Chlorine in PDB 5h2f: Crystal Structure of the Psbm-Deletion Mutant of Photosystem II

All present enzymatic activity of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II:
1.10.3.9;

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f was solved by S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.954, 226.993, 285.886, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.6

The structure of Crystal Structure of the Psbm-Deletion Mutant of Photosystem II also contains other interesting chemical elements:

Magnesium	(Mg)	74 atoms
Manganese	(Mn)	8 atoms
Iron	(Fe)	6 atoms
Calcium	(Ca)	7 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II (pdb code 5h2f). 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 the Psbm-Deletion Mutant of Photosystem II, PDB code: 5h2f:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


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 the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:29.8 occ:1.00 NZ D:LYS317 3.2 20.7 1.0 O D:HOH530 3.2 25.8 1.0 ND2 A:ASN181 3.2 23.4 1.0 N A:GLU333 3.3 21.9 1.0 O A:HOH565 3.5 32.0 1.0 CA A:HIS332 3.7 23.7 1.0 CB A:HIS332 3.7 24.9 1.0 CE D:LYS317 3.9 20.8 1.0 C A:HIS332 4.0 23.8 1.0 CG A:GLU333 4.1 23.0 1.0 CG A:ASN181 4.1 22.3 1.0 OD1 A:ASN181 4.1 24.0 1.0 CG2 A:VAL185 4.1 25.5 1.0 CD2 D:LEU321 4.1 18.9 1.0 CA A:GLU333 4.3 23.9 1.0 CD1 D:LEU321 4.4 20.2 1.0 CB D:LYS317 4.4 21.0 1.0 O A:HOH534 4.4 26.6 1.0 O D:HOH531 4.4 20.9 1.0 CG D:LEU321 4.6 21.2 1.0 O D:LYS317 4.7 22.3 1.0 CG D:LYS317 4.8 21.0 1.0 CG A:HIS332 4.8 26.0 1.0 CB A:GLU333 4.8 22.4 1.0 OE2 A:GLU333 4.8 25.1 1.0 CD A:GLU333 5.0 25.1 1.0 O D:HOH560 5.0 34.5 1.0 CD D:LYS317 5.0 21.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


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 the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:28.0 occ:1.00 O C:HOH676 3.0 28.4 1.0 O A:HOH592 3.0 29.0 1.0 N A:ASN338 3.2 24.5 1.0 N C:GLU354 3.3 27.6 1.0 N A:PHE339 3.7 32.5 1.0 CA A:HIS337 3.7 25.9 1.0 CA C:GLY353 3.8 26.5 1.0 CD2 A:PHE339 3.8 24.5 1.0 C A:HIS337 4.0 23.9 1.0 C C:GLY353 4.0 28.1 1.0 O A:ALA336 4.1 23.0 1.0 CA A:ASN338 4.2 27.6 1.0 CB C:GLU354 4.2 28.6 1.0 CB A:HIS337 4.3 24.2 1.0 CA C:GLU354 4.3 28.6 1.0 CB A:PHE339 4.4 27.7 1.0 CB A:ASN338 4.4 27.9 1.0 O C:HOH660 4.4 22.4 1.0 CG A:PHE339 4.4 29.3 1.0 C A:ASN338 4.4 31.6 1.0 O A:HOH611 4.5 28.2 1.0 CE2 A:PHE339 4.5 28.1 1.0 CA A:PHE339 4.6 27.9 1.0 O A:PHE339 4.6 30.1 1.0 CG C:GLU354 4.6 29.5 1.0 O C:GLY352 4.8 29.1 1.0 CD2 A:HIS337 4.9 25.0 1.0 N A:HIS337 4.9 22.8 1.0 N C:THR355 4.9 27.7 1.0 CG A:HIS337 4.9 24.9 1.0 C A:ALA336 4.9 26.0 1.0 NE2 C:GLN313 5.0 23.5 1.0 O C:HOH611 5.0 27.1 1.0 CG A:ASN338 5.0 29.6 1.0 N C:GLY353 5.0 26.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


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 the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl405 b:31.7 occ:1.00 NZ d:LYS317 3.0 27.7 1.0 O d:HOH535 3.1 32.0 1.0 O a:HOH536 3.3 30.5 1.0 ND2 a:ASN181 3.4 26.2 1.0 N a:GLU333 3.4 24.8 1.0 CB a:HIS332 3.7 28.5 1.0 CA a:HIS332 3.8 28.6 1.0 CE d:LYS317 3.8 27.1 1.0 OD1 a:ASN181 4.0 31.0 1.0 CG a:GLU333 4.1 28.1 1.0 C a:HIS332 4.1 27.3 1.0 CG2 a:VAL185 4.1 22.6 1.0 CG a:ASN181 4.1 30.2 1.0 CD2 d:LEU321 4.2 25.3 1.0 CD1 d:LEU321 4.3 26.7 1.0 O d:HOH544 4.3 25.7 1.0 CB d:LYS317 4.3 24.9 1.0 CA a:GLU333 4.4 28.5 1.0 O a:HOH570 4.6 32.2 1.0 CG d:LEU321 4.6 29.2 1.0 CG a:HIS332 4.7 26.4 1.0 O d:LYS317 4.7 27.9 1.0 CG d:LYS317 4.8 25.6 1.0 CB a:GLU333 4.8 26.7 1.0 CD2 a:HIS332 4.9 29.6 1.0 CD a:GLU333 4.9 30.9 1.0 OE2 a:GLU333 4.9 27.7 1.0 O d:HOH547 4.9 31.8 1.0 CD d:LYS317 4.9 25.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Psbm-Deletion Mutant of Photosystem II


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 the Psbm-Deletion Mutant of Photosystem II within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl406 b:32.9 occ:1.00 O c:HOH1082 3.0 25.9 1.0 O a:HOH558 3.1 28.4 1.0 N a:ASN338 3.2 32.1 1.0 N c:GLU354 3.4 27.8 1.0 CD2 a:PHE339 3.6 29.7 1.0 N a:PHE339 3.7 29.3 1.0 CA a:HIS337 3.7 33.7 1.0 CA c:GLY353 3.8 30.8 1.0 C a:HIS337 3.9 37.3 1.0 C c:GLY353 4.1 28.1 1.0 CA a:ASN338 4.1 32.6 1.0 O a:ALA336 4.2 30.4 1.0 O c:HOH1127 4.2 29.9 1.0 CG a:PHE339 4.3 29.2 1.0 CB a:PHE339 4.3 26.9 1.0 CB a:ASN338 4.3 31.2 1.0 CB c:GLU354 4.3 29.5 1.0 CE2 a:PHE339 4.3 30.8 1.0 CB a:HIS337 4.3 29.5 1.0 C a:ASN338 4.4 33.0 1.0 CA c:GLU354 4.5 32.0 1.0 CG c:GLU354 4.5 34.2 1.0 CA a:PHE339 4.5 29.6 1.0 O c:HOH1133 4.6 28.8 1.0 O a:PHE339 4.7 32.9 1.0 N a:HIS337 4.8 27.4 1.0 CG a:ASN338 4.9 29.8 1.0 N c:THR355 4.9 29.8 1.0 C a:ALA336 4.9 29.8 1.0 CD2 a:HIS337 4.9 34.3 1.0 O c:GLY352 5.0 32.4 1.0 NE2 c:GLN313 5.0 27.9 1.0 O c:HOH1053 5.0 31.9 1.0

S.Uto, K.Kawakami, Y.Umena, M.Iwai, M.Ikeuchi, J.R.Shen, N.Kamiya. Mutual Relationships Between Structural and Functional Changes in A Psbm-Deletion Mutant of Photosystem II. Faraday Discuss. V. 198 107 2017.
ISSN: ISSN 1359-6640
PubMed: 28272640
DOI: 10.1039/C6FD00213G