Chlorine 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:

Magnesium

(Mg)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus (pdb code 6pru). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus, PDB code: 6pru:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl605 b:61.7 occ:1.00 O A:HOH765 2.8 24.4 1.0 HB3 A:ASP466 2.9 30.2 1.0 O A:HOH826 3.6 47.5 1.0 CB A:ASP466 3.8 25.2 1.0 HA A:ASP466 3.8 25.5 1.0 HG1 A:THR472 3.9 29.4 1.0 O A:PHE465 3.9 23.0 1.0 N A:ASP466 4.0 18.6 1.0 C A:PHE465 4.0 20.2 1.0 CA A:ASP466 4.1 21.2 1.0 O A:ALA464 4.1 20.6 1.0 HB2 A:ASP466 4.2 30.2 1.0 HB A:THR472 4.2 24.0 1.0 HB3 A:ALA464 4.2 28.1 1.0 OG1 A:THR472 4.3 24.5 1.0 H A:ASP466 4.3 22.3 1.0 HB1 A:ALA464 4.6 28.1 1.0 C A:ALA464 4.6 18.6 1.0 O A:HOH841 4.6 58.5 1.0 CB A:THR472 4.8 20.0 1.0 CB A:ALA464 4.8 23.4 1.0 H A:THR472 4.8 24.3 1.0 CG A:ASP466 4.9 29.0 1.0 CA A:PHE465 4.9 18.2 1.0 HA A:PHE465 4.9 21.9 1.0 N A:PHE465 5.0 16.9 1.0

Chlorine binding site 2 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl606 b:64.1 occ:1.00 OE1 A:GLN505 2.7 32.3 0.4 O A:HOH790 3.0 52.8 1.0 HA A:ALA502 3.2 23.5 1.0 HB2 A:ALA502 3.4 26.1 1.0 OE1 A:GLN505 3.5 31.6 0.6 CD A:GLN505 3.7 36.4 0.4 CA A:ALA502 3.9 19.6 1.0 HE22 A:GLN505 3.9 42.6 0.6 CD A:GLN505 4.0 36.7 0.6 CB A:ALA502 4.0 21.8 1.0 HE22 A:GLN505 4.0 45.8 0.4 HB1 A:ALA502 4.1 26.1 1.0 NE2 A:GLN505 4.2 35.5 0.6 NE2 A:GLN505 4.3 38.2 0.4 HG2 A:GLU501 4.3 34.7 0.4 HB2 A:GLN505 4.3 29.4 0.4 HG3 A:GLU501 4.3 33.1 0.6 HB2 A:GLN505 4.4 28.0 0.6 N A:ALA502 4.5 19.4 1.0 H A:ALA502 4.7 23.3 1.0 HE21 A:GLN505 4.8 42.6 0.6 CG A:GLN505 4.9 26.3 0.4 HB3 A:ALA502 4.9 26.1 1.0 CG A:GLN505 5.0 25.1 0.6 CB A:GLN505 5.0 24.5 0.4 OE1 A:GLU501 5.0 42.3 0.4 C A:GLU501 5.0 27.3 0.6 C A:GLU501 5.0 25.9 0.4

Chlorine binding site 3 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl607 b:60.7 occ:1.00 O A:HOH708 3.1 25.6 1.0 O A:GLN505 4.1 23.4 0.4 O A:GLN505 4.1 22.4 0.6 HA3 A:GLY506 4.8 25.6 1.0

Chlorine binding site 4 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:37.8 occ:0.53 CL A:CL608 0.0 37.8 0.5 CL A:CL608 1.9 55.5 0.5 H A:GLU501 2.0 27.8 0.4 H A:GLU501 2.0 26.9 0.6 HB2 A:GLU501 2.9 29.9 0.4 N A:GLU501 2.9 23.2 0.4 N A:GLU501 2.9 22.5 0.6 HB3 A:GLU501 2.9 29.9 0.4 HB2 A:GLU501 2.9 27.8 0.6 HB3 A:GLU501 3.0 27.8 0.6 HB A:VAL500 3.0 31.4 1.0 H A:VAL500 3.2 22.8 1.0 CB A:GLU501 3.2 24.9 0.4 O A:HOH835 3.3 58.5 1.0 O A:HOH734 3.3 24.4 1.0 CB A:GLU501 3.3 23.2 0.6 N A:VAL500 3.5 19.0 1.0 CA A:GLU501 3.6 20.6 0.4 CA A:GLU501 3.7 20.3 0.6 CB A:VAL500 3.8 26.2 1.0 C A:VAL500 3.8 23.1 1.0 CA A:VAL500 3.9 22.0 1.0 HG11 A:VAL500 4.2 30.2 1.0 HA A:GLU501 4.2 24.8 0.4 H A:ALA502 4.2 23.3 1.0 C A:TRP499 4.2 22.3 1.0 HA A:GLU501 4.2 24.4 0.6 O A:HIS498 4.4 23.8 1.0 N A:TRP499 4.4 23.0 1.0 C A:HIS498 4.5 21.3 1.0 H A:TRP499 4.6 27.6 1.0 CG1 A:VAL500 4.6 25.1 1.0 OE1 A:GLU501 4.6 42.3 0.4 CG A:GLU501 4.6 28.9 0.4 HH12 A:ARG504 4.7 46.8 0.6 CG A:GLU501 4.7 27.6 0.6 HA A:TRP499 4.7 26.0 1.0 CA A:TRP499 4.7 21.7 1.0 C A:GLU501 4.8 25.9 0.4 N A:ALA502 4.8 19.4 1.0 C A:GLU501 4.8 27.3 0.6 HG2 A:GLU501 4.8 33.1 0.6 HH11 A:ARG504 4.9 46.8 0.6 HA A:VAL500 4.9 26.4 1.0 O A:ARG496 4.9 23.8 1.0 NH1 A:ARG504 4.9 39.0 0.6 CG2 A:VAL500 4.9 22.7 1.0 O A:TRP499 5.0 18.5 1.0 HG22 A:VAL500 5.0 27.3 1.0

Chlorine binding site 5 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:55.5 occ:0.47 CL A:CL608 0.0 55.5 0.5 CL A:CL608 1.9 37.8 0.5 H A:VAL500 2.6 22.8 1.0 HB A:VAL500 3.0 31.4 1.0 O A:ARG496 3.2 23.8 1.0 N A:VAL500 3.3 19.0 1.0 H A:GLU501 3.3 27.8 0.4 H A:TRP499 3.3 27.6 1.0 H A:GLU501 3.3 26.9 0.6 N A:TRP499 3.4 23.0 1.0 O A:PHE495 3.5 20.3 1.0 C A:HIS498 3.5 21.3 1.0 CB A:VAL500 3.8 26.2 1.0 C A:ARG496 3.8 21.9 1.0 N A:HIS498 3.9 23.9 1.0 O A:HOH835 3.9 58.5 1.0 O A:HIS498 3.9 23.8 1.0 HA A:ARG496 4.0 29.8 1.0 H A:HIS498 4.0 28.7 1.0 HA A:HIS498 4.0 29.6 1.0 O A:HOH734 4.0 24.4 1.0 CA A:HIS498 4.0 24.6 1.0 CA A:VAL500 4.1 22.0 1.0 C A:TRP499 4.1 22.3 1.0 N A:GLU501 4.1 23.2 0.4 N A:GLU501 4.1 22.5 0.6 C A:GLU497 4.1 23.4 0.5 HG21 A:VAL500 4.2 27.3 1.0 C A:GLU497 4.2 23.4 0.5 CA A:TRP499 4.2 21.7 1.0 HG22 A:VAL500 4.2 27.3 1.0 O A:GLU497 4.3 24.7 0.5 CG2 A:VAL500 4.4 22.7 1.0 CA A:ARG496 4.5 24.8 1.0 HA A:TRP499 4.5 26.0 1.0 N A:GLU497 4.6 22.2 0.5 O A:GLU497 4.6 24.7 0.5 N A:GLU497 4.6 22.4 0.5 C A:VAL500 4.6 23.1 1.0 HB3 A:GLU501 4.6 29.9 0.4 C A:PHE495 4.7 22.3 1.0 HB3 A:GLU501 4.7 27.8 0.6 HB2 A:GLU501 4.7 29.9 0.4 HB2 A:GLU501 4.8 27.8 0.6 CA A:GLU497 4.8 23.6 0.5 HA A:GLU497 4.9 28.3 0.5 CA A:GLU497 4.9 23.6 0.5 HA A:VAL500 4.9 26.4 1.0 HG11 A:VAL500 4.9 30.2 1.0 CG1 A:VAL500 5.0 25.1 1.0 HA A:GLU497 5.0 28.3 0.5

Chlorine binding site 6 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:66.8 occ:1.00 O A:HOH789 3.0 40.4 0.5 O B:HOH817 3.0 46.2 0.5 HA A:HIS584 3.2 45.4 1.0 HH11 B:ARG438 3.6 51.8 0.5 HH12 B:ARG438 3.7 51.8 0.5 O A:HIS584 3.9 31.8 1.0 NH1 B:ARG438 4.0 43.2 0.5 CA A:HIS584 4.1 37.9 1.0 O A:LEU583 4.2 32.6 1.0 C A:HIS584 4.2 36.7 1.0 C A:LEU583 4.8 39.2 1.0 HD2 B:ARG438 4.8 58.9 0.5 N A:HIS584 4.8 31.1 1.0 O A:ARG582 4.9 27.5 1.0 HD2 B:ARG438 4.9 59.5 0.5 HB3 A:HIS584 4.9 46.9 1.0 O A:HOH794 5.0 40.9 1.0

Chlorine binding site 7 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl611 b:34.8 occ:0.50 CL B:CL611 0.0 34.8 0.5 CL B:CL611 2.2 58.2 0.5 HG1 B:THR512 2.3 41.6 1.0 H B:TRP561 2.4 39.6 1.0 HD1 B:TRP561 2.5 28.8 1.0 OG1 B:THR512 2.8 34.6 1.0 HA B:GLN560 3.0 37.3 1.0 HB3 B:ALA510 3.1 30.1 1.0 N B:TRP561 3.2 33.0 1.0 CD1 B:TRP561 3.3 24.0 1.0 HB2 B:TRP561 3.4 38.7 1.0 N B:THR512 3.6 26.7 1.0 HA B:THR512 3.6 37.6 1.0 H B:THR512 3.6 32.1 1.0 HG3 B:GLN560 3.8 53.4 1.0 HB2 B:ALA510 3.8 30.1 1.0 CB B:ALA510 3.9 25.0 1.0 CA B:GLN560 3.9 31.1 1.0 C B:THR511 3.9 26.0 1.0 CB B:THR512 3.9 30.8 1.0 CA B:THR512 3.9 31.4 1.0 C B:ALA510 3.9 36.5 1.0 CB B:TRP561 3.9 32.3 1.0 N B:THR511 4.0 29.2 1.0 O B:ARG559 4.0 31.1 1.0 CG B:TRP561 4.0 23.0 1.0 C B:GLN560 4.0 26.1 1.0 O B:ALA510 4.1 31.1 1.0 O B:HOH789 4.1 43.5 1.0 CA B:TRP561 4.1 31.8 1.0 HA B:THR511 4.2 32.5 1.0 H B:THR511 4.2 35.0 1.0 O B:TRP561 4.2 30.6 1.0 CA B:THR511 4.3 27.1 1.0 HG2 B:GLN560 4.3 53.4 1.0 HB B:THR512 4.4 36.9 1.0 CG B:GLN560 4.4 44.5 1.0 NE1 B:TRP561 4.4 26.4 1.0 O B:THR511 4.4 23.9 1.0 CA B:ALA510 4.5 24.1 1.0 HE1 B:TRP561 4.6 31.7 1.0 HB1 B:ALA510 4.6 30.1 1.0 C B:TRP561 4.7 33.8 1.0 CB B:GLN560 4.7 36.5 1.0 O B:HOH767 4.7 40.0 1.0 C B:ARG559 4.8 30.5 1.0 HA B:ALA510 4.8 28.9 1.0 HB3 B:TRP561 4.9 38.7 1.0 N B:GLN560 4.9 32.1 1.0 HA B:TRP561 5.0 38.1 1.0 HB2 B:GLN560 5.0 43.8 1.0

Chlorine binding site 8 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl611 b:58.2 occ:0.50 CL B:CL611 0.0 58.2 0.5 CL B:CL611 2.2 34.8 0.5 O B:TRP561 3.0 30.6 1.0 H B:TRP561 3.1 39.6 1.0 HG3 B:GLN560 3.4 53.4 1.0 HB2 B:TRP561 3.4 38.7 1.0 HB3 B:ALA510 3.6 30.1 1.0 N B:TRP561 3.6 33.0 1.0 HG2 B:GLN560 3.6 53.4 1.0 HB2 B:ALA510 3.7 30.1 1.0 HG1 B:THR512 3.7 41.6 1.0 HD13 B:ILE566 3.9 35.0 1.0 C B:TRP561 3.9 33.8 1.0 CG B:GLN560 4.0 44.5 1.0 HA B:GLN560 4.0 37.3 1.0 HD1 B:TRP561 4.1 28.8 1.0 CB B:ALA510 4.1 25.0 1.0 CA B:TRP561 4.1 31.8 1.0 OG1 B:THR512 4.2 34.6 1.0 CB B:TRP561 4.2 32.3 1.0 C B:GLN560 4.4 26.1 1.0 CA B:GLN560 4.6 31.1 1.0 HB1 B:ALA510 4.6 30.1 1.0 CD1 B:TRP561 4.8 24.0 1.0 CD1 B:ILE566 4.8 29.2 1.0 HE21 B:GLN560 4.9 72.7 1.0 CB B:GLN560 4.9 36.5 1.0 HB3 B:TRP561 4.9 38.7 1.0 O B:ALA510 4.9 31.1 1.0 HD11 B:ILE566 4.9 35.0 1.0 CG B:TRP561 4.9 23.0 1.0 O B:HOH767 5.0 40.0 1.0

Chlorine binding site 9 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl612 b:81.1 occ:1.00 O B:HOH709 2.7 41.9 1.0 MG B:MG608 2.8 35.8 1.0 HE21 B:GLN505 3.2 60.6 1.0 HG2 B:GLN505 3.3 41.8 1.0 OE2 B:GLU501 3.7 33.1 1.0 NE2 B:GLN505 3.8 50.5 1.0 HB3 B:ARG504 3.8 32.4 1.0 HE B:ARG504 3.8 56.0 1.0 HH11 B:ARG504 3.9 62.6 1.0 HG3 B:GLN505 3.9 41.8 1.0 CG B:GLN505 4.0 34.9 1.0 OD2 B:ASP544 4.1 30.1 0.4 NE B:ARG504 4.1 46.7 1.0 NH1 B:ARG504 4.2 52.2 1.0 CD B:GLN505 4.3 51.1 1.0 HB2 B:ARG504 4.3 32.4 1.0 CZ B:ARG504 4.3 54.2 1.0 HE22 B:GLN505 4.4 60.6 1.0 OD1 B:ASP544 4.4 30.8 0.6 OD2 B:ASP544 4.4 29.7 0.6 OD1 B:ASP544 4.5 33.6 0.4 CD B:GLU501 4.5 29.6 1.0 CB B:ARG504 4.5 27.0 1.0 CG B:ASP544 4.6 35.8 0.4 HH12 B:ARG504 4.7 62.6 1.0 HD3 B:ARG504 4.7 49.7 1.0 OE1 B:GLU501 4.8 28.1 1.0 CG B:ASP544 4.8 38.0 0.6 CD B:ARG504 4.9 41.4 1.0 HA B:GLN505 5.0 26.7 1.0

Chlorine binding site 10 out of 12 in the Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Photoconvertible Crystals of Pixj From Thermosynechococcus Elongatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl613 b:73.1 occ:1.00 O B:HOH749 3.2 28.8 1.0 HB3 B:ASP466 3.4 35.3 0.6 HB3 B:ASP466 3.6 33.2 0.4 HA B:ASP466 3.7 33.2 0.4 HB1 B:ALA464 3.8 25.8 1.0 HB B:THR472 3.8 28.7 1.0 HH22 B:ARG440 3.8 48.3 0.5 O B:ALA464 3.9 19.8 1.0 O B:PHE465 3.9 25.8 1.0 HA B:ASP466 3.9 31.8 0.6 C B:PHE465 3.9 23.4 1.0 N B:ASP466 3.9 24.7 0.4 N B:ASP466 3.9 24.4 0.6 HB2 B:ALA464 4.0 25.8 1.0 HG1 B:THR472 4.0 34.5 1.0 O B:HOH837 4.1 37.9 0.5 H B:ASP466 4.2 29.7 0.4 CA B:ASP466 4.2 27.7 0.4 H B:ASP466 4.2 29.3 0.6 CB B:ASP466 4.2 29.4 0.6 CA B:ASP466 4.2 26.5 0.6 C B:ALA464 4.3 18.2 1.0 CB B:ALA464 4.3 21.5 1.0 CB B:ASP466 4.3 27.7 0.4 OG1 B:THR472 4.4 28.8 1.0 HB2 B:ASP466 4.5 35.3 0.6 CB B:THR472 4.6 23.9 1.0 HH12 B:ARG440 4.6 51.9 0.5 N B:PHE465 4.6 19.2 1.0 NH2 B:ARG440 4.6 40.2 0.5 HG12 B:VAL474 4.6 29.0 1.0 CA B:PHE465 4.7 20.6 1.0 HB2 B:ASP466 4.7 33.2 0.4 H B:THR472 4.7 28.8 1.0 HA B:PHE465 4.8 24.8 1.0 O B:HOH744 4.9 31.4 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