.4 1.0 OE1 A:GLU571 4.2 53.9 1.0 NE2 B:GLN568 4.4 67.2 1.0 HD21 B:LEU454 4.4 71.9 1.0 O B:LEU454 4.5 34.9 1.0 OE1 B:GLN568 4.7 52.0 1.0 OD2 A:ASP567 4.8 35.8 0.6 OD1 A:ASP567 4.8 33.8 0.6 CD B:GLN568 4.9 52.4 1.0 CA B:LEU454 4.9 33.7 1.0 HE21 B:GLN568 4.9 80.6 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