Chlorine in PDB 5gth: Native Xfel Structure of Photosystem II (Dark Dataset)

All present enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset):
1.10.3.9;

The structure of Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth was solved by M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.520, 231.230, 287.460, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 18.6

The structure of Native Xfel Structure of Photosystem II (Dark Dataset) also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the Native Xfel Structure of Photosystem II (Dark Dataset) (pdb code 5gth). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:24.1 occ:1.00 O D:HOH591 3.0 24.1 1.0 NZ D:LYS317 3.0 20.3 1.0 ND2 A:ASN181 3.4 19.9 1.0 O A:HOH580 3.4 27.1 1.0 N A:GLU333 3.4 21.0 1.0 CE D:LYS317 3.7 26.5 1.0 CG A:GLU333 4.0 32.7 1.0 O D:HOH512 4.0 30.9 1.0 CA A:HIS332 4.0 22.2 1.0 CB A:HIS332 4.1 26.9 1.0 OD1 A:ASN181 4.2 24.2 1.0 C A:HIS332 4.2 25.2 1.0 CG A:ASN181 4.2 30.1 1.0 CA A:GLU333 4.3 29.6 1.0 CG2 A:VAL185 4.3 24.3 1.0 CB D:LYS317 4.4 19.5 1.0 O A:HOH590 4.5 30.3 1.0 CD1 D:LEU321 4.5 21.1 1.0 CD2 D:LEU321 4.6 20.4 1.0 CB A:GLU333 4.7 21.5 1.0 CG D:LYS317 4.7 20.0 1.0 CG D:LEU321 4.8 20.1 1.0 CD D:LYS317 4.8 20.4 1.0 CD A:GLU333 4.9 30.9 1.0 OE2 A:GLU333 5.0 21.5 1.0

Chlorine binding site 2 out of 4 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:27.6 occ:1.00 N A:ASN338 3.2 27.1 1.0 O C:HOH650 3.2 25.5 1.0 O A:HOH570 3.3 28.4 1.0 N C:GLU354 3.3 24.3 1.0 CA C:GLY353 3.6 24.8 1.0 N A:PHE339 3.7 27.6 1.0 CA A:HIS337 3.7 34.9 1.0 CD2 A:PHE339 3.8 25.9 1.0 C C:GLY353 3.9 44.4 1.0 C A:HIS337 3.9 34.6 1.0 O A:ALA336 4.1 34.3 1.0 CA A:ASN338 4.1 26.6 1.0 CB A:ASN338 4.3 29.1 1.0 CB A:HIS337 4.3 23.3 1.0 CB C:GLU354 4.3 23.9 1.0 CB A:PHE339 4.3 25.6 1.0 O A:HOH611 4.4 31.7 1.0 CG A:PHE339 4.4 50.4 1.0 C A:ASN338 4.4 28.6 1.0 CA C:GLU354 4.4 24.2 1.0 O C:HOH667 4.5 25.9 1.0 CA A:PHE339 4.6 31.4 1.0 CE2 A:PHE339 4.6 34.5 1.0 O A:PHE339 4.7 24.6 1.0 CG C:GLU354 4.7 28.6 1.0 CD2 A:HIS337 4.8 38.9 1.0 N A:HIS337 4.8 26.7 1.0 N C:GLY353 4.8 25.2 1.0 N C:THR355 4.9 25.1 1.0 C A:ALA336 4.9 24.2 1.0 O C:GLY352 4.9 25.9 1.0 CG A:HIS337 4.9 33.8 1.0 CG A:ASN338 4.9 24.6 1.0

Chlorine binding site 3 out of 4 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl402 b:31.2 occ:1.00 O d:HOH580 2.9 30.6 1.0 NZ d:LYS317 3.1 24.4 1.0 ND2 a:ASN181 3.3 24.2 1.0 N a:GLU333 3.5 25.9 1.0 O a:HOH570 3.5 25.3 1.0 CE d:LYS317 3.7 26.3 1.0 CB a:HIS332 3.7 26.3 1.0 CA a:HIS332 3.8 26.1 1.0 CG2 a:VAL185 4.1 25.8 1.0 CG a:GLU333 4.1 31.8 1.0 OD1 a:ASN181 4.1 24.5 1.0 C a:HIS332 4.1 29.4 1.0 CG a:ASN181 4.2 30.1 1.0 CD1 d:LEU321 4.2 25.7 1.0 O a:HOH519 4.4 33.3 1.0 CD2 d:LEU321 4.4 25.4 1.0 CA a:GLU333 4.4 26.1 1.0 CB d:LYS317 4.4 23.4 1.0 O a:HOH606 4.5 29.6 1.0 CG d:LEU321 4.5 24.9 1.0 CG a:HIS332 4.8 27.8 1.0 CG d:LYS317 4.9 24.8 1.0 CB a:GLU333 4.9 26.4 1.0 CD d:LYS317 4.9 23.5 1.0 OE2 a:GLU333 5.0 26.3 1.0 CD a:GLU333 5.0 28.5 1.0

Chlorine binding site 4 out of 4 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range: probe atom residue distance (Å) B Occ a:Cl403 b:34.8 occ:1.00 O c:HOH638 3.0 45.0 1.0 N a:ASN338 3.1 30.2 1.0 O a:HOH592 3.1 40.2 1.0 N c:GLU354 3.4 29.9 1.0 CA c:GLY353 3.6 34.5 1.0 CD2 a:PHE339 3.6 32.4 1.0 N a:PHE339 3.6 31.4 1.0 CA a:HIS337 3.7 35.6 1.0 C a:HIS337 3.9 31.7 1.0 C c:GLY353 3.9 39.2 1.0 CA a:ASN338 4.0 30.7 1.0 O a:ALA336 4.2 40.7 1.0 CB a:ASN338 4.3 35.3 1.0 O c:HOH655 4.3 32.5 1.0 CE2 a:PHE339 4.3 38.9 1.0 CB c:GLU354 4.3 35.5 1.0 CB a:PHE339 4.3 32.5 1.0 CG a:PHE339 4.3 49.7 1.0 C a:ASN338 4.3 31.3 1.0 CB a:HIS337 4.4 29.2 1.0 CA c:GLU354 4.4 29.6 1.0 CA a:PHE339 4.5 32.1 1.0 O c:HOH698 4.6 30.4 1.0 O a:PHE339 4.7 33.3 1.0 CG c:GLU354 4.7 28.9 1.0 O c:GLY352 4.8 31.8 1.0 N c:GLY353 4.8 30.8 1.0 N c:THR355 4.9 30.8 1.0 N a:HIS337 4.9 31.5 1.0 CG a:ASN338 4.9 30.9 1.0 C a:ALA336 5.0 28.4 1.0

M.Suga, F.Akita, M.Sugahara, M.Kubo, Y.Nakajima, T.Nakane, K.Yamashita, Y.Umena, M.Nakabayashi, T.Yamane, T.Nakano, M.Suzuki, T.Masuda, S.Inoue, T.Kimura, T.Nomura, S.Yonekura, L.J.Yu, T.Sakamoto, T.Motomura, J.H.Chen, Y.Kato, T.Noguchi, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, E.Nango, R.Tanaka, H.Naitow, Y.Matsuura, A.Yamashita, M.Yamamoto, O.Nureki, M.Yabashi, T.Ishikawa, S.Iwata, J.R.Shen. Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400