Chlorine in PDB 7yq7: Crystal Structure of Photosystem II Expressing PSBA3 Gene Only

All present enzymatic activity of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only:
1.10.3.9;

The structure of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only, PDB code: 7yq7 was solved by Y.Nakajima, M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.804, 228.456, 286.852, 90, 90, 90
R / Rfree (%)	14.7 / 17.7

The structure of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only also contains other interesting chemical elements:

Iron	(Fe)	6 atoms
Magnesium	(Mg)	72 atoms
Manganese	(Mn)	8 atoms
Calcium	(Ca)	7 atoms

The binding sites of Chlorine atom in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only (pdb code 7yq7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only, PDB code: 7yq7:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:27.9 occ:1.00 O D:HOH598 3.0 26.2 1.0 NZ D:LYS317 3.3 28.6 1.0 ND2 A:ASN181 3.3 22.6 1.0 O A:HOH576 3.4 30.8 1.0 N A:GLU333 3.4 25.9 1.0 CB A:HIS332 3.7 21.9 1.0 CA A:HIS332 3.7 25.3 1.0 CE D:LYS317 4.1 23.8 1.0 C A:HIS332 4.1 27.1 1.0 CG A:GLU333 4.1 27.1 1.0 OD1 A:ASN181 4.2 26.2 1.0 CG A:ASN181 4.2 24.7 1.0 CG2 A:VAL185 4.2 26.7 1.0 CD2 D:LEU321 4.3 22.4 1.0 CA A:GLU333 4.4 26.1 1.0 CB D:LYS317 4.4 25.1 1.0 CD1 D:LEU321 4.4 24.2 1.0 O A:HOH544 4.5 27.9 1.0 O A:HOH559 4.5 24.9 1.0 CG D:LEU321 4.6 25.9 1.0 CG A:HIS332 4.7 24.3 1.0 CG D:LYS317 4.8 19.8 1.0 CB A:GLU333 4.8 26.6 1.0 O D:LYS317 4.9 23.2 1.0 OE2 A:GLU333 4.9 28.5 1.0 CD A:GLU333 5.0 29.7 1.0 O D:HOH568 5.0 35.2 1.0 CD2 A:HIS332 5.0 25.3 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:28.1 occ:1.00 O C:HOH743 3.0 28.6 1.0 O A:HOH558 3.1 30.5 1.0 N A:ASN338 3.2 24.4 1.0 N C:GLU354 3.4 25.1 1.0 CD2 A:PHE339 3.7 28.8 1.0 CA A:HIS337 3.7 27.4 1.0 N A:PHE339 3.7 27.2 1.0 CA C:GLY353 3.8 26.2 1.0 C A:HIS337 4.0 30.2 1.0 C C:GLY353 4.1 30.1 1.0 CA A:ASN338 4.1 24.3 1.0 O A:ALA336 4.2 26.8 1.0 CB C:GLU354 4.2 28.8 1.0 CB A:HIS337 4.3 22.5 1.0 O C:HOH719 4.3 28.7 1.0 CA C:GLU354 4.4 25.7 1.0 CB A:ASN338 4.4 31.6 1.0 CG A:PHE339 4.4 30.0 1.0 CB A:PHE339 4.4 30.0 1.0 CE2 A:PHE339 4.4 30.1 1.0 C A:ASN338 4.4 27.6 1.0 CA A:PHE339 4.6 28.9 1.0 O C:HOH783 4.6 28.9 1.0 CG C:GLU354 4.7 30.1 1.0 O A:PHE339 4.7 30.1 1.0 N A:HIS337 4.8 24.9 1.0 N C:THR355 4.9 22.8 1.0 O C:GLY352 4.9 32.0 1.0 CD2 A:HIS337 5.0 25.9 1.0 C A:ALA336 5.0 28.6 1.0 CG A:ASN338 5.0 32.2 1.0 CG A:HIS337 5.0 28.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl406 b:31.7 occ:1.00 O d:HOH576 3.1 30.9 1.0 NZ d:LYS317 3.2 27.8 1.0 O a:HOH590 3.3 33.1 1.0 ND2 a:ASN181 3.3 29.2 1.0 N a:GLU333 3.4 25.9 1.0 CB a:HIS332 3.7 26.0 1.0 CA a:HIS332 3.8 24.6 1.0 CG a:GLU333 4.0 29.7 1.0 CE d:LYS317 4.0 28.2 1.0 C a:HIS332 4.1 29.8 1.0 OD1 a:ASN181 4.1 26.3 1.0 CG a:ASN181 4.2 30.8 1.0 CG2 a:VAL185 4.3 27.6 1.0 CD2 d:LEU321 4.3 26.0 1.0 O d:HOH529 4.3 26.9 1.0 CA a:GLU333 4.4 27.4 1.0 CB d:LYS317 4.4 30.5 1.0 CD1 d:LEU321 4.5 23.1 1.0 O a:HOH541 4.5 29.7 1.0 CG d:LEU321 4.6 28.1 1.0 CG a:HIS332 4.7 29.5 1.0 CG d:LYS317 4.7 26.4 1.0 CB a:GLU333 4.8 29.1 1.0 OE2 a:GLU333 4.8 30.1 1.0 CD a:GLU333 4.9 31.1 1.0 O d:LYS317 4.9 26.6 1.0 O d:HOH563 4.9 40.6 1.0 CD2 a:HIS332 5.0 26.9 1.0 CD d:LYS317 5.0 27.0 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Photosystem II Expressing PSBA3 Gene Only


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Photosystem II Expressing PSBA3 Gene Only within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl407 b:33.0 occ:1.00 O c:HOH694 3.0 29.2 1.0 N a:ASN338 3.1 31.7 1.0 O a:HOH575 3.2 32.8 1.0 N c:GLU354 3.4 30.7 1.0 CD2 a:PHE339 3.7 36.4 1.0 CA a:HIS337 3.7 28.9 1.0 N a:PHE339 3.7 30.9 1.0 CA c:GLY353 3.8 29.1 1.0 C a:HIS337 3.9 31.8 1.0 C c:GLY353 4.1 30.4 1.0 CA a:ASN338 4.1 31.0 1.0 O a:ALA336 4.1 31.2 1.0 CB c:GLU354 4.2 36.8 1.0 CB a:HIS337 4.3 25.4 1.0 CB a:ASN338 4.3 34.2 1.0 CG a:PHE339 4.4 35.0 1.0 CE2 a:PHE339 4.4 37.4 1.0 CB a:PHE339 4.4 34.4 1.0 CA c:GLU354 4.4 30.7 1.0 C a:ASN338 4.4 36.0 1.0 O c:HOH700 4.4 31.4 1.0 CA a:PHE339 4.6 30.2 1.0 CG c:GLU354 4.7 35.1 1.0 O c:HOH787 4.7 31.1 1.0 O a:PHE339 4.7 32.9 1.0 N a:HIS337 4.8 26.5 1.0 C a:ALA336 4.9 31.8 1.0 O c:GLY352 4.9 34.0 1.0 CG a:ASN338 4.9 38.7 1.0 N c:THR355 4.9 28.8 1.0 CD2 a:HIS337 4.9 26.1 1.0 CG a:HIS337 5.0 28.3 1.0

Y.Nakajima, N.Ugai-Amo, N.Tone, A.Nakagawa, M.Iwai, M.Ikeuchi, M.Sugiura, M.Suga, J.R.Shen. Crystal Structures of Photosystem II From A Cyanobacterium Expressing Psba 2 in Comparison to Psba 3 Reveal Differences in the D1 Subunit. J.Biol.Chem. V. 298 02668 2022.
ISSN: ESSN 1083-351X
PubMed: 36334624
DOI: 10.1016/J.JBC.2022.102668