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Calcium 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:

Chlorine (Cl) 4 atoms
Manganese (Mn) 16 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 70 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 2.00 Angstrom Resolution (pdb code 8f4c). 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 2.00 Angstrom Resolution, PDB code: 8f4c:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8f4c

Go back to Calcium Binding Sites List in 8f4c
Calcium binding site 1 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:29.9
occ:0.65
 CA1 A:OEY601 0.0 29.9 0.7
CA1 A:OEX602 0.2 30.3 0.3
O1 A:OEY601 2.3 27.6 0.7
O A:HOH716 2.3 31.9 0.7
OD2 A:ASP170 2.3 28.6 0.7
O1 A:OEX602 2.4 21.5 0.3
O5 A:OEX602 2.4 29.1 0.3
O A:ALA344 2.4 31.4 0.7
O2 A:OEX602 2.5 31.3 0.3
O A:HOH805 2.5 25.8 0.3
O2 A:OEY601 2.5 24.3 0.7
O A:HOH716 2.5 32.4 0.3
OD2 A:ASP170 2.5 29.1 0.3
O A:HOH805 2.5 28.1 0.7
O A:ALA344 2.6 33.5 0.3
O6 A:OEY601 2.6 28.6 0.7
O5 A:OEY601 2.7 30.9 0.7
OE1 A:GLU189 2.8 29.9 0.3
OE1 A:GLU189 3.2 30.2 0.7
CG A:ASP170 3.3 30.1 0.3
CG A:ASP170 3.3 28.5 0.7
MN2 A:OEY601 3.3 26.9 0.7
MN1 A:OEX602 3.4 28.4 0.3
C A:ALA344 3.4 30.6 0.7
MN1 A:OEY601 3.4 26.9 0.7
MN2 A:OEX602 3.4 28.4 0.3
MN3 A:OEX602 3.5 28.4 0.3
OE2 A:GLU189 3.5 29.4 0.3
MN3 A:OEY601 3.5 26.7 0.7
C A:ALA344 3.5 31.1 0.3
CD A:GLU189 3.5 29.6 0.3
OXT A:ALA344 3.7 26.6 0.7
OD1 A:ASP170 3.7 27.7 0.3
O3 A:OEY601 3.8 30.2 0.7
MN4 A:OEX602 3.8 33.6 0.3
OXT A:ALA344 3.8 27.8 0.3
O3 A:OEX602 3.8 31.9 0.3
O4 A:OEX602 3.8 33.1 0.3
OD1 A:ASP170 3.8 27.3 0.7
OE2 A:GLU189 3.9 32.4 0.7
CD A:GLU189 3.9 30.2 0.7
MN4 A:OEY601 4.0 28.8 0.7
O4 A:OEY601 4.1 28.2 0.7
O A:HOH809 4.2 33.9 1.0
O A:HOH733 4.4 25.6 1.0
NH1 C:ARG357 4.5 25.3 0.3
CB A:ASP170 4.5 25.9 0.3
NH1 C:ARG357 4.5 24.7 0.7
CB A:ASP170 4.5 23.5 0.7
OE1 A:GLN165 4.5 30.4 0.7
O A:HOH777 4.6 30.8 0.3
OH A:TYR161 4.6 25.0 0.3
NH2 C:ARG357 4.7 29.5 0.3
O A:HOH777 4.7 31.9 0.7
CA A:ALA344 4.7 31.4 0.7
OH A:TYR161 4.7 27.7 0.7
NH2 C:ARG357 4.8 25.1 0.7
OE1 A:GLN165 4.8 29.3 0.3
CA A:ALA344 4.8 31.2 0.3
OD1 A:ASP342 4.9 24.1 0.7
OD2 A:ASP342 5.0 25.1 0.3
OE1 C:GLU354 5.0 28.4 0.7
OE2 C:GLU354 5.0 29.6 0.3
OD2 A:ASP342 5.0 26.6 0.7

Calcium binding site 2 out of 4 in 8f4c

Go back to Calcium Binding Sites List in 8f4c
Calcium binding site 2 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:30.3
occ:0.35
 CA1 A:OEX602 0.0 30.3 0.3
CA1 A:OEY601 0.2 29.9 0.7
O A:HOH716 2.2 31.9 0.7
O1 A:OEY601 2.3 27.6 0.7
O A:ALA344 2.3 31.4 0.7
O A:HOH716 2.3 32.4 0.3
O1 A:OEX602 2.3 21.5 0.3
OD2 A:ASP170 2.4 28.6 0.7
O A:ALA344 2.4 33.5 0.3
O2 A:OEX602 2.5 31.3 0.3
O A:HOH805 2.5 25.8 0.3
O2 A:OEY601 2.5 24.3 0.7
OD2 A:ASP170 2.5 29.1 0.3
O5 A:OEX602 2.6 29.1 0.3
O A:HOH805 2.6 28.1 0.7
O6 A:OEY601 2.7 28.6 0.7
OE1 A:GLU189 2.8 29.9 0.3
O5 A:OEY601 2.8 30.9 0.7
OE1 A:GLU189 3.2 30.2 0.7
C A:ALA344 3.3 30.6 0.7
MN2 A:OEY601 3.4 26.9 0.7
CG A:ASP170 3.4 30.1 0.3
CG A:ASP170 3.4 28.5 0.7
C A:ALA344 3.4 31.1 0.3
MN2 A:OEX602 3.4 28.4 0.3
MN1 A:OEX602 3.4 28.4 0.3
MN1 A:OEY601 3.5 26.9 0.7
OE2 A:GLU189 3.5 29.4 0.3
CD A:GLU189 3.5 29.6 0.3
OXT A:ALA344 3.6 26.6 0.7
MN3 A:OEX602 3.6 28.4 0.3
MN3 A:OEY601 3.7 26.7 0.7
OXT A:ALA344 3.7 27.8 0.3
OD1 A:ASP170 3.8 27.7 0.3
O3 A:OEY601 3.9 30.2 0.7
O3 A:OEX602 3.9 31.9 0.3
OE2 A:GLU189 3.9 32.4 0.7
CD A:GLU189 3.9 30.2 0.7
OD1 A:ASP170 3.9 27.3 0.7
MN4 A:OEX602 4.0 33.6 0.3
O4 A:OEX602 4.0 33.1 0.3
O A:HOH809 4.0 33.9 1.0
MN4 A:OEY601 4.2 28.8 0.7
O4 A:OEY601 4.2 28.2 0.7
OE1 A:GLN165 4.4 30.4 0.7
O A:HOH733 4.4 25.6 1.0
NH1 C:ARG357 4.4 25.3 0.3
NH1 C:ARG357 4.4 24.7 0.7
CB A:ASP170 4.5 25.9 0.3
OH A:TYR161 4.5 25.0 0.3
CB A:ASP170 4.5 23.5 0.7
CA A:ALA344 4.5 31.4 0.7
OH A:TYR161 4.6 27.7 0.7
OE1 A:GLN165 4.6 29.3 0.3
NH2 C:ARG357 4.7 29.5 0.3
CA A:ALA344 4.7 31.2 0.3
O A:HOH777 4.8 30.8 0.3
O A:HOH777 4.8 31.9 0.7
NH2 C:ARG357 4.8 25.1 0.7
OD1 A:ASP342 4.9 24.1 0.7
OD2 A:ASP342 5.0 25.1 0.3

Calcium binding site 3 out of 4 in 8f4c

Go back to Calcium Binding Sites List in 8f4c
Calcium binding site 3 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:29.0
occ:0.65
 CA1 a:OEY601 0.0 29.0 0.7
CA1 a:OEX602 0.1 30.5 0.3
OD2 a:ASP170 2.3 28.3 0.7
O1 a:OEY601 2.3 29.0 0.7
O a:HOH755 2.3 29.7 0.7
O a:HOH755 2.3 31.9 0.3
O5 a:OEX602 2.4 31.9 0.3
O1 a:OEX602 2.4 26.4 0.3
O a:HOH778 2.4 24.9 0.3
O a:ALA344 2.5 28.7 0.7
OD2 a:ASP170 2.5 29.0 0.3
O2 a:OEY601 2.5 27.8 0.7
O2 a:OEX602 2.5 24.5 0.3
O6 a:OEY601 2.5 32.9 0.7
O a:HOH778 2.6 28.1 0.7
O a:ALA344 2.6 30.3 0.3
O5 a:OEY601 2.6 30.4 0.7
OE1 a:GLU189 2.8 27.8 0.3
OE1 a:GLU189 3.1 29.5 0.7
CG a:ASP170 3.3 27.8 0.3
CG a:ASP170 3.3 29.7 0.7
MN2 a:OEY601 3.4 26.7 0.7
MN1 a:OEX602 3.4 29.1 0.3
MN1 a:OEY601 3.4 27.6 0.7
C a:ALA344 3.5 28.4 0.7
MN2 a:OEX602 3.5 28.1 0.3
MN3 a:OEX602 3.5 27.6 0.3
OE2 a:GLU189 3.5 28.6 0.3
MN3 a:OEY601 3.5 30.0 0.7
CD a:GLU189 3.6 29.1 0.3
C a:ALA344 3.6 28.7 0.3
OD1 a:ASP170 3.6 26.6 0.3
OXT a:ALA344 3.8 29.0 0.7
OD1 a:ASP170 3.8 32.4 0.7
O3 a:OEY601 3.8 32.2 0.7
OXT a:ALA344 3.9 27.3 0.3
CD a:GLU189 3.9 29.9 0.7
O3 a:OEX602 3.9 29.7 0.3
OE2 a:GLU189 3.9 29.3 0.7
MN4 a:OEX602 4.0 31.9 0.3
MN4 a:OEY601 4.0 32.9 0.7
O4 a:OEX602 4.2 25.3 0.3
O a:HOH781 4.2 34.7 1.0
NH1 c:ARG357 4.4 25.7 0.7
O4 a:OEY601 4.4 29.6 0.7
O a:HOH718 4.4 27.6 1.0
CB a:ASP170 4.5 25.9 0.3
CB a:ASP170 4.5 24.3 0.7
NH1 c:ARG357 4.5 24.3 0.3
O a:HOH744 4.6 30.0 0.3
OH a:TYR161 4.6 26.5 0.7
NH2 c:ARG357 4.7 29.3 0.7
OE1 a:GLN165 4.7 28.2 0.3
O a:HOH744 4.7 29.9 0.7
OH a:TYR161 4.7 27.9 0.3
OE1 a:GLN165 4.8 28.6 0.7
CA a:ALA344 4.8 25.7 0.7
NH2 c:ARG357 4.8 24.9 0.3
CA a:ALA344 4.9 29.4 0.3
CG1 a:VAL185 4.9 24.9 0.3

Calcium binding site 4 out of 4 in 8f4c

Go back to Calcium Binding Sites List in 8f4c
Calcium binding site 4 out of 4 in the Rt Xfel Structure of the Two-Flash State of Photosystem II (2F, S3- Rich) at 2.00 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 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca602

b:30.5
occ:0.35
 CA1 a:OEX602 0.0 30.5 0.3
CA1 a:OEY601 0.1 29.0 0.7
O1 a:OEY601 2.3 29.0 0.7
O a:HOH755 2.3 29.7 0.7
O a:HOH755 2.3 31.9 0.3
OD2 a:ASP170 2.3 28.3 0.7
O a:ALA344 2.3 28.7 0.7
O1 a:OEX602 2.3 26.4 0.3
O a:ALA344 2.5 30.3 0.3
O2 a:OEY601 2.5 27.8 0.7
O2 a:OEX602 2.5 24.5 0.3
O5 a:OEX602 2.5 31.9 0.3
OD2 a:ASP170 2.5 29.0 0.3
O a:HOH778 2.5 24.9 0.3
O6 a:OEY601 2.6 32.9 0.7
O a:HOH778 2.7 28.1 0.7
O5 a:OEY601 2.7 30.4 0.7
OE1 a:GLU189 2.8 27.8 0.3
OE1 a:GLU189 3.1 29.5 0.7
MN2 a:OEY601 3.3 26.7 0.7
CG a:ASP170 3.3 27.8 0.3
C a:ALA344 3.3 28.4 0.7
CG a:ASP170 3.4 29.7 0.7
MN1 a:OEX602 3.4 29.1 0.3
MN1 a:OEY601 3.4 27.6 0.7
MN2 a:OEX602 3.4 28.1 0.3
C a:ALA344 3.5 28.7 0.3
MN3 a:OEX602 3.5 27.6 0.3
OE2 a:GLU189 3.5 28.6 0.3
CD a:GLU189 3.6 29.1 0.3
MN3 a:OEY601 3.6 30.0 0.7
OXT a:ALA344 3.7 29.0 0.7
OD1 a:ASP170 3.7 26.6 0.3
OXT a:ALA344 3.8 27.3 0.3
O3 a:OEY601 3.8 32.2 0.7
OD1 a:ASP170 3.9 32.4 0.7
CD a:GLU189 3.9 29.9 0.7
O3 a:OEX602 3.9 29.7 0.3
OE2 a:GLU189 3.9 29.3 0.7
MN4 a:OEX602 4.1 31.9 0.3
MN4 a:OEY601 4.1 32.9 0.7
O a:HOH781 4.1 34.7 1.0
O4 a:OEX602 4.3 25.3 0.3
NH1 c:ARG357 4.3 25.7 0.7
NH1 c:ARG357 4.4 24.3 0.3
O4 a:OEY601 4.5 29.6 0.7
CB a:ASP170 4.5 25.9 0.3
O a:HOH718 4.5 27.6 1.0
CB a:ASP170 4.5 24.3 0.7
OE1 a:GLN165 4.6 28.2 0.3
OH a:TYR161 4.6 26.5 0.7
CA a:ALA344 4.6 25.7 0.7
OE1 a:GLN165 4.7 28.6 0.7
NH2 c:ARG357 4.7 29.3 0.7
O a:HOH744 4.7 30.0 0.3
OH a:TYR161 4.7 27.9 0.3
CA a:ALA344 4.7 29.4 0.3
NH2 c:ARG357 4.8 24.9 0.3
O a:HOH744 4.9 29.9 0.7
O a:HOH803 5.0 38.8 1.0
OD1 a:ASP342 5.0 28.8 0.7
CZ c:ARG357 5.0 28.3 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: Fri Jul 19 08:43:56 2024

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