Chlorine in PDB 8f4k: Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k 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) 33.52 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 116.991, 221.755, 307.964, 90, 90, 90
R / Rfree (%) 18.5 / 24.1

Other elements in 8f4k:

The structure of Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution (pdb code 8f4k). 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 Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution, PDB code: 8f4k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8f4k

Go back to Chlorine Binding Sites List in 8f4k
Chlorine binding site 1 out of 4 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:33.7
occ:1.00
 O D:HOH563 2.9 33.6 1.0
NZ D:LYS317 3.3 27.9 1.0
OD1 A:ASN181 3.3 42.6 0.3
N A:GLU333 3.4 38.3 0.3
O A:HOH762 3.4 27.8 1.0
OD1 A:ASN181 3.4 35.2 0.7
N A:GLU333 3.4 36.7 0.7
CB A:HIS332 3.7 37.3 0.3
CA A:HIS332 3.7 38.2 0.3
CA A:HIS332 3.8 32.9 0.7
CB A:HIS332 3.8 36.5 0.7
CG A:GLU333 4.0 34.1 0.3
CG A:GLU333 4.0 32.0 0.7
C A:HIS332 4.0 37.7 0.3
ND2 A:ASN181 4.1 30.6 0.7
C A:HIS332 4.1 34.8 0.7
ND2 A:ASN181 4.1 30.9 0.3
CG A:ASN181 4.1 31.9 0.7
CG A:ASN181 4.1 35.6 0.3
CE D:LYS317 4.2 36.2 1.0
O D:HOH505 4.2 32.4 1.0
CA A:GLU333 4.3 38.3 0.3
CA A:GLU333 4.3 34.5 0.7
CG2 A:VAL185 4.4 35.5 0.3
CG2 A:VAL185 4.4 25.6 0.7
CD2 D:LEU321 4.4 25.9 1.0
CB D:LYS317 4.4 37.6 1.0
CD1 D:LEU321 4.5 27.8 1.0
O A:HOH774 4.5 34.2 1.0
CG D:LEU321 4.7 36.4 1.0
CG D:LYS317 4.7 34.9 1.0
CB A:GLU333 4.8 33.0 0.3
O D:HOH529 4.8 35.5 1.0
CG A:HIS332 4.8 37.5 0.3
CB A:GLU333 4.8 29.2 0.7
CG A:HIS332 4.8 30.0 0.7
CD A:GLU333 4.9 37.2 0.3
O D:LYS317 4.9 33.7 1.0
OE2 A:GLU333 5.0 37.1 0.3

Chlorine binding site 2 out of 4 in 8f4k

Go back to Chlorine Binding Sites List in 8f4k
Chlorine binding site 2 out of 4 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:33.5
occ:1.00
 O A:HOH771 2.9 28.4 1.0
O C:HOH676 3.0 29.2 1.0
N A:ASN338 3.1 34.9 0.7
N A:ASN338 3.2 35.3 0.3
N C:GLU354 3.3 33.2 0.7
N C:GLU354 3.4 37.5 0.3
CD2 A:PHE339 3.6 31.2 0.7
CA A:HIS337 3.7 34.5 0.7
N A:PHE339 3.7 36.2 0.3
N A:PHE339 3.7 34.8 0.7
CA C:GLY353 3.7 26.5 0.7
CA A:HIS337 3.7 37.7 0.3
CA C:GLY353 3.8 36.6 0.3
CD2 A:PHE339 3.8 34.2 0.3
C A:HIS337 3.9 32.2 0.7
C A:HIS337 3.9 35.8 0.3
CA A:ASN338 4.0 29.9 0.7
C C:GLY353 4.0 32.4 0.7
C C:GLY353 4.1 38.7 0.3
CA A:ASN338 4.1 33.9 0.3
O A:ALA336 4.2 36.9 0.7
CB A:ASN338 4.2 32.7 0.7
CB C:GLU354 4.2 32.5 0.7
O A:ALA336 4.2 41.3 0.3
O C:HOH675 4.2 29.1 1.0
CB A:HIS337 4.3 30.1 0.7
CE2 A:PHE339 4.3 31.8 0.7
CB C:GLU354 4.3 42.2 0.3
C A:ASN338 4.3 33.3 0.7
CB A:HIS337 4.3 35.7 0.3
CG A:PHE339 4.3 34.0 0.7
CA C:GLU354 4.4 37.0 0.7
CB A:PHE339 4.4 35.5 0.3
C A:ASN338 4.4 37.0 0.3
CB A:ASN338 4.4 37.4 0.3
CB A:PHE339 4.4 35.7 0.7
CA C:GLU354 4.4 42.4 0.3
CG A:PHE339 4.5 38.2 0.3
O A:HOH787 4.5 42.1 1.0
O A:PHE339 4.5 36.2 0.3
CE2 A:PHE339 4.5 36.2 0.3
CA A:PHE339 4.5 37.6 0.3
CA A:PHE339 4.6 38.1 0.7
O A:PHE339 4.6 34.8 0.7
CG C:GLU354 4.7 41.4 0.3
N A:HIS337 4.8 32.8 0.7
N C:THR355 4.8 38.5 0.3
N C:THR355 4.8 31.0 0.7
N A:HIS337 4.9 39.1 0.3
CG C:GLU354 4.9 32.5 0.7
CG A:ASN338 4.9 37.6 0.3
C A:ALA336 5.0 33.0 0.7
CD2 A:HIS337 5.0 35.6 0.3
N C:GLY353 5.0 31.3 0.7
O C:GLY352 5.0 37.3 1.0
C A:ALA336 5.0 40.9 0.3
N C:GLY353 5.0 40.7 0.3

Chlorine binding site 3 out of 4 in 8f4k

Go back to Chlorine Binding Sites List in 8f4k
Chlorine binding site 3 out of 4 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:34.2
occ:1.00
 O d:HOH550 3.1 33.4 1.0
O a:HOH774 3.1 29.1 1.0
N a:GLU333 3.3 35.8 0.3
N a:GLU333 3.3 29.6 0.7
NZ d:LYS317 3.4 34.3 1.0
OD1 a:ASN181 3.4 34.0 0.7
OD1 a:ASN181 3.5 42.1 0.3
CA a:HIS332 3.5 36.3 0.3
CB a:HIS332 3.5 37.9 0.3
CA a:HIS332 3.7 31.3 0.7
CB a:HIS332 3.7 33.7 0.7
CG a:GLU333 3.8 28.9 0.7
CG a:GLU333 3.8 36.2 0.3
C a:HIS332 3.9 38.8 0.3
C a:HIS332 4.0 32.7 0.7
CE d:LYS317 4.0 32.3 1.0
CG2 a:VAL185 4.1 23.2 0.7
CD1 d:LEU321 4.2 33.7 1.0
CG2 a:VAL185 4.2 37.2 0.3
ND2 a:ASN181 4.2 36.4 0.3
CA a:GLU333 4.2 29.7 0.7
CG a:ASN181 4.3 38.1 0.3
CA a:GLU333 4.3 37.7 0.3
O a:HOH716 4.3 29.8 1.0
CD2 d:LEU321 4.3 30.4 1.0
CG a:ASN181 4.4 30.3 0.7
O a:HOH756 4.5 39.0 1.0
CB d:LYS317 4.5 31.7 1.0
ND2 a:ASN181 4.6 29.5 0.7
CG a:HIS332 4.6 38.1 0.3
CB a:GLU333 4.6 25.9 0.7
CB a:GLU333 4.7 37.1 0.3
CG a:HIS332 4.7 29.6 0.7
O d:LYS317 4.8 33.7 1.0
CD a:GLU333 4.8 36.8 0.3
CD a:GLU333 4.8 33.4 0.7
OE2 a:GLU333 4.8 32.9 0.7
OE2 a:GLU333 4.9 36.9 0.3
N a:HIS332 4.9 33.7 0.3
CD2 a:HIS332 4.9 31.5 0.7
CG d:LEU321 4.9 33.1 1.0
CD2 a:HIS332 5.0 38.9 0.3

Chlorine binding site 4 out of 4 in 8f4k

Go back to Chlorine Binding Sites List in 8f4k
Chlorine binding site 4 out of 4 in the Rt Xfel Structure of the Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 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 Three-Flash State of Photosystem II (3F, S0- Rich) at 2.16 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl605

b:35.5
occ:1.00
 O c:HOH648 3.0 35.7 1.0
N a:ASN338 3.1 36.1 0.7
N a:ASN338 3.1 40.0 0.3
O a:HOH724 3.1 36.5 1.0
N c:GLU354 3.4 35.0 0.7
N c:GLU354 3.5 33.9 0.3
CA a:HIS337 3.6 31.2 0.7
N a:PHE339 3.6 33.4 0.3
CA a:HIS337 3.6 35.0 0.3
N a:PHE339 3.6 30.6 0.7
CD2 a:PHE339 3.8 34.6 0.7
CD2 a:PHE339 3.8 35.4 0.3
C a:HIS337 3.8 37.8 0.7
CA c:GLY353 3.9 33.9 0.3
C a:HIS337 3.9 39.0 0.3
CA c:GLY353 3.9 33.1 0.7
CA a:ASN338 4.1 37.5 0.3
CA a:ASN338 4.1 30.0 0.7
CB c:GLU354 4.1 32.6 0.7
C c:GLY353 4.1 35.8 0.7
O a:ALA336 4.1 37.7 0.3
O a:ALA336 4.2 40.6 0.7
CB a:HIS337 4.2 33.7 0.7
C c:GLY353 4.2 39.2 0.3
CB a:HIS337 4.2 35.4 0.3
C a:ASN338 4.3 36.8 0.3
CB a:PHE339 4.3 38.6 0.3
CB a:PHE339 4.3 35.4 0.7
C a:ASN338 4.3 36.7 0.7
CB c:GLU354 4.3 36.3 0.3
CB a:ASN338 4.3 33.7 0.7
CB a:ASN338 4.3 36.5 0.3
CG a:PHE339 4.4 34.1 0.7
CA c:GLU354 4.4 34.5 0.7
O a:PHE339 4.4 40.8 0.3
CG a:PHE339 4.4 38.2 0.3
O a:PHE339 4.5 38.0 0.7
CA a:PHE339 4.5 38.7 0.3
CA c:GLU354 4.5 36.4 0.3
O c:HOH656 4.5 30.4 1.0
CA a:PHE339 4.5 33.3 0.7
CE2 a:PHE339 4.5 33.7 0.7
CG c:GLU354 4.6 34.4 0.7
CE2 a:PHE339 4.6 35.1 0.3
O c:HOH684 4.7 38.1 1.0
N a:HIS337 4.7 33.2 0.7
N a:HIS337 4.7 36.0 0.3
CG c:GLU354 4.8 36.2 0.3
O c:GLY352 4.9 32.2 1.0
N c:THR355 4.9 32.5 0.7
C a:ALA336 4.9 37.6 0.3
C a:ALA336 4.9 35.8 0.7
CG a:ASN338 4.9 41.3 0.3
N c:THR355 4.9 34.5 0.3
C a:PHE339 4.9 39.1 0.3
C a:PHE339 4.9 34.2 0.7
CD2 a:HIS337 5.0 35.7 0.3
CG a:HIS337 5.0 38.3 0.3
CG a:HIS337 5.0 37.3 0.7

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: Tue Jul 30 09:18:07 2024

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