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Chlorine in PDB 8ez5: Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution, PDB code: 8ez5 was solved by A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.65 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.958, 221.646, 307.786, 90, 90, 90
R / Rfree (%) 18.6 / 23.5

Other elements in 8ez5:

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Manganese (Mn) 16 atoms
Magnesium (Mg) 70 atoms
Calcium (Ca) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution (pdb code 8ez5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution, PDB code: 8ez5:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8ez5

Go back to Chlorine Binding Sites List in 8ez5
Chlorine binding site 1 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:34.0
occ:1.00
 O D:HOH580 3.1 36.6 1.0
NZ D:LYS317 3.2 25.3 1.0
N A:GLU333 3.3 33.9 0.3
N A:GLU333 3.3 30.4 0.7
OD1 A:ASN181 3.4 36.8 0.7
OD1 A:ASN181 3.4 34.1 0.3
O A:HOH755 3.4 30.0 1.0
CB A:HIS332 3.7 30.6 0.7
CB A:HIS332 3.7 31.9 0.3
CA A:HIS332 3.7 31.6 0.7
CA A:HIS332 3.7 32.8 0.3
CG A:GLU333 3.9 30.2 0.3
CG A:GLU333 4.0 28.2 0.7
C A:HIS332 4.0 30.4 0.7
C A:HIS332 4.0 34.1 0.3
CE D:LYS317 4.1 32.4 1.0
ND2 A:ASN181 4.1 24.4 0.7
CG A:ASN181 4.1 28.1 0.7
ND2 A:ASN181 4.2 29.0 0.3
CG A:ASN181 4.2 32.8 0.3
CG2 A:VAL185 4.2 30.4 0.3
CD1 D:LEU321 4.3 24.2 1.0
CG2 A:VAL185 4.3 29.6 0.7
CA A:GLU333 4.3 36.8 0.3
CA A:GLU333 4.3 31.9 0.7
O A:HOH712 4.4 32.7 1.0
CB D:LYS317 4.5 28.1 1.0
O A:HOH766 4.5 37.2 1.0
CD2 D:LEU321 4.7 24.9 1.0
CG D:LEU321 4.7 31.1 1.0
CG A:HIS332 4.7 33.8 0.3
CG D:LYS317 4.7 32.9 1.0
CG A:HIS332 4.7 30.8 0.7
CB A:GLU333 4.8 28.1 0.3
CB A:GLU333 4.8 26.3 0.7
O D:HOH526 4.9 34.4 1.0
O D:LYS317 4.9 32.6 1.0
CD A:GLU333 4.9 31.0 0.7
OE2 A:GLU333 5.0 30.4 0.7
CD A:GLU333 5.0 34.2 0.3

Chlorine binding site 2 out of 4 in 8ez5

Go back to Chlorine Binding Sites List in 8ez5
Chlorine binding site 2 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:34.2
occ:1.00
 O A:HOH764 2.9 32.4 1.0
O C:HOH668 3.1 29.6 1.0
N A:ASN338 3.2 29.0 0.7
N A:ASN338 3.2 35.0 0.3
N C:GLU354 3.3 33.4 0.3
N C:GLU354 3.4 30.8 0.7
N A:PHE339 3.6 33.6 0.3
CA A:HIS337 3.7 31.8 0.7
CA A:HIS337 3.7 33.5 0.3
N A:PHE339 3.7 31.0 0.7
CD2 A:PHE339 3.7 36.7 0.3
CA C:GLY353 3.8 27.5 0.3
CD2 A:PHE339 3.8 28.7 0.7
CA C:GLY353 3.8 30.4 0.7
C A:HIS337 3.9 29.6 0.7
C A:HIS337 3.9 31.5 0.3
C C:GLY353 4.0 32.4 0.3
C C:GLY353 4.1 32.5 0.7
CA A:ASN338 4.1 32.0 0.3
CA A:ASN338 4.1 28.2 0.7
O A:ALA336 4.1 32.1 0.3
O A:ALA336 4.2 34.7 0.7
CB C:GLU354 4.2 36.5 0.7
CB C:GLU354 4.2 31.4 0.3
CB A:HIS337 4.2 32.1 0.3
CB A:HIS337 4.3 27.9 0.7
CB A:PHE339 4.3 33.4 0.3
O A:HOH800 4.3 37.2 1.0
C A:ASN338 4.4 33.4 0.3
CA C:GLU354 4.4 35.3 0.3
CA C:GLU354 4.4 35.6 0.7
CB A:PHE339 4.4 30.4 0.7
C A:ASN338 4.4 31.2 0.7
CB A:ASN338 4.4 35.5 0.3
CG A:PHE339 4.4 34.3 0.3
O C:HOH682 4.4 32.4 1.0
CB A:ASN338 4.4 32.8 0.7
CG A:PHE339 4.5 32.3 0.7
CE2 A:PHE339 4.5 34.4 0.3
O A:PHE339 4.5 30.0 0.7
CA A:PHE339 4.5 35.1 0.3
CA A:PHE339 4.6 31.4 0.7
CG C:GLU354 4.6 34.8 0.7
CE2 A:PHE339 4.6 31.1 0.7
O A:PHE339 4.6 38.1 0.3
N A:HIS337 4.8 34.5 0.3
N A:HIS337 4.8 32.2 0.7
CD2 A:HIS337 4.8 29.3 0.3
N C:THR355 4.9 32.0 0.7
N C:THR355 4.9 27.4 0.3
CG A:HIS337 4.9 32.5 0.3
CD2 A:HIS337 4.9 28.2 0.7
C A:ALA336 4.9 32.6 0.3
C A:ALA336 4.9 35.0 0.7
CG A:HIS337 5.0 29.6 0.7
C A:PHE339 5.0 32.2 0.7
CG A:ASN338 5.0 31.8 0.7

Chlorine binding site 3 out of 4 in 8ez5

Go back to Chlorine Binding Sites List in 8ez5
Chlorine binding site 3 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:32.2
occ:1.00
 O d:HOH571 3.1 28.4 1.0
NZ d:LYS317 3.1 30.4 1.0
N a:GLU333 3.3 31.0 0.3
N a:GLU333 3.3 28.5 0.7
O a:HOH756 3.3 29.1 1.0
OD1 a:ASN181 3.4 33.7 0.3
OD1 a:ASN181 3.5 35.7 0.7
CA a:HIS332 3.6 29.9 0.7
CB a:HIS332 3.6 30.9 0.7
CA a:HIS332 3.7 29.0 0.3
CG a:GLU333 3.7 30.9 0.3
CB a:HIS332 3.8 34.8 0.3
CG a:GLU333 3.8 28.9 0.7
C a:HIS332 3.9 32.1 0.7
CE d:LYS317 3.9 33.5 1.0
C a:HIS332 4.0 30.6 0.3
O a:HOH755 4.0 28.4 1.0
CA a:GLU333 4.2 31.7 0.3
CD1 d:LEU321 4.2 32.8 1.0
ND2 a:ASN181 4.2 30.2 0.7
CG2 a:VAL185 4.2 30.0 0.3
CG2 a:VAL185 4.2 29.8 0.7
CG a:ASN181 4.2 32.1 0.3
CA a:GLU333 4.2 30.5 0.7
CG a:ASN181 4.3 31.8 0.7
ND2 a:ASN181 4.3 32.7 0.3
CD2 d:LEU321 4.3 27.1 1.0
CB d:LYS317 4.5 25.8 1.0
CB a:GLU333 4.6 31.2 0.3
O a:HOH759 4.6 33.4 1.0
CB a:GLU333 4.6 29.1 0.7
CG a:HIS332 4.7 30.6 0.7
CG a:HIS332 4.7 33.1 0.3
CD a:GLU333 4.8 30.7 0.7
CD a:GLU333 4.8 32.5 0.3
OE2 a:GLU333 4.8 30.0 0.7
O d:LYS317 4.9 29.5 1.0
CG d:LEU321 4.9 35.2 1.0
CD2 a:HIS332 4.9 33.5 0.3
O d:HOH535 4.9 30.4 1.0
N a:HIS332 5.0 27.9 0.7
CD2 a:HIS332 5.0 32.2 0.7
OE2 a:GLU333 5.0 30.7 0.3

Chlorine binding site 4 out of 4 in 8ez5

Go back to Chlorine Binding Sites List in 8ez5
Chlorine binding site 4 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.09 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl605

b:33.3
occ:1.00
 O c:HOH650 3.0 30.3 1.0
N a:ASN338 3.1 34.8 0.3
N a:ASN338 3.1 34.3 0.7
O a:HOH714 3.3 32.7 1.0
N c:GLU354 3.4 33.5 0.3
N c:GLU354 3.4 26.9 0.7
CA a:HIS337 3.6 31.7 0.3
CA a:HIS337 3.6 29.6 0.7
CD2 a:PHE339 3.6 35.9 0.3
N a:PHE339 3.6 27.6 0.7
N a:PHE339 3.7 31.3 0.3
C a:HIS337 3.8 34.2 0.3
CD2 a:PHE339 3.9 29.5 0.7
C a:HIS337 3.9 33.3 0.7
CA c:GLY353 3.9 27.9 0.7
CA c:GLY353 3.9 33.0 0.3
CA a:ASN338 4.1 32.4 0.7
CA a:ASN338 4.1 32.3 0.3
O a:ALA336 4.1 31.3 0.7
CB a:HIS337 4.1 30.0 0.3
C c:GLY353 4.1 35.2 0.3
C c:GLY353 4.2 33.7 0.7
CB c:GLU354 4.2 33.6 0.3
O a:ALA336 4.2 36.8 0.3
CB a:HIS337 4.2 28.5 0.7
CB c:GLU354 4.3 29.8 0.7
CB a:PHE339 4.3 36.5 0.3
CB a:PHE339 4.3 31.8 0.7
C a:ASN338 4.3 30.8 0.7
CG a:PHE339 4.3 33.1 0.3
C a:ASN338 4.3 34.6 0.3
CB a:ASN338 4.3 30.5 0.7
CA c:GLU354 4.4 33.8 0.3
CB a:ASN338 4.4 31.2 0.3
CE2 a:PHE339 4.4 32.9 0.3
O a:PHE339 4.4 40.1 0.3
O c:HOH663 4.4 26.3 1.0
CA c:GLU354 4.4 30.3 0.7
O a:PHE339 4.4 33.8 0.7
CG a:PHE339 4.5 33.1 0.7
CA a:PHE339 4.5 33.0 0.7
CA a:PHE339 4.5 36.2 0.3
CE2 a:PHE339 4.7 28.2 0.7
N a:HIS337 4.7 36.5 0.3
N a:HIS337 4.7 30.7 0.7
CG c:GLU354 4.8 30.7 0.7
O c:HOH698 4.8 33.2 1.0
N c:THR355 4.8 32.5 0.3
C a:ALA336 4.9 32.9 0.7
N c:THR355 4.9 27.5 0.7
NE2 c:GLN313 4.9 29.3 1.0
C a:ALA336 4.9 36.0 0.3
C a:PHE339 4.9 33.0 0.3
C a:PHE339 4.9 32.5 0.7
CG a:HIS337 4.9 38.1 0.3
CG c:GLU354 4.9 37.9 0.3
CG a:ASN338 5.0 36.0 0.7
CD2 a:HIS337 5.0 30.0 0.7
CG a:HIS337 5.0 32.9 0.7
O c:GLY352 5.0 27.9 1.0

Reference:

A.Bhowmick, R.Hussein, I.Bogacz, P.S.Simon, M.Ibrahim, R.Chatterjee, M.D.Doyle, M.H.Cheah, T.Fransson, P.Chernev, I.-S.Kim, H.Makita, M.Dasgupta, C.J.Kaminsky, M.Zhang, J.Gatcke, S.Haupt, I.I.Nangca, S.M.Keable, O.Aydin, K.Tono, S.Owada, L.B.Gee, F.D.Fuller, A.Batyuk, R.Alonso-Mori, J.M.Holton, D.W.Paley, N.W.Moriarty, F.Mamedov, P.D.Adams, A.S.Brewster, H.Dobbek, N.K.Sauter, U.Bergmann, A.Zouni, J.Messinger, J.Kern, J.Yano, V.K.Yachandra. Structural Evidence For Intermediates During O2 Formation in Photosystem II To Be Published.
Page generated: Sun Jul 13 11:05:00 2025

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