Chlorine in PDB 8f4c: Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution, PDB code: 8f4c 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) 19.80 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.328, 222.786, 309.116, 90, 90, 90
R / Rfree (%) 18 / 22.4

Other elements in 8f4c:

The structure of Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 Angstrom Resolution also contains other interesting chemical elements:

Manganese (Mn) 16 atoms
Iron (Fe) 6 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 2.00 Angstrom Resolution (pdb code 8f4c). 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 2.00 Angstrom Resolution, PDB code: 8f4c:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8f4c

Go back to Chlorine Binding Sites List in 8f4c
Chlorine binding site 1 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:28.9
occ:1.00
 O D:HOH563 3.0 26.2 1.0
NZ D:LYS317 3.0 26.8 1.0
O A:HOH726 3.3 31.5 1.0
N A:GLU333 3.3 27.1 0.7
N A:GLU333 3.4 30.5 0.3
OD1 A:ASN181 3.4 27.6 0.7
OD1 A:ASN181 3.4 32.5 0.3
CB A:HIS332 3.7 23.0 0.3
CA A:HIS332 3.8 29.1 0.3
CG A:GLU333 3.8 25.0 0.7
CA A:HIS332 3.8 27.9 0.7
CB A:HIS332 3.8 27.9 0.7
CG A:GLU333 3.9 26.0 0.3
CE D:LYS317 3.9 25.7 1.0
C A:HIS332 4.0 27.8 0.3
C A:HIS332 4.0 27.3 0.7
ND2 A:ASN181 4.1 23.9 0.3
O D:HOH544 4.1 28.1 1.0
CG A:ASN181 4.2 26.3 0.3
ND2 A:ASN181 4.2 22.6 0.7
CG A:ASN181 4.2 25.1 0.7
CA A:GLU333 4.3 27.2 0.7
CG2 A:VAL185 4.3 24.4 0.7
CG2 A:VAL185 4.3 23.5 0.3
CA A:GLU333 4.3 30.8 0.3
O A:HOH781 4.4 29.7 1.0
CD1 D:LEU321 4.5 27.3 1.0
CD2 D:LEU321 4.5 24.5 1.0
CB D:LYS317 4.5 26.9 1.0
CB A:GLU333 4.6 23.6 0.7
CG D:LYS317 4.7 25.2 1.0
CG A:HIS332 4.7 30.3 0.3
O D:HOH519 4.7 29.7 1.0
CB A:GLU333 4.7 24.9 0.3
CG D:LEU321 4.8 26.3 1.0
CD A:GLU333 4.8 25.4 0.7
CG A:HIS332 4.8 26.0 0.7
CD A:GLU333 4.9 27.8 0.3
O D:LYS317 4.9 26.7 1.0
OE2 A:GLU333 4.9 27.9 0.3
OE2 A:GLU333 4.9 27.5 0.7
CD D:LYS317 5.0 27.3 1.0
CD2 A:HIS332 5.0 26.4 0.3

Chlorine binding site 2 out of 4 in 8f4c

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Chlorine binding site 2 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:29.7
occ:1.00
 O A:HOH785 3.0 32.7 1.0
O C:HOH703 3.1 27.0 1.0
N A:ASN338 3.1 31.7 0.7
N A:ASN338 3.2 29.5 0.3
N C:GLU354 3.2 27.1 0.3
N C:GLU354 3.4 26.8 0.7
CA A:HIS337 3.5 28.3 0.3
CA A:HIS337 3.6 27.3 0.7
N A:PHE339 3.7 30.1 0.7
CD2 A:PHE339 3.7 29.6 0.7
CA C:GLY353 3.8 25.7 0.3
CA C:GLY353 3.8 27.9 0.7
N A:PHE339 3.8 26.9 0.3
C A:HIS337 3.8 27.4 0.3
C A:HIS337 3.8 28.8 0.7
CD2 A:PHE339 4.0 22.5 0.3
C C:GLY353 4.0 30.9 0.3
CB A:HIS337 4.0 26.5 0.3
CB C:GLU354 4.0 29.9 0.3
CA A:ASN338 4.1 29.5 0.7
O A:ALA336 4.1 32.4 0.3
C C:GLY353 4.1 27.6 0.7
O A:ALA336 4.1 29.8 0.7
CA A:ASN338 4.2 23.8 0.3
CB C:GLU354 4.2 26.4 0.7
CA C:GLU354 4.2 29.3 0.3
CB A:HIS337 4.2 25.2 0.7
CB A:ASN338 4.3 29.8 0.7
CB A:PHE339 4.3 25.8 0.7
C A:ASN338 4.3 28.3 0.7
CA C:GLU354 4.3 28.2 0.7
CG A:PHE339 4.4 31.6 0.7
CB A:PHE339 4.5 24.8 0.3
C A:ASN338 4.5 24.5 0.3
CE2 A:PHE339 4.5 26.8 0.7
CB A:ASN338 4.5 31.3 0.3
O C:HOH699 4.5 25.6 1.0
CA A:PHE339 4.5 28.1 0.7
CG A:PHE339 4.6 30.2 0.3
O A:PHE339 4.6 26.9 0.3
O A:PHE339 4.6 27.5 0.7
O C:HOH732 4.6 32.0 1.0
CA A:PHE339 4.7 28.7 0.3
N A:HIS337 4.7 27.0 0.3
CE2 A:PHE339 4.7 28.6 0.3
N A:HIS337 4.7 25.7 0.7
CG A:HIS337 4.8 26.8 0.3
CD2 A:HIS337 4.8 27.2 0.3
C A:ALA336 4.8 32.1 0.3
CG C:GLU354 4.8 28.8 0.7
N C:THR355 4.9 28.6 0.7
C A:ALA336 4.9 29.0 0.7
N C:THR355 4.9 26.2 0.3
CG A:ASN338 5.0 32.0 0.7

Chlorine binding site 3 out of 4 in 8f4c

Go back to Chlorine Binding Sites List in 8f4c
Chlorine binding site 3 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl604

b:30.2
occ:1.00
 O a:HOH762 3.2 29.2 1.0
O d:HOH578 3.2 25.1 1.0
OD1 a:ASN181 3.3 31.5 0.7
OD1 a:ASN181 3.3 28.2 0.3
N a:GLU333 3.4 26.5 0.3
N a:GLU333 3.4 29.4 0.7
NZ d:LYS317 3.4 26.9 1.0
CB a:HIS332 3.6 28.2 0.3
CA a:HIS332 3.7 27.6 0.3
CA a:HIS332 3.7 28.9 0.7
CB a:HIS332 3.7 28.7 0.7
CG a:GLU333 3.8 27.6 0.7
CG a:GLU333 3.9 27.9 0.3
C a:HIS332 4.0 26.8 0.7
C a:HIS332 4.0 27.2 0.3
CE d:LYS317 4.1 23.4 1.0
O d:HOH526 4.1 24.8 1.0
CG2 a:VAL185 4.2 28.6 0.7
CG a:ASN181 4.2 28.9 0.7
CD2 d:LEU321 4.2 27.7 1.0
CG a:ASN181 4.2 26.8 0.3
ND2 a:ASN181 4.2 25.1 0.7
ND2 a:ASN181 4.2 22.5 0.3
CG2 a:VAL185 4.2 25.8 0.3
CA a:GLU333 4.3 29.2 0.7
CA a:GLU333 4.3 25.9 0.3
O a:HOH767 4.4 34.6 1.0
CD1 d:LEU321 4.5 28.7 1.0
CB d:LYS317 4.5 22.6 1.0
CG a:HIS332 4.6 28.4 0.3
CB a:GLU333 4.7 27.3 0.7
CG a:HIS332 4.7 26.9 0.7
CB a:GLU333 4.7 24.9 0.3
O d:HOH509 4.8 30.0 1.0
CD a:GLU333 4.8 30.6 0.7
OE2 a:GLU333 4.9 30.6 0.7
CD2 a:HIS332 4.9 29.3 0.3
CD2 a:HIS332 4.9 29.1 0.7
CG d:LYS317 5.0 22.9 1.0
CD a:GLU333 5.0 27.7 0.3
CG d:LEU321 5.0 34.5 1.0
O d:LYS317 5.0 28.2 1.0

Chlorine binding site 4 out of 4 in 8f4c

Go back to Chlorine Binding Sites List in 8f4c
Chlorine binding site 4 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Cl605

b:30.2
occ:1.00
 O c:HOH686 3.1 24.7 1.0
O a:HOH758 3.1 33.4 1.0
N a:ASN338 3.1 27.7 0.3
N a:ASN338 3.2 25.8 0.7
N c:GLU354 3.4 27.7 0.3
N c:GLU354 3.4 27.1 0.7
CA a:HIS337 3.6 21.7 0.3
CA a:HIS337 3.6 27.7 0.7
N a:PHE339 3.6 24.6 0.7
CD2 a:PHE339 3.7 26.2 0.7
N a:PHE339 3.7 27.1 0.3
C a:HIS337 3.8 27.8 0.3
C a:HIS337 3.9 29.7 0.7
CD2 a:PHE339 3.9 26.1 0.3
CA c:GLY353 3.9 25.5 0.7
CA c:GLY353 3.9 23.8 0.3
CB c:GLU354 4.1 24.7 0.3
O a:ALA336 4.1 32.2 0.3
CA a:ASN338 4.1 28.5 0.7
CA a:ASN338 4.1 24.9 0.3
CB c:GLU354 4.1 29.6 0.7
CB a:HIS337 4.1 24.7 0.3
O a:ALA336 4.1 30.7 0.7
C c:GLY353 4.2 25.0 0.3
C c:GLY353 4.2 29.6 0.7
CB a:HIS337 4.2 26.7 0.7
CB a:PHE339 4.2 28.3 0.7
CG a:PHE339 4.3 26.5 0.7
CA c:GLU354 4.3 26.7 0.3
CB a:PHE339 4.3 27.9 0.3
C a:ASN338 4.3 28.7 0.7
CA c:GLU354 4.3 28.7 0.7
CB a:ASN338 4.3 26.2 0.3
CB a:ASN338 4.4 26.9 0.7
C a:ASN338 4.4 27.2 0.3
CA a:PHE339 4.5 29.0 0.7
CG a:PHE339 4.5 30.5 0.3
O a:PHE339 4.5 30.7 0.7
O c:HOH668 4.5 26.2 1.0
CE2 a:PHE339 4.5 27.8 0.7
O a:PHE339 4.5 32.1 0.3
CA a:PHE339 4.6 29.8 0.3
O c:HOH713 4.6 27.2 1.0
N a:HIS337 4.7 25.4 0.3
CE2 a:PHE339 4.7 24.5 0.3
N a:HIS337 4.8 28.2 0.7
CD2 a:HIS337 4.8 29.5 0.7
CD2 a:HIS337 4.8 28.9 0.3
C a:ALA336 4.8 31.1 0.3
CG a:HIS337 4.8 30.7 0.3
CG a:HIS337 4.9 30.0 0.7
CG c:GLU354 4.9 29.4 0.3
N c:THR355 4.9 27.3 0.3
N c:THR355 4.9 26.4 0.7
C a:ALA336 4.9 31.1 0.7
CG a:ASN338 4.9 32.6 0.7
C a:PHE339 5.0 27.8 0.7
NE2 c:GLN313 5.0 29.4 1.0
CG a:ASN338 5.0 30.1 0.3
O c:GLY352 5.0 30.4 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: Tue Jul 30 09:13:40 2024

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