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Calcium 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
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8ez5

Go back to Calcium Binding Sites List in 8ez5
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:32.3
occ:0.65
 CA1 A:OEY601 0.0 32.3 0.7
CA1 A:OEX602 0.1 38.0 0.3
O1 A:OEY601 2.3 26.1 0.7
O A:HOH732 2.3 32.1 0.7
O1 A:OEX602 2.3 31.4 0.3
O5 A:OEX602 2.4 35.2 0.3
O A:HOH732 2.4 35.4 0.3
OD2 A:ASP170 2.4 35.0 0.3
OD2 A:ASP170 2.4 29.4 0.7
O2 A:OEX602 2.4 31.8 0.3
O A:ALA344 2.5 36.2 0.3
O2 A:OEY601 2.5 28.3 0.7
O A:HOH786 2.5 36.6 0.3
O A:HOH786 2.5 31.1 0.7
O6 A:OEY601 2.5 35.0 0.7
O5 A:OEY601 2.6 31.5 0.7
O A:ALA344 2.6 31.8 0.7
OE1 A:GLU189 2.9 37.2 0.3
MN2 A:OEX602 3.3 34.9 0.3
CG A:ASP170 3.3 34.2 0.3
MN2 A:OEY601 3.3 29.0 0.7
MN1 A:OEY601 3.3 26.7 0.7
MN1 A:OEX602 3.4 32.6 0.3
C A:ALA344 3.4 38.9 0.3
CG A:ASP170 3.4 29.0 0.7
MN3 A:OEX602 3.4 32.6 0.3
OE2 A:GLU189 3.5 35.4 0.3
MN3 A:OEY601 3.5 30.8 0.7
C A:ALA344 3.5 31.5 0.7
OE1 A:GLU189 3.6 28.5 0.7
CD A:GLU189 3.6 32.0 0.3
OXT A:ALA344 3.7 39.7 0.3
OD1 A:ASP170 3.7 35.9 0.3
O3 A:OEY601 3.7 33.2 0.7
O3 A:OEX602 3.7 35.6 0.3
OXT A:ALA344 3.8 31.1 0.7
O4 A:OEX602 3.8 31.3 0.3
MN4 A:OEX602 3.9 36.0 0.3
OD1 A:ASP170 3.9 33.0 0.7
MN4 A:OEY601 3.9 32.2 0.7
OE2 A:GLU189 3.9 31.5 0.7
CD A:GLU189 4.1 31.4 0.7
O A:HOH716 4.2 34.0 1.0
O4 A:OEY601 4.2 26.9 0.7
NH1 C:ARG357 4.3 29.5 0.7
CB A:ASP170 4.4 28.4 0.3
O A:HOH741 4.4 28.6 1.0
NH1 C:ARG357 4.5 38.3 0.3
CB A:ASP170 4.5 28.6 0.7
O A:HOH805 4.5 42.4 1.0
NH2 C:ARG357 4.6 31.6 0.3
O A:HOH747 4.6 35.1 0.3
OH A:TYR161 4.6 28.8 0.7
OH A:TYR161 4.6 31.8 0.3
CA A:ALA344 4.7 38.9 0.3
OE1 A:GLN165 4.7 29.3 0.7
NH2 C:ARG357 4.7 32.0 0.7
O A:HOH747 4.7 34.2 0.7
OE1 A:GLN165 4.7 33.2 0.3
CA A:ALA344 4.8 32.8 0.7
OD1 A:ASP342 4.9 29.1 0.7
OE1 C:GLU354 4.9 28.9 0.7
OD1 A:ASP342 4.9 32.6 0.3
OE2 C:GLU354 4.9 36.1 0.3
OE1 C:GLU354 4.9 36.3 0.3
OD2 A:ASP342 5.0 29.1 0.7
CZ C:ARG357 5.0 29.9 0.7
OD2 A:ASP342 5.0 32.4 0.3

Calcium binding site 2 out of 4 in 8ez5

Go back to Calcium Binding Sites List in 8ez5
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:38.0
occ:0.35
 CA1 A:OEX602 0.0 38.0 0.3
CA1 A:OEY601 0.1 32.3 0.7
O A:HOH732 2.2 32.1 0.7
O1 A:OEY601 2.3 26.1 0.7
O A:HOH732 2.3 35.4 0.3
O1 A:OEX602 2.4 31.4 0.3
O A:ALA344 2.4 36.2 0.3
OD2 A:ASP170 2.5 35.0 0.3
OD2 A:ASP170 2.5 29.4 0.7
O5 A:OEX602 2.5 35.2 0.3
O A:HOH786 2.5 36.6 0.3
O A:HOH786 2.5 31.1 0.7
O2 A:OEX602 2.5 31.8 0.3
O2 A:OEY601 2.6 28.3 0.7
O A:ALA344 2.6 31.8 0.7
O6 A:OEY601 2.6 35.0 0.7
O5 A:OEY601 2.7 31.5 0.7
OE1 A:GLU189 2.8 37.2 0.3
MN2 A:OEX602 3.3 34.9 0.3
CG A:ASP170 3.3 34.2 0.3
C A:ALA344 3.4 38.9 0.3
MN2 A:OEY601 3.4 29.0 0.7
MN1 A:OEY601 3.4 26.7 0.7
MN1 A:OEX602 3.4 32.6 0.3
CG A:ASP170 3.4 29.0 0.7
OE2 A:GLU189 3.5 35.4 0.3
C A:ALA344 3.5 31.5 0.7
OE1 A:GLU189 3.5 28.5 0.7
MN3 A:OEX602 3.5 32.6 0.3
CD A:GLU189 3.5 32.0 0.3
MN3 A:OEY601 3.6 30.8 0.7
OXT A:ALA344 3.7 39.7 0.3
OD1 A:ASP170 3.8 35.9 0.3
OXT A:ALA344 3.8 31.1 0.7
O3 A:OEY601 3.8 33.2 0.7
O3 A:OEX602 3.8 35.6 0.3
O4 A:OEX602 3.9 31.3 0.3
OE2 A:GLU189 3.9 31.5 0.7
OD1 A:ASP170 4.0 33.0 0.7
MN4 A:OEX602 4.0 36.0 0.3
MN4 A:OEY601 4.0 32.2 0.7
CD A:GLU189 4.1 31.4 0.7
O A:HOH716 4.1 34.0 1.0
NH1 C:ARG357 4.3 29.5 0.7
O4 A:OEY601 4.3 26.9 0.7
O A:HOH741 4.4 28.6 1.0
O A:HOH805 4.4 42.4 1.0
CB A:ASP170 4.5 28.4 0.3
NH1 C:ARG357 4.5 38.3 0.3
OH A:TYR161 4.5 28.8 0.7
CB A:ASP170 4.5 28.6 0.7
OE1 A:GLN165 4.6 29.3 0.7
OH A:TYR161 4.6 31.8 0.3
CA A:ALA344 4.6 38.9 0.3
OE1 A:GLN165 4.6 33.2 0.3
NH2 C:ARG357 4.6 31.6 0.3
O A:HOH747 4.7 35.1 0.3
NH2 C:ARG357 4.7 32.0 0.7
CA A:ALA344 4.8 32.8 0.7
O A:HOH747 4.8 34.2 0.7
OD1 A:ASP342 4.9 29.1 0.7
OD1 A:ASP342 4.9 32.6 0.3
OE1 C:GLU354 4.9 28.9 0.7
OD2 A:ASP342 5.0 29.1 0.7
CG A:GLU189 5.0 34.1 0.3

Calcium binding site 3 out of 4 in 8ez5

Go back to Calcium Binding Sites List in 8ez5
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:32.7
occ:0.65
 CA1 a:OEY601 0.0 32.7 0.7
CA1 a:OEX602 0.1 36.9 0.3
O a:HOH705 2.1 34.3 0.3
O1 a:OEY601 2.3 31.6 0.7
O a:HOH705 2.3 33.7 0.7
O1 a:OEX602 2.4 30.1 0.3
OD2 a:ASP170 2.5 38.8 0.3
O6 a:OEY601 2.5 38.2 0.7
O2 a:OEY601 2.5 30.5 0.7
O a:ALA344 2.5 33.1 0.3
O a:HOH785 2.5 34.5 0.3
OD2 a:ASP170 2.5 30.6 0.7
O a:HOH785 2.5 29.8 0.7
O2 a:OEX602 2.6 31.3 0.3
O5 a:OEY601 2.6 33.2 0.7
O a:ALA344 2.6 34.6 0.7
O5 a:OEX602 2.6 35.3 0.3
OE1 a:GLU189 2.7 37.9 0.3
OE1 a:GLU189 3.0 33.3 0.7
CG a:ASP170 3.2 36.7 0.3
MN2 a:OEY601 3.3 27.9 0.7
MN1 a:OEX602 3.3 33.9 0.3
MN1 a:OEY601 3.3 30.1 0.7
MN2 a:OEX602 3.4 34.0 0.3
CG a:ASP170 3.4 32.2 0.7
MN3 a:OEX602 3.4 31.1 0.3
C a:ALA344 3.4 35.7 0.3
CD a:GLU189 3.5 38.5 0.3
OE2 a:GLU189 3.5 34.1 0.3
MN3 a:OEY601 3.5 31.7 0.7
C a:ALA344 3.5 33.0 0.7
OD1 a:ASP170 3.5 33.0 0.3
OXT a:ALA344 3.7 31.1 0.3
OXT a:ALA344 3.7 27.4 0.7
O3 a:OEY601 3.7 31.3 0.7
O3 a:OEX602 3.8 32.3 0.3
OD1 a:ASP170 3.8 33.7 0.7
CD a:GLU189 3.9 32.3 0.7
MN4 a:OEX602 3.9 37.0 0.3
OE2 a:GLU189 4.0 32.3 0.7
O a:HOH741 4.0 39.4 1.0
MN4 a:OEY601 4.1 29.8 0.7
O a:HOH742 4.2 35.2 1.0
O4 a:OEX602 4.2 29.9 0.3
CB a:ASP170 4.4 28.9 0.3
NH1 c:ARG357 4.4 28.1 0.7
O4 a:OEY601 4.4 29.9 0.7
NH1 c:ARG357 4.5 35.2 0.3
CB a:ASP170 4.5 28.0 0.7
OH a:TYR161 4.6 31.9 0.3
OE1 a:GLN165 4.7 34.2 0.3
NH2 c:ARG357 4.7 31.7 0.3
O a:HOH739 4.7 28.8 0.3
OE1 a:GLN165 4.7 28.1 0.7
OH a:TYR161 4.7 28.2 0.7
CA a:ALA344 4.8 35.4 0.3
O a:HOH739 4.8 33.0 0.7
CA a:ALA344 4.9 31.4 0.7
NH2 c:ARG357 4.9 30.3 0.7
CG1 a:VAL185 4.9 28.2 0.7
CG a:GLU189 5.0 37.1 0.3
OD2 a:ASP342 5.0 37.1 0.3
OE1 c:GLU354 5.0 33.8 0.3
OE2 c:GLU354 5.0 34.5 0.3

Calcium binding site 4 out of 4 in 8ez5

Go back to Calcium Binding Sites List in 8ez5
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:36.9
occ:0.35
 CA1 a:OEX602 0.0 36.9 0.3
CA1 a:OEY601 0.1 32.7 0.7
O1 a:OEY601 2.2 31.6 0.7
O a:HOH705 2.2 34.3 0.3
O1 a:OEX602 2.3 30.1 0.3
O a:HOH705 2.4 33.7 0.7
O6 a:OEY601 2.4 38.2 0.7
O2 a:OEY601 2.4 30.5 0.7
O5 a:OEY601 2.5 33.2 0.7
O2 a:OEX602 2.5 31.3 0.3
O5 a:OEX602 2.5 35.3 0.3
O a:HOH785 2.5 34.5 0.3
OD2 a:ASP170 2.5 38.8 0.3
O a:HOH785 2.6 29.8 0.7
O a:ALA344 2.6 33.1 0.3
OD2 a:ASP170 2.6 30.6 0.7
O a:ALA344 2.7 34.6 0.7
OE1 a:GLU189 2.7 37.9 0.3
OE1 a:GLU189 3.0 33.3 0.7
MN1 a:OEX602 3.2 33.9 0.3
MN1 a:OEY601 3.2 30.1 0.7
CG a:ASP170 3.3 36.7 0.3
MN2 a:OEY601 3.3 27.9 0.7
MN2 a:OEX602 3.3 34.0 0.3
MN3 a:OEX602 3.3 31.1 0.3
MN3 a:OEY601 3.4 31.7 0.7
OE2 a:GLU189 3.4 34.1 0.3
CG a:ASP170 3.4 32.2 0.7
CD a:GLU189 3.4 38.5 0.3
C a:ALA344 3.5 35.7 0.3
OD1 a:ASP170 3.5 33.0 0.3
C a:ALA344 3.6 33.0 0.7
O3 a:OEY601 3.6 31.3 0.7
OXT a:ALA344 3.7 31.1 0.3
O3 a:OEX602 3.7 32.3 0.3
OXT a:ALA344 3.7 27.4 0.7
CD a:GLU189 3.8 32.3 0.7
OD1 a:ASP170 3.8 33.7 0.7
MN4 a:OEX602 3.9 37.0 0.3
OE2 a:GLU189 3.9 32.3 0.7
MN4 a:OEY601 4.0 29.8 0.7
O a:HOH741 4.1 39.4 1.0
O4 a:OEX602 4.2 29.9 0.3
O a:HOH742 4.2 35.2 1.0
O4 a:OEY601 4.4 29.9 0.7
CB a:ASP170 4.4 28.9 0.3
NH1 c:ARG357 4.5 28.1 0.7
NH1 c:ARG357 4.5 35.2 0.3
CB a:ASP170 4.6 28.0 0.7
O a:HOH739 4.6 28.8 0.3
NH2 c:ARG357 4.7 31.7 0.3
OH a:TYR161 4.7 31.9 0.3
O a:HOH739 4.7 33.0 0.7
OE1 a:GLN165 4.8 34.2 0.3
CA a:ALA344 4.8 35.4 0.3
OH a:TYR161 4.8 28.2 0.7
OE1 a:GLN165 4.8 28.1 0.7
OD2 a:ASP342 4.9 37.1 0.3
CG1 a:VAL185 4.9 28.2 0.7
OE2 c:GLU354 4.9 34.5 0.3
OE1 c:GLU354 4.9 33.8 0.3
OD2 a:ASP342 4.9 31.0 0.7
NH2 c:ARG357 4.9 30.3 0.7
CG a:GLU189 4.9 37.1 0.3
CA a:ALA344 4.9 31.4 0.7
OD1 a:ASP342 4.9 38.0 0.3
OD1 a:ASP342 5.0 30.9 0.7
OE1 c:GLU354 5.0 30.9 0.7
CG1 a:VAL185 5.0 27.7 0.3

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: Thu Jul 10 04:30:16 2025

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