Atomistry » Chlorine » PDB 5wkx-5ws6 » 5ws6
Atomistry »
  Chlorine »
    PDB 5wkx-5ws6 »
      5ws6 »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy