Calcium in PDB 7d1u: Cryo-Em Structure of Psii at 2.08 Angstrom Resolution

All present enzymatic activity of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution:
1.10.3.9;

The structure of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution also contains other interesting chemical elements:

Chlorine	(Cl)	4 atoms
Magnesium	(Mg)	72 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution (pdb code 7d1u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution, PDB code: 7d1u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:13.1 occ:1.00 CA1 A:OEX401 0.0 13.1 1.0 OD1 A:ASP170 2.4 9.5 1.0 O A:HOH625 2.6 12.4 1.0 O5 A:OEX401 2.6 13.1 1.0 O A:ALA344 2.6 15.4 1.0 O2 A:OEX401 2.7 13.1 1.0 O1 A:OEX401 2.7 13.1 1.0 O A:HOH537 2.7 11.9 1.0 CG A:ASP170 3.1 9.5 1.0 OD2 A:ASP170 3.2 9.5 1.0 MN2 A:OEX401 3.4 13.1 1.0 MN3 A:OEX401 3.4 13.1 1.0 OE1 A:GLU189 3.5 9.8 1.0 MN1 A:OEX401 3.6 13.1 1.0 C A:ALA344 3.6 15.5 1.0 MN4 A:OEX401 3.8 13.2 1.0 O4 A:OEX401 3.8 13.1 1.0 OXT A:ALA344 3.8 15.5 1.0 O3 A:OEX401 4.0 13.1 1.0 CD A:GLU189 4.2 9.8 1.0 OE2 A:GLU189 4.3 9.9 1.0 CB A:ASP170 4.4 9.4 1.0 NH1 C:ARG357 4.4 13.5 1.0 OE1 A:GLN165 4.5 9.9 1.0 NH2 C:ARG357 4.5 13.5 1.0 OH A:TYR161 4.6 8.9 1.0 O A:HOH512 4.6 9.8 1.0 O A:HOH554 4.7 12.5 1.0 O A:HOH565 4.8 17.1 1.0 CZ C:ARG357 4.9 13.5 1.0 CA A:ALA344 4.9 15.5 1.0 O A:HOH560 4.9 15.0 1.0 O A:HOH559 4.9 11.1 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Psii at 2.08 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Psii at 2.08 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ a:Ca401 b:13.1 occ:1.00 CA1 a:OEX401 0.0 13.1 1.0 OD1 a:ASP170 2.4 9.5 1.0 O a:HOH624 2.6 12.2 1.0 O5 a:OEX401 2.6 13.1 1.0 O a:ALA344 2.6 15.3 1.0 O2 a:OEX401 2.7 13.1 1.0 O1 a:OEX401 2.7 13.1 1.0 O a:HOH537 2.7 12.0 1.0 CG a:ASP170 3.1 9.5 1.0 OD2 a:ASP170 3.2 9.5 1.0 MN2 a:OEX401 3.4 13.1 1.0 MN3 a:OEX401 3.4 13.1 1.0 OE1 a:GLU189 3.5 9.8 1.0 MN1 a:OEX401 3.6 13.1 1.0 C a:ALA344 3.6 15.4 1.0 MN4 a:OEX401 3.8 13.2 1.0 O4 a:OEX401 3.8 13.1 1.0 OXT a:ALA344 3.8 15.4 1.0 O3 a:OEX401 4.0 13.1 1.0 CD a:GLU189 4.2 9.7 1.0 OE2 a:GLU189 4.3 9.8 1.0 CB a:ASP170 4.4 9.4 1.0 NH1 c:ARG357 4.4 13.6 1.0 OE1 a:GLN165 4.5 9.9 1.0 NH2 c:ARG357 4.5 13.5 1.0 OH a:TYR161 4.6 8.9 1.0 O a:HOH512 4.6 9.7 1.0 O a:HOH554 4.7 12.4 1.0 O a:HOH564 4.8 17.0 1.0 CZ c:ARG357 4.9 13.5 1.0 CA a:ALA344 4.9 15.4 1.0 O a:HOH561 4.9 14.9 1.0 O a:HOH559 4.9 11.1 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