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Chlorine in PDB 5ws6: Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

Enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset

All present enzymatic activity of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset:
1.10.3.9;

Protein crystallography data

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset, PDB code: 5ws6 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) 20.00 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.960, 230.220, 286.020, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.5

Other elements in 5ws6:

The structure of Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset also contains other interesting chemical elements:

Magnesium (Mg) 72 atoms
Manganese (Mn) 16 atoms
Iron (Fe) 8 atoms
Calcium (Ca) 12 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Native Xfel Structure of Photosystem II (Preflash Two-Flash Dataset (pdb code 5ws6). 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 (Preflash Two-Flash Dataset, PDB code: 5ws6:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5ws6

Go back to Chlorine Binding Sites List in 5ws6
Chlorine binding site 1 out of 4 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:44.2
occ:1.00
 O D:HOH587 3.0 48.4 1.0
NZ D:LYS317 3.0 44.1 1.0
ND2 A:ASN181 3.3 36.5 1.0
O A:HOH576 3.3 47.6 1.0
N A:GLU333 3.3 41.7 0.2
N A:GLU333 3.3 39.3 0.8
CE D:LYS317 3.7 41.8 1.0
CB A:HIS332 3.7 42.0 0.2
CG A:GLU333 3.8 45.5 0.2
CG A:GLU333 3.8 48.1 0.8
CA A:HIS332 3.8 42.6 0.2
CA A:HIS332 3.9 41.2 0.8
CB A:HIS332 4.0 42.8 0.8
C A:HIS332 4.0 43.6 0.2
OD1 A:ASN181 4.1 44.8 1.0
C A:HIS332 4.1 45.6 0.8
CG A:ASN181 4.1 46.3 1.0
O D:HOH532 4.1 40.5 1.0
CG2 A:VAL185 4.2 43.4 0.2
CA A:GLU333 4.2 42.4 0.2
CG2 A:VAL185 4.2 43.2 0.8
CA A:GLU333 4.2 42.6 0.8
CD1 D:LEU321 4.4 38.6 1.0
O A:HOH587 4.4 51.7 1.0
CB D:LYS317 4.5 45.5 1.0
CB A:GLU333 4.6 43.6 0.2
CD2 D:LEU321 4.6 39.0 1.0
CD A:GLU333 4.6 48.4 0.2
CG A:HIS332 4.6 45.0 0.2
CB A:GLU333 4.6 42.2 0.8
OE2 A:GLU333 4.7 48.7 0.2
CG D:LEU321 4.8 37.3 1.0
CG D:LYS317 4.8 43.5 1.0
CD A:GLU333 4.8 49.5 0.8
CD2 A:HIS332 4.8 43.3 0.2
CD D:LYS317 4.8 41.6 1.0
OE2 A:GLU333 4.9 48.4 0.8
CG A:HIS332 4.9 48.6 0.8

Chlorine binding site 2 out of 4 in 5ws6

Go back to Chlorine Binding Sites List in 5ws6
Chlorine binding site 2 out of 4 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl347

b:49.8
occ:1.00
 O A:HOH574 3.0 52.5 1.0
O C:HOH655 3.1 45.8 1.0
N A:ASN338 3.2 45.0 1.0
N C:GLU354 3.3 44.9 0.8
N C:GLU354 3.4 46.8 0.2
CA C:GLY353 3.6 44.0 1.0
N A:PHE339 3.6 46.5 1.0
CA A:HIS337 3.7 48.8 0.8
CA A:HIS337 3.7 47.3 0.2
CD2 A:PHE339 3.8 45.2 1.0
C C:GLY353 3.9 50.2 1.0
C A:HIS337 4.0 49.4 0.8
C A:HIS337 4.0 48.3 0.2
CA A:ASN338 4.1 49.3 1.0
O A:ALA336 4.1 46.4 1.0
CB A:HIS337 4.2 45.2 0.2
CB A:HIS337 4.2 44.4 0.8
CB C:GLU354 4.2 50.1 0.8
CB A:ASN338 4.3 49.1 1.0
CB A:PHE339 4.3 47.4 1.0
CB C:GLU354 4.3 50.6 0.2
C A:ASN338 4.3 53.8 1.0
CA C:GLU354 4.4 47.8 0.8
CA C:GLU354 4.4 47.3 0.2
CG A:PHE339 4.4 50.5 1.0
O A:HOH615 4.4 54.4 1.0
O C:HOH654 4.4 51.2 1.0
CA A:PHE339 4.5 50.5 1.0
O A:PHE339 4.6 46.8 1.0
CE2 A:PHE339 4.6 43.5 1.0
CD2 A:HIS337 4.6 45.9 0.8
CG C:GLU354 4.7 54.9 0.8
CG C:GLU354 4.8 53.8 0.2
CG A:HIS337 4.8 44.2 0.8
CD2 A:HIS337 4.8 45.1 0.2
N A:HIS337 4.8 44.8 0.8
N C:GLY353 4.9 47.4 1.0
O C:GLY352 4.9 44.5 1.0
N C:THR355 4.9 41.7 1.0
CG A:ASN338 4.9 49.3 1.0
N A:HIS337 4.9 46.6 0.2
CG A:HIS337 4.9 44.1 0.2
C A:ALA336 4.9 50.0 1.0

Chlorine binding site 3 out of 4 in 5ws6

Go back to Chlorine Binding Sites List in 5ws6
Chlorine binding site 3 out of 4 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl402

b:51.6
occ:1.00
 NZ d:LYS317 3.0 48.7 1.0
O d:HOH590 3.0 54.7 1.0
O a:HOH532 3.3 48.8 1.0
ND2 a:ASN181 3.3 47.5 1.0
N a:GLU333 3.4 41.8 0.8
N a:GLU333 3.4 42.7 0.2
CB a:HIS332 3.7 45.0 0.2
CE d:LYS317 3.8 50.2 1.0
CG a:GLU333 3.8 51.1 0.8
CB a:HIS332 3.8 46.5 0.8
CA a:HIS332 3.8 42.5 0.8
CA a:HIS332 3.8 44.1 0.2
CG a:GLU333 4.0 49.8 0.2
C a:HIS332 4.1 43.7 0.8
OD1 a:ASN181 4.1 46.3 1.0
C a:HIS332 4.1 43.8 0.2
CG a:ASN181 4.1 43.9 1.0
CG2 a:VAL185 4.2 42.5 0.8
O a:HOH534 4.3 51.4 1.0
CA a:GLU333 4.3 43.1 0.8
CG2 a:VAL185 4.3 43.3 0.2
CD2 d:LEU321 4.3 40.5 1.0
CA a:GLU333 4.3 44.3 0.2
CD1 d:LEU321 4.4 45.2 1.0
O a:HOH590 4.4 55.8 1.0
CB d:LYS317 4.5 40.4 1.0
CG d:LEU321 4.6 49.0 1.0
CB a:GLU333 4.7 46.5 0.8
CG a:HIS332 4.7 46.0 0.2
CB a:GLU333 4.7 45.8 0.2
CG a:HIS332 4.8 45.9 0.8
CD a:GLU333 4.8 52.5 0.8
CG d:LYS317 4.9 45.3 1.0
OE2 a:GLU333 4.9 52.8 0.2
CD a:GLU333 4.9 52.1 0.2
CD2 a:HIS332 4.9 45.2 0.2
OE2 a:GLU333 4.9 53.8 0.8
CD d:LYS317 4.9 47.3 1.0
O d:LYS317 5.0 53.7 1.0
CD2 a:HIS332 5.0 43.4 0.8

Chlorine binding site 4 out of 4 in 5ws6

Go back to Chlorine Binding Sites List in 5ws6
Chlorine binding site 4 out of 4 in the Native Xfel Structure of Photosystem II (Preflash Two-Flash 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 (Preflash Two-Flash Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl347

b:53.5
occ:1.00
 O c:HOH676 2.9 51.5 1.0
N a:ASN338 3.0 49.3 1.0
O a:HOH608 3.1 60.5 1.0
N c:GLU354 3.3 49.2 0.2
N c:GLU354 3.3 48.5 0.8
N a:PHE339 3.5 53.4 1.0
CA a:HIS337 3.5 47.8 0.2
CA a:HIS337 3.5 48.9 0.8
CD2 a:PHE339 3.6 59.4 1.0
CA c:GLY353 3.6 48.3 1.0
C a:HIS337 3.8 48.8 0.2
C a:HIS337 3.8 47.5 0.8
C c:GLY353 4.0 50.2 1.0
CA a:ASN338 4.0 51.5 1.0
CB a:HIS337 4.1 46.3 0.2
O a:ALA336 4.1 64.0 1.0
CB a:HIS337 4.1 44.5 0.8
CB c:GLU354 4.2 51.2 0.2
C a:ASN338 4.3 50.2 1.0
CB a:ASN338 4.3 57.1 1.0
CG a:PHE339 4.3 58.5 1.0
CB a:PHE339 4.3 56.0 1.0
CB c:GLU354 4.3 52.0 0.8
CE2 a:PHE339 4.3 62.6 1.0
CA c:GLU354 4.4 50.1 0.2
O c:HOH659 4.4 51.8 1.0
CA c:GLU354 4.4 48.7 0.8
CA a:PHE339 4.4 56.8 1.0
O a:PHE339 4.5 60.5 1.0
O c:HOH697 4.7 52.7 1.0
N a:HIS337 4.7 48.1 0.2
N a:HIS337 4.7 48.0 0.8
CG c:GLU354 4.8 51.9 0.2
CG a:HIS337 4.8 47.0 0.2
C a:ALA336 4.8 49.4 1.0
CG a:ASN338 4.9 56.6 1.0
N c:GLY353 4.9 51.9 1.0
CG a:HIS337 4.9 46.9 0.8
O c:GLY352 4.9 49.6 1.0
CD2 a:HIS337 4.9 47.7 0.2
N c:THR355 4.9 49.6 1.0
CD2 a:HIS337 4.9 48.4 0.8
CG c:GLU354 4.9 53.5 0.8
C a:PHE339 5.0 55.3 1.0
O a:HIS337 5.0 50.1 0.2
O a:HIS337 5.0 52.3 0.8
NE2 c:GLN313 5.0 49.8 1.0

Reference:

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
Page generated: Sat Jul 12 10:24:36 2025

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