Calcium 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
Chlorine	(Cl)	4 atoms
Iron	(Fe)	6 atoms
Manganese	(Mn)	8 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Psii at 1.95 Angstrom Resolution, PDB code: 7d1t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Psii at 1.95 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 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.3 occ:0.87 CA1 A:OEX401 0.0 11.3 0.9 O2 A:OEX401 2.4 11.5 0.9 OD1 A:ASP170 2.4 8.4 1.0 O1 A:OEX401 2.6 11.5 0.9 O5 A:OEX401 2.7 11.4 0.9 O A:ALA344 2.8 16.0 0.5 O A:HOH629 2.8 11.8 1.0 O A:HOH509 2.9 11.8 1.0 CG A:ASP170 3.2 8.4 1.0 MN3 A:OEX401 3.3 11.5 0.9 MN2 A:OEX401 3.5 11.7 0.9 OD2 A:ASP170 3.5 8.4 1.0 MN1 A:OEX401 3.5 11.4 0.9 C A:ALA344 3.7 16.1 0.5 MN4 A:OEX401 3.7 11.3 0.9 OE1 A:GLU189 3.8 8.5 1.0 OXT A:ALA344 3.8 16.0 0.5 O4 A:OEX401 3.9 11.5 0.9 NH1 C:ARG357 4.3 12.9 1.0 O3 A:OEX401 4.3 11.5 0.9 NH2 C:ARG357 4.4 12.8 1.0 CB A:ASP170 4.4 8.3 1.0 CD A:GLU189 4.4 8.5 1.0 OE1 A:GLN165 4.4 8.9 1.0 OE2 A:GLU189 4.5 8.6 1.0 O A:HOH563 4.5 13.1 1.0 O A:HOH523 4.7 8.6 1.0 OH A:TYR161 4.7 7.7 1.0 CZ C:ARG357 4.8 12.8 1.0 O A:HOH628 4.9 11.0 1.0 OE2 C:GLU354 5.0 13.3 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Psii at 1.95 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 1.95 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ a:Ca401 b:11.3 occ:0.87 CA1 a:OEX401 0.0 11.3 0.9 O2 a:OEX401 2.4 11.5 0.9 OD1 a:ASP170 2.4 8.4 1.0 O1 a:OEX401 2.6 11.5 0.9 O5 a:OEX401 2.7 11.4 0.9 O a:ALA344 2.8 16.0 0.5 O a:HOH629 2.8 11.8 1.0 O a:HOH509 2.9 11.8 1.0 CG a:ASP170 3.2 8.4 1.0 MN3 a:OEX401 3.3 11.5 0.9 MN2 a:OEX401 3.5 11.7 0.9 OD2 a:ASP170 3.5 8.4 1.0 MN1 a:OEX401 3.5 11.4 0.9 C a:ALA344 3.7 16.1 0.5 MN4 a:OEX401 3.7 11.3 0.9 OE1 a:GLU189 3.8 8.5 1.0 OXT a:ALA344 3.8 16.0 0.5 O4 a:OEX401 3.9 11.5 0.9 NH1 c:ARG357 4.3 12.9 1.0 O3 a:OEX401 4.3 11.5 0.9 NH2 c:ARG357 4.4 12.8 1.0 CB a:ASP170 4.4 8.3 1.0 CD a:GLU189 4.4 8.5 1.0 OE1 a:GLN165 4.4 8.9 1.0 OE2 a:GLU189 4.5 8.6 1.0 O a:HOH563 4.5 13.1 1.0 O a:HOH523 4.7 8.6 1.0 OH a:TYR161 4.7 7.7 1.0 CZ c:ARG357 4.8 12.8 1.0 O a:HOH628 4.9 11.0 1.0 OE2 c:GLU354 5.0 13.3 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