Chlorine in PDB 7d1t: Cryo-Em Structure of Psii at 1.95 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution:
1.10.3.9;

The structure of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution also contains other interesting chemical elements:

Magnesium	(Mg)	72 atoms
Iron	(Fe)	6 atoms
Manganese	(Mn)	8 atoms
Calcium	(Ca)	2 atoms

The binding sites of Chlorine atom in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution (pdb code 7d1t). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution, PDB code: 7d1t:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:17.3 occ:1.00 NZ D:LYS317 3.0 11.1 1.0 O D:HOH593 3.0 13.3 1.0 N A:GLU333 3.2 12.4 1.0 O A:HOH529 3.3 12.9 1.0 OD1 A:ASN181 3.5 6.4 1.0 CA A:HIS332 3.6 12.1 1.0 CB A:HIS332 3.7 12.0 1.0 CE D:LYS317 3.8 11.1 1.0 C A:HIS332 3.9 12.2 1.0 O A:HOH580 4.1 13.8 1.0 CD2 D:LEU321 4.1 10.1 1.0 ND2 A:ASN181 4.2 6.5 1.0 CG A:GLU333 4.2 12.7 1.0 CA A:GLU333 4.2 12.6 1.0 CB D:LYS317 4.2 10.9 1.0 CG2 A:VAL185 4.3 6.9 1.0 CG A:ASN181 4.3 6.4 1.0 CD1 D:LEU321 4.3 10.1 1.0 CG D:LEU321 4.4 10.1 1.0 CG D:LYS317 4.7 11.0 1.0 CG A:HIS332 4.8 11.9 1.0 O D:LYS317 4.8 10.7 1.0 CB A:GLU333 4.8 12.6 1.0 CD D:LYS317 4.9 11.1 1.0 N A:HIS332 4.9 12.0 1.0 O A:HOH620 4.9 14.7 1.0 O A:MET331 4.9 12.0 1.0 O A:HOH534 4.9 30.0 1.0

Chlorine binding site 2 out of 4 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:14.9 occ:1.00 O C:HOH757 2.7 13.3 1.0 N C:GLU354 3.0 13.2 1.0 O A:HOH547 3.2 17.3 1.0 N A:ASN338 3.2 14.4 1.0 O C:HOH766 3.4 16.7 1.0 CA A:HIS337 3.6 14.1 1.0 CA C:GLY353 3.6 13.4 1.0 CB C:GLU354 3.8 13.2 1.0 C C:GLY353 3.8 13.3 1.0 O A:ALA336 3.9 13.9 1.0 C A:HIS337 3.9 14.2 1.0 CD2 A:PHE339 3.9 14.7 1.0 CA C:GLU354 4.0 13.2 1.0 N A:PHE339 4.0 14.7 1.0 CA A:ASN338 4.1 14.6 1.0 CB A:ASN338 4.2 14.6 1.0 CG C:GLU354 4.2 13.3 1.0 CB A:HIS337 4.3 14.1 1.0 C A:ASN338 4.5 14.7 1.0 CE2 A:PHE339 4.6 14.7 1.0 N A:HIS337 4.7 14.0 1.0 CG A:PHE339 4.7 14.7 1.0 C A:ALA336 4.7 13.8 1.0 CB A:PHE339 4.7 14.8 1.0 O C:HOH676 4.7 14.1 1.0 CD2 A:HIS337 4.8 14.2 1.0 N C:THR355 4.8 13.0 1.0 O A:HOH553 4.8 14.8 1.0 CG A:HIS337 4.9 14.2 1.0 C C:GLU354 4.9 13.1 1.0 CG A:ASN338 4.9 14.6 1.0 CA A:PHE339 5.0 14.8 1.0 O C:GLY352 5.0 13.7 1.0 N C:GLY353 5.0 13.6 1.0

Chlorine binding site 3 out of 4 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl403 b:17.3 occ:1.00 NZ d:LYS317 3.0 11.1 1.0 O d:HOH592 3.0 13.3 1.0 N a:GLU333 3.2 12.4 1.0 O a:HOH529 3.3 12.9 1.0 OD1 a:ASN181 3.5 6.4 1.0 CA a:HIS332 3.6 12.1 1.0 CB a:HIS332 3.7 12.0 1.0 CE d:LYS317 3.8 11.1 1.0 C a:HIS332 3.9 12.2 1.0 O a:HOH580 4.1 13.8 1.0 CD2 d:LEU321 4.1 10.1 1.0 ND2 a:ASN181 4.2 6.5 1.0 CG a:GLU333 4.2 12.7 1.0 CA a:GLU333 4.2 12.6 1.0 CB d:LYS317 4.2 10.9 1.0 CG2 a:VAL185 4.3 6.9 1.0 CG a:ASN181 4.3 6.4 1.0 CD1 d:LEU321 4.3 10.1 1.0 CG d:LEU321 4.4 10.1 1.0 CG d:LYS317 4.7 11.0 1.0 CG a:HIS332 4.8 11.9 1.0 O d:LYS317 4.8 10.7 1.0 CB a:GLU333 4.8 12.6 1.0 CD d:LYS317 4.9 11.1 1.0 N a:HIS332 4.9 12.0 1.0 O a:HOH620 4.9 14.7 1.0 O a:MET331 4.9 12.0 1.0 O a:HOH534 4.9 30.0 1.0

Chlorine binding site 4 out of 4 in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cryo-Em Structure of Psii at 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl404 b:14.9 occ:1.00 O c:HOH757 2.7 13.3 1.0 N c:GLU354 3.0 13.2 1.0 O a:HOH547 3.2 17.3 1.0 N a:ASN338 3.2 14.4 1.0 O c:HOH766 3.4 16.7 1.0 CA a:HIS337 3.6 14.1 1.0 CA c:GLY353 3.6 13.4 1.0 CB c:GLU354 3.8 13.2 1.0 C c:GLY353 3.8 13.3 1.0 O a:ALA336 3.9 13.9 1.0 C a:HIS337 3.9 14.2 1.0 CD2 a:PHE339 3.9 14.7 1.0 CA c:GLU354 4.0 13.2 1.0 N a:PHE339 4.0 14.7 1.0 CA a:ASN338 4.1 14.6 1.0 CB a:ASN338 4.2 14.6 1.0 CG c:GLU354 4.2 13.3 1.0 CB a:HIS337 4.3 14.1 1.0 C a:ASN338 4.5 14.7 1.0 CE2 a:PHE339 4.6 14.7 1.0 CG a:PHE339 4.7 14.7 1.0 N a:HIS337 4.7 14.0 1.0 C a:ALA336 4.7 13.8 1.0 CB a:PHE339 4.7 14.8 1.0 O c:HOH676 4.7 14.1 1.0 CD2 a:HIS337 4.8 14.2 1.0 N c:THR355 4.8 13.0 1.0 O a:HOH553 4.8 14.8 1.0 CG a:HIS337 4.9 14.2 1.0 C c:GLU354 4.9 13.1 1.0 CG a:ASN338 4.9 14.6 1.0 CA a:PHE339 5.0 14.8 1.0 O c:GLY352 5.0 13.7 1.0 N c:GLY353 5.0 13.6 1.0

K.Kato, N.Miyazaki, T.Hamaguchi, Y.Nakajima, F.Akita, K.Yonekura, J.R.Shen. High-Resolution Cryo-Em Structure of Photosystem II Reveals Damage From High-Dose Electron Beams Commun Biol 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-01919-3