Chlorine in PDB 7cjj: Photosystem II Structure in the S2 State

All present enzymatic activity of Photosystem II Structure in the S2 State:
1.10.3.9;

The structure of Photosystem II Structure in the S2 State, PDB code: 7cjj was solved by H.Li, J.-R.Shen, M.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	125.75, 231.63, 288.4, 90, 90, 90
R / Rfree (%)	16.8 / 21.8

The structure of Photosystem II Structure in the S2 State also contains other interesting chemical elements:

Calcium	(Ca)	11 atoms
Iron	(Fe)	8 atoms
Manganese	(Mn)	16 atoms
Magnesium	(Mg)	72 atoms

The binding sites of Chlorine atom in the Photosystem II Structure in the S2 State (pdb code 7cjj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Photosystem II Structure in the S2 State, PDB code: 7cjj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Photosystem II Structure in the S2 State within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:39.8 occ:1.00 NZ D:LYS317 3.1 38.7 1.0 O A:HOH550 3.2 43.1 1.0 O D:HOH543 3.3 38.7 1.0 ND2 A:ASN181 3.3 35.3 1.0 N A:GLU333 3.4 36.5 0.7 N A:GLU333 3.4 36.8 0.3 CE D:LYS317 3.8 35.4 1.0 CB A:HIS332 3.9 37.6 1.0 CA A:HIS332 3.9 35.7 1.0 CG A:GLU333 3.9 42.3 0.7 OD1 A:ASN181 4.0 42.1 1.0 CG A:GLU333 4.0 41.9 0.3 CG A:ASN181 4.1 36.9 1.0 C A:HIS332 4.1 38.1 1.0 CG2 A:VAL185 4.2 35.5 1.0 CA A:GLU333 4.3 36.8 0.7 CA A:GLU333 4.3 37.2 0.3 O D:HOH542 4.3 40.8 1.0 CD1 D:LEU321 4.4 37.9 1.0 O A:HOH593 4.5 39.6 1.0 CB D:LYS317 4.6 35.0 1.0 CD2 D:LEU321 4.6 41.0 1.0 CB A:GLU333 4.7 37.5 0.7 CG D:LYS317 4.8 34.3 1.0 CG D:LEU321 4.8 41.2 1.0 CB A:GLU333 4.8 38.5 0.3 CG A:HIS332 4.8 41.0 1.0 CD D:LYS317 4.9 35.8 1.0 CD A:GLU333 4.9 46.0 0.7 O D:LYS317 4.9 43.0 1.0 CD A:GLU333 5.0 45.8 0.3 CD2 A:HIS332 5.0 37.4 1.0 OE2 A:GLU333 5.0 48.2 0.3 OE2 A:GLU333 5.0 48.9 0.7

Chlorine binding site 2 out of 4 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Photosystem II Structure in the S2 State within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl501 b:43.8 occ:1.00 O C:HOH684 3.0 39.0 1.0 N A:ASN338 3.2 42.3 1.0 O A:HOH606 3.2 49.4 1.0 N C:GLU354 3.3 39.6 0.3 N C:GLU354 3.4 39.1 0.7 N A:PHE339 3.6 43.6 1.0 CA A:HIS337 3.7 44.0 1.0 CD2 A:PHE339 3.8 43.6 1.0 CA C:GLY353 3.8 38.4 1.0 C A:HIS337 3.9 45.3 1.0 C C:GLY353 4.1 44.5 1.0 CA A:ASN338 4.1 43.0 1.0 CB C:GLU354 4.1 39.9 0.3 CB A:HIS337 4.2 43.7 1.0 O A:ALA336 4.2 41.4 1.0 CB C:GLU354 4.2 37.3 0.7 CB A:PHE339 4.3 42.6 1.0 C A:ASN338 4.3 45.0 1.0 CA C:GLU354 4.3 38.8 0.3 O C:HOH695 4.4 39.5 1.0 CA C:GLU354 4.4 37.8 0.7 CB A:ASN338 4.4 43.9 1.0 CG A:PHE339 4.4 39.7 1.0 CA A:PHE339 4.4 46.0 1.0 O A:PHE339 4.5 42.7 1.0 O C:HOH742 4.5 44.9 1.0 CE2 A:PHE339 4.6 39.9 1.0 CD2 A:HIS337 4.8 40.4 1.0 N A:HIS337 4.8 41.2 1.0 N C:THR355 4.8 38.5 1.0 CG A:HIS337 4.9 41.8 1.0 O C:GLY352 4.9 39.9 1.0 C A:PHE339 4.9 48.0 1.0 CG A:ASN338 5.0 46.5 1.0 C A:ALA336 5.0 44.2 1.0

Chlorine binding site 3 out of 4 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Photosystem II Structure in the S2 State within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl402 b:46.1 occ:1.00 O d:HOH581 3.1 51.0 1.0 NZ d:LYS317 3.2 45.1 1.0 O a:HOH511 3.3 47.4 1.0 ND2 a:ASN181 3.3 37.2 1.0 N a:GLU333 3.5 39.9 0.7 N a:GLU333 3.5 41.1 0.3 CA a:HIS332 3.8 42.0 1.0 CE d:LYS317 3.8 45.5 1.0 CB a:HIS332 3.8 39.3 1.0 CG a:GLU333 3.9 45.0 0.7 CG a:GLU333 4.0 45.4 0.3 C a:HIS332 4.1 41.1 1.0 CG2 a:VAL185 4.2 40.1 1.0 CG a:ASN181 4.2 39.9 1.0 OD1 a:ASN181 4.2 39.4 1.0 CD2 d:LEU321 4.3 38.4 1.0 CD1 d:LEU321 4.4 41.6 1.0 CA a:GLU333 4.4 43.4 0.7 O a:HOH607 4.4 54.6 1.0 CA a:GLU333 4.4 43.5 0.3 O a:HOH529 4.4 40.1 1.0 CB d:LYS317 4.6 40.0 1.0 CG d:LEU321 4.6 46.4 1.0 CG a:HIS332 4.8 41.9 1.0 CB a:GLU333 4.8 45.6 0.7 CG d:LYS317 4.8 42.5 1.0 CB a:GLU333 4.8 45.3 0.3 CD a:GLU333 4.9 48.5 0.7 CD d:LYS317 4.9 47.5 1.0 OE2 a:GLU333 4.9 48.7 0.3 OE2 a:GLU333 5.0 49.8 0.7 CD2 a:HIS332 5.0 44.2 1.0 CD a:GLU333 5.0 47.9 0.3

Chlorine binding site 4 out of 4 in the Photosystem II Structure in the S2 State


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Photosystem II Structure in the S2 State within 5.0Å range: probe atom residue distance (Å) B Occ c:Cl501 b:46.3 occ:1.00 O c:HOH670 3.0 46.1 1.0 O a:HOH620 3.0 50.1 1.0 N a:ASN338 3.2 47.6 1.0 N c:GLU354 3.3 48.6 0.7 N c:GLU354 3.3 48.0 0.3 N a:PHE339 3.6 44.8 1.0 CA a:HIS337 3.7 42.5 1.0 CD2 a:PHE339 3.7 50.0 1.0 CA c:GLY353 3.7 47.3 1.0 C a:HIS337 3.9 48.2 1.0 C c:GLY353 4.0 47.1 1.0 CA a:ASN338 4.1 44.1 1.0 O a:ALA336 4.2 54.0 1.0 CB a:HIS337 4.2 42.5 1.0 CB c:GLU354 4.2 45.2 0.3 CB c:GLU354 4.2 42.7 0.7 CB a:PHE339 4.3 45.9 1.0 CG a:PHE339 4.3 51.6 1.0 C a:ASN338 4.3 46.1 1.0 CB a:ASN338 4.3 50.7 1.0 CA c:GLU354 4.4 47.8 0.3 CA c:GLU354 4.4 49.1 0.7 CE2 a:PHE339 4.4 54.0 1.0 CA a:PHE339 4.5 51.1 1.0 O c:HOH682 4.5 45.8 1.0 O a:PHE339 4.6 51.6 1.0 O c:HOH747 4.6 53.9 1.0 N a:HIS337 4.8 46.6 1.0 CG c:GLU354 4.8 45.8 0.3 NE2 c:GLN313 4.9 45.8 1.0 CD2 a:HIS337 4.9 46.5 1.0 N c:THR355 4.9 44.0 1.0 C a:ALA336 4.9 46.0 1.0 CG a:HIS337 4.9 43.0 1.0 O c:GLY352 4.9 45.2 1.0 C a:PHE339 5.0 52.3 1.0 CG a:ASN338 5.0 52.5 1.0

H.Li, Y.Nakajima, T.Nomura, M.Sugahara, S.Yonekura, S.K.Chan, T.Nakane, T.Yamane, Y.Umena, M.Suzuki, T.Masuda, T.Motomura, H.Naitow, Y.Matsuura, T.Kimura, K.Tono, S.Owada, Y.Joti, R.Tanaka, E.Nango, F.Akita, M.Kubo, S.Iwata, J.-R.Shen, M.Suga. Capturing Structural Changes of the S1 to S2 Transition of Photosystem II Using Time-Resolved Serial Femtosecond Crystallography Iucrj 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521002177