Calcium 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:

Chlorine (Cl) 4 atoms
Manganese (Mn) 16 atoms
Magnesium (Mg) 70 atoms
Iron (Fe) 6 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 8f4k

Go back to Calcium Binding Sites List in 8f4k
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:32.8
occ:0.65
 CA1 A:OEX601 0.0 32.8 0.7
CA1 A:OEY602 0.1 40.0 0.3
O1 A:OEY602 2.3 32.5 0.3
O A:HOH752 2.3 39.0 0.3
O A:HOH752 2.3 32.0 0.7
O1 A:OEX601 2.3 31.5 0.7
OD2 A:ASP170 2.3 35.1 0.7
O2 A:OEX601 2.5 32.3 0.7
O A:HOH797 2.5 37.4 0.3
OD2 A:ASP170 2.5 36.9 0.3
O A:ALA344 2.5 36.2 0.7
O2 A:OEY602 2.6 35.5 0.3
O A:HOH797 2.6 33.0 0.7
O A:ALA344 2.6 37.0 0.3
O6 A:OEY602 2.6 38.9 0.3
O5 A:OEX601 2.6 32.1 0.7
O5 A:OEY602 2.7 37.5 0.3
OE1 A:GLU189 2.9 34.2 0.7
CG A:ASP170 3.3 32.1 0.7
MN1 A:OEX601 3.4 29.9 0.7
MN1 A:OEY602 3.4 34.3 0.3
MN2 A:OEY602 3.4 36.1 0.3
MN2 A:OEX601 3.4 32.2 0.7
OE1 A:GLU189 3.4 35.2 0.3
CG A:ASP170 3.5 36.5 0.3
OE2 A:GLU189 3.5 30.2 0.7
C A:ALA344 3.5 35.4 0.7
C A:ALA344 3.5 36.6 0.3
MN3 A:OEX601 3.5 31.1 0.7
CD A:GLU189 3.6 30.4 0.7
MN3 A:OEY602 3.6 38.4 0.3
O3 A:OEX601 3.7 36.5 0.7
OXT A:ALA344 3.8 34.0 0.7
OD1 A:ASP170 3.8 27.8 0.7
O3 A:OEY602 3.8 38.9 0.3
OXT A:ALA344 3.8 37.1 0.3
O A:HOH706 3.8 32.7 1.0
OE2 A:GLU189 3.9 37.6 0.3
OD1 A:ASP170 4.0 40.3 0.3
MN4 A:OEY602 4.0 40.0 0.3
CD A:GLU189 4.0 37.9 0.3
O4 A:OEX601 4.1 31.1 0.7
MN4 A:OEX601 4.1 32.8 0.7
O4 A:OEY602 4.3 33.6 0.3
NH1 C:ARG357 4.3 36.6 0.3
NH1 C:ARG357 4.3 30.9 0.7
O A:HOH720 4.5 29.1 1.0
OH A:TYR161 4.5 35.6 0.3
CB A:ASP170 4.5 29.8 0.7
CB A:ASP170 4.6 35.3 0.3
OH A:TYR161 4.6 31.8 0.7
OE1 A:GLN165 4.6 35.5 0.3
OE1 A:GLN165 4.7 33.6 0.7
NH2 C:ARG357 4.7 38.7 0.3
O A:HOH733 4.8 40.8 0.3
CA A:ALA344 4.8 38.4 0.3
CA A:ALA344 4.8 31.6 0.7
O A:HOH733 4.8 29.1 0.7
O A:HOH795 4.8 46.8 1.0
NH2 C:ARG357 4.9 30.6 0.7
OD1 A:ASP342 4.9 35.6 0.3
OD1 A:ASP342 4.9 34.1 0.7
OD2 A:ASP342 4.9 35.8 0.7
OE1 C:GLU354 4.9 35.4 0.3
OD2 A:ASP342 5.0 35.2 0.3
CZ C:ARG357 5.0 35.5 0.3

Calcium binding site 2 out of 4 in 8f4k

Go back to Calcium Binding Sites List in 8f4k
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:40.0
occ:0.35
 CA1 A:OEY602 0.0 40.0 0.3
CA1 A:OEX601 0.1 32.8 0.7
O1 A:OEY602 2.3 32.5 0.3
OD2 A:ASP170 2.3 35.1 0.7
O1 A:OEX601 2.3 31.5 0.7
O A:HOH752 2.3 39.0 0.3
O2 A:OEX601 2.4 32.3 0.7
O A:HOH752 2.4 32.0 0.7
OD2 A:ASP170 2.5 36.9 0.3
O2 A:OEY602 2.5 35.5 0.3
O A:HOH797 2.5 37.4 0.3
O5 A:OEX601 2.5 32.1 0.7
O A:ALA344 2.6 36.2 0.7
O6 A:OEY602 2.6 38.9 0.3
O A:HOH797 2.6 33.0 0.7
O5 A:OEY602 2.6 37.5 0.3
O A:ALA344 2.6 37.0 0.3
OE1 A:GLU189 3.0 34.2 0.7
CG A:ASP170 3.3 32.1 0.7
MN2 A:OEY602 3.3 36.1 0.3
MN1 A:OEX601 3.4 29.9 0.7
MN1 A:OEY602 3.4 34.3 0.3
MN2 A:OEX601 3.4 32.2 0.7
CG A:ASP170 3.4 36.5 0.3
MN3 A:OEX601 3.4 31.1 0.7
OE2 A:GLU189 3.5 30.2 0.7
C A:ALA344 3.5 35.4 0.7
OE1 A:GLU189 3.5 35.2 0.3
C A:ALA344 3.5 36.6 0.3
MN3 A:OEY602 3.5 38.4 0.3
CD A:GLU189 3.6 30.4 0.7
O3 A:OEX601 3.7 36.5 0.7
OD1 A:ASP170 3.7 27.8 0.7
O3 A:OEY602 3.7 38.9 0.3
OXT A:ALA344 3.8 34.0 0.7
OXT A:ALA344 3.8 37.1 0.3
O A:HOH706 3.8 32.7 1.0
OD1 A:ASP170 3.9 40.3 0.3
MN4 A:OEY602 3.9 40.0 0.3
OE2 A:GLU189 4.0 37.6 0.3
O4 A:OEX601 4.0 31.1 0.7
MN4 A:OEX601 4.0 32.8 0.7
CD A:GLU189 4.1 37.9 0.3
O4 A:OEY602 4.2 33.6 0.3
NH1 C:ARG357 4.3 36.6 0.3
NH1 C:ARG357 4.3 30.9 0.7
O A:HOH720 4.5 29.1 1.0
CB A:ASP170 4.5 29.8 0.7
CB A:ASP170 4.5 35.3 0.3
OH A:TYR161 4.6 35.6 0.3
NH2 C:ARG357 4.6 38.7 0.3
OH A:TYR161 4.7 31.8 0.7
OE1 A:GLN165 4.7 35.5 0.3
O A:HOH733 4.7 40.8 0.3
OE1 A:GLN165 4.7 33.6 0.7
O A:HOH733 4.8 29.1 0.7
NH2 C:ARG357 4.8 30.6 0.7
CA A:ALA344 4.8 38.4 0.3
CA A:ALA344 4.8 31.6 0.7
OD1 A:ASP342 4.9 35.6 0.3
OE1 C:GLU354 4.9 35.4 0.3
OD1 A:ASP342 4.9 34.1 0.7
O A:HOH795 4.9 46.8 1.0
OD2 A:ASP342 4.9 35.8 0.7
OE2 C:GLU354 4.9 35.0 0.7
CZ C:ARG357 4.9 35.5 0.3
OD2 A:ASP342 5.0 35.2 0.3
OE1 C:GLU354 5.0 33.7 0.7

Calcium binding site 3 out of 4 in 8f4k

Go back to Calcium Binding Sites List in 8f4k
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:36.5
occ:0.65
 CA1 a:OEX601 0.0 36.5 0.7
CA1 a:OEY602 0.1 40.5 0.3
O a:HOH765 2.2 40.3 0.3
O1 a:OEY602 2.3 36.9 0.3
O1 a:OEX601 2.3 34.3 0.7
O a:HOH765 2.3 36.2 0.7
OD2 a:ASP170 2.4 37.3 0.7
O2 a:OEX601 2.5 29.9 0.7
O6 a:OEY602 2.5 43.5 0.3
O a:ALA344 2.5 40.6 0.3
O2 a:OEY602 2.5 36.2 0.3
O a:HOH786 2.5 33.2 0.7
O a:HOH786 2.6 37.6 0.3
O5 a:OEX601 2.6 36.8 0.7
O a:ALA344 2.6 33.7 0.7
OD2 a:ASP170 2.6 37.2 0.3
O5 a:OEY602 2.7 39.4 0.3
OE1 a:GLU189 2.7 29.5 0.7
OE1 a:GLU189 3.0 40.8 0.3
CG a:ASP170 3.3 33.5 0.7
MN2 a:OEY602 3.4 35.3 0.3
MN1 a:OEY602 3.4 37.7 0.3
MN1 a:OEX601 3.4 31.4 0.7
MN2 a:OEX601 3.4 32.3 0.7
CG a:ASP170 3.4 38.8 0.3
C a:ALA344 3.5 39.0 0.3
CD a:GLU189 3.5 29.4 0.7
C a:ALA344 3.6 36.5 0.7
MN3 a:OEX601 3.6 31.7 0.7
MN3 a:OEY602 3.6 38.7 0.3
OE2 a:GLU189 3.6 32.4 0.7
OXT a:ALA344 3.7 34.2 0.3
OD1 a:ASP170 3.7 32.3 0.7
O3 a:OEX601 3.8 33.5 0.7
O3 a:OEY602 3.8 38.1 0.3
OXT a:ALA344 3.8 33.1 0.7
OD1 a:ASP170 3.8 40.6 0.3
CD a:GLU189 3.9 39.6 0.3
OE2 a:GLU189 4.0 38.6 0.3
MN4 a:OEX601 4.1 31.0 0.7
MN4 a:OEY602 4.2 36.9 0.3
O4 a:OEX601 4.2 33.2 0.7
O a:HOH764 4.2 31.3 1.0
O a:HOH703 4.3 38.0 1.0
NH1 c:ARG357 4.4 34.5 0.7
NH1 c:ARG357 4.4 33.7 0.3
CB a:ASP170 4.5 29.7 0.7
O4 a:OEY602 4.5 37.1 0.3
OH a:TYR161 4.6 32.0 0.7
CB a:ASP170 4.6 35.2 0.3
OE1 a:GLN165 4.6 32.8 0.7
O a:HOH790 4.6 42.5 1.0
OE1 a:GLN165 4.6 35.8 0.3
OH a:TYR161 4.7 34.5 0.3
O a:HOH740 4.8 27.0 0.7
CA a:ALA344 4.8 37.4 0.3
O a:HOH740 4.9 39.0 0.3
NH2 c:ARG357 4.9 37.3 0.3
CA a:ALA344 4.9 34.7 0.7
CG a:GLU189 4.9 34.1 0.7
NH2 c:ARG357 4.9 33.6 0.7
CG1 a:VAL185 5.0 36.0 0.3
CG1 a:VAL185 5.0 31.8 0.7
OE1 c:GLU354 5.0 33.8 0.7
OD1 a:ASP342 5.0 37.6 0.3

Calcium binding site 4 out of 4 in 8f4k

Go back to Calcium Binding Sites List in 8f4k
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:40.5
occ:0.35
 CA1 a:OEY602 0.0 40.5 0.3
CA1 a:OEX601 0.1 36.5 0.7
O1 a:OEY602 2.2 36.9 0.3
O a:HOH765 2.3 40.3 0.3
O1 a:OEX601 2.3 34.3 0.7
OD2 a:ASP170 2.4 37.3 0.7
O a:HOH765 2.4 36.2 0.7
O2 a:OEX601 2.4 29.9 0.7
O6 a:OEY602 2.5 43.5 0.3
O2 a:OEY602 2.5 36.2 0.3
O5 a:OEX601 2.5 36.8 0.7
O a:HOH786 2.5 33.2 0.7
O a:HOH786 2.5 37.6 0.3
O5 a:OEY602 2.6 39.4 0.3
O a:ALA344 2.6 40.6 0.3
OD2 a:ASP170 2.6 37.2 0.3
O a:ALA344 2.7 33.7 0.7
OE1 a:GLU189 2.7 29.5 0.7
OE1 a:GLU189 3.0 40.8 0.3
CG a:ASP170 3.2 33.5 0.7
MN2 a:OEY602 3.3 35.3 0.3
MN1 a:OEX601 3.3 31.4 0.7
MN1 a:OEY602 3.3 37.7 0.3
MN2 a:OEX601 3.4 32.3 0.7
CG a:ASP170 3.4 38.8 0.3
MN3 a:OEX601 3.5 31.7 0.7
MN3 a:OEY602 3.5 38.7 0.3
C a:ALA344 3.5 39.0 0.3
CD a:GLU189 3.5 29.4 0.7
OE2 a:GLU189 3.6 32.4 0.7
OD1 a:ASP170 3.6 32.3 0.7
C a:ALA344 3.6 36.5 0.7
OXT a:ALA344 3.7 34.2 0.3
O3 a:OEY602 3.7 38.1 0.3
O3 a:OEX601 3.7 33.5 0.7
OD1 a:ASP170 3.8 40.6 0.3
OXT a:ALA344 3.8 33.1 0.7
CD a:GLU189 3.9 39.6 0.3
MN4 a:OEX601 4.0 31.0 0.7
OE2 a:GLU189 4.0 38.6 0.3
MN4 a:OEY602 4.1 36.9 0.3
O4 a:OEX601 4.1 33.2 0.7
O a:HOH764 4.3 31.3 1.0
O a:HOH703 4.4 38.0 1.0
O4 a:OEY602 4.4 37.1 0.3
NH1 c:ARG357 4.4 34.5 0.7
NH1 c:ARG357 4.5 33.7 0.3
CB a:ASP170 4.5 29.7 0.7
CB a:ASP170 4.5 35.2 0.3
OH a:TYR161 4.6 32.0 0.7
O a:HOH740 4.7 27.0 0.7
OE1 a:GLN165 4.7 32.8 0.7
O a:HOH790 4.7 42.5 1.0
OE1 a:GLN165 4.7 35.8 0.3
OH a:TYR161 4.7 34.5 0.3
O a:HOH740 4.8 39.0 0.3
NH2 c:ARG357 4.8 37.3 0.3
CA a:ALA344 4.9 37.4 0.3
NH2 c:ARG357 4.9 33.6 0.7
CG1 a:VAL185 4.9 36.0 0.3
CG a:GLU189 4.9 34.1 0.7
CG1 a:VAL185 4.9 31.8 0.7
OE1 c:GLU354 4.9 33.8 0.7
CA a:ALA344 5.0 34.7 0.7
OD1 a:ASP342 5.0 37.6 0.3
OE1 c:GLU354 5.0 37.1 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: Tue Apr 4 19:47:37 2023

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