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Calcium in PDB 8f4d: Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution, PDB code: 8f4d 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) 33.74 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.103, 222.196, 308.415, 90, 90, 90
R / Rfree (%) 18.8 / 24.3

Other elements in 8f4d:

The structure of Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution (pdb code 8f4d). 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 Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution, PDB code: 8f4d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8f4d

Go back to Calcium Binding Sites List in 8f4d
Calcium binding site 1 out of 4 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 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 Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:34.8
occ:0.65
 CA1 A:OEY601 0.0 34.8 0.7
CA1 A:OEX602 0.1 37.1 0.3
O A:HOH715 2.2 32.4 0.7
OD2 A:ASP170 2.3 38.7 0.7
O1 A:OEY601 2.4 30.1 0.7
O1 A:OEX602 2.4 37.1 0.3
O A:HOH715 2.4 39.7 0.3
OD2 A:ASP170 2.4 34.6 0.3
O A:ALA344 2.5 39.6 0.3
O2 A:OEY601 2.5 32.4 0.7
O A:ALA344 2.5 36.2 0.7
O2 A:OEX602 2.5 26.7 0.3
O A:HOH781 2.5 29.5 0.3
O5 A:OEX602 2.5 39.5 0.3
O5 A:OEY601 2.6 33.1 0.7
O A:HOH781 2.6 31.7 0.7
O6 A:OEY601 2.7 32.9 0.7
OE1 A:GLU189 3.2 31.9 0.7
CG A:ASP170 3.3 33.1 0.7
CG A:ASP170 3.3 35.9 0.3
OE1 A:GLU189 3.3 35.7 0.3
C A:ALA344 3.4 31.7 0.3
MN2 A:OEX602 3.4 31.9 0.3
MN1 A:OEX602 3.4 36.3 0.3
MN2 A:OEY601 3.4 33.6 0.7
C A:ALA344 3.4 36.1 0.7
MN1 A:OEY601 3.5 29.5 0.7
MN3 A:OEY601 3.5 32.3 0.7
MN3 A:OEX602 3.5 34.6 0.3
OE2 A:GLU189 3.5 36.5 0.3
OXT A:ALA344 3.6 27.8 0.3
OXT A:ALA344 3.7 34.3 0.7
O3 A:OEX602 3.7 38.7 0.3
OD1 A:ASP170 3.7 31.9 0.3
CD A:GLU189 3.8 33.0 0.3
O3 A:OEY601 3.8 33.0 0.7
OD1 A:ASP170 3.8 34.2 0.7
MN4 A:OEX602 3.9 38.1 0.3
OE2 A:GLU189 3.9 34.4 0.7
CD A:GLU189 4.0 30.8 0.7
O4 A:OEX602 4.0 32.7 0.3
O4 A:OEY601 4.1 31.6 0.7
O A:HOH778 4.1 33.1 1.0
MN4 A:OEY601 4.1 34.1 0.7
O A:HOH705 4.3 29.9 1.0
NH1 C:ARG357 4.3 33.7 0.3
CB A:ASP170 4.3 28.3 0.7
NH1 C:ARG357 4.4 28.0 0.7
CB A:ASP170 4.4 30.2 0.3
OH A:TYR161 4.5 38.0 0.3
OE1 A:GLN165 4.6 38.7 0.7
NH2 C:ARG357 4.6 33.7 0.3
OH A:TYR161 4.7 24.7 0.7
OE1 A:GLN165 4.7 40.4 0.3
CA A:ALA344 4.7 33.2 0.3
NH2 C:ARG357 4.7 30.1 0.7
O A:HOH755 4.7 34.9 0.7
CA A:ALA344 4.7 31.5 0.7
OE2 C:GLU354 4.8 32.2 0.3
O A:HOH755 4.8 32.5 0.3
OD1 A:ASP342 4.9 32.9 0.3
OE1 C:GLU354 5.0 32.5 0.7
CG A:GLN165 5.0 39.2 0.3
OE1 C:GLU354 5.0 37.0 0.3
CZ C:ARG357 5.0 30.6 0.3

Calcium binding site 2 out of 4 in 8f4d

Go back to Calcium Binding Sites List in 8f4d
Calcium binding site 2 out of 4 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 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 Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:37.1
occ:0.35
 CA1 A:OEX602 0.0 37.1 0.3
CA1 A:OEY601 0.1 34.8 0.7
O A:HOH715 2.2 32.4 0.7
OD2 A:ASP170 2.3 38.7 0.7
O1 A:OEY601 2.4 30.1 0.7
O1 A:OEX602 2.4 37.1 0.3
O A:HOH715 2.4 39.7 0.3
O A:ALA344 2.4 39.6 0.3
O A:ALA344 2.5 36.2 0.7
OD2 A:ASP170 2.5 34.6 0.3
O2 A:OEY601 2.5 32.4 0.7
O A:HOH781 2.5 29.5 0.3
O2 A:OEX602 2.6 26.7 0.3
O5 A:OEX602 2.6 39.5 0.3
O A:HOH781 2.6 31.7 0.7
O5 A:OEY601 2.6 33.1 0.7
O6 A:OEY601 2.7 32.9 0.7
OE1 A:GLU189 3.1 31.9 0.7
OE1 A:GLU189 3.3 35.7 0.3
CG A:ASP170 3.3 33.1 0.7
C A:ALA344 3.3 31.7 0.3
MN1 A:OEX602 3.4 36.3 0.3
CG A:ASP170 3.4 35.9 0.3
MN2 A:OEX602 3.4 31.9 0.3
C A:ALA344 3.4 36.1 0.7
MN2 A:OEY601 3.4 33.6 0.7
MN1 A:OEY601 3.5 29.5 0.7
OE2 A:GLU189 3.5 36.5 0.3
MN3 A:OEY601 3.6 32.3 0.7
OXT A:ALA344 3.6 27.8 0.3
MN3 A:OEX602 3.6 34.6 0.3
OXT A:ALA344 3.6 34.3 0.7
CD A:GLU189 3.7 33.0 0.3
O3 A:OEX602 3.7 38.7 0.3
O3 A:OEY601 3.8 33.0 0.7
OD1 A:ASP170 3.8 31.9 0.3
OD1 A:ASP170 3.9 34.2 0.7
OE2 A:GLU189 3.9 34.4 0.7
CD A:GLU189 3.9 30.8 0.7
MN4 A:OEX602 4.0 38.1 0.3
O A:HOH778 4.0 33.1 1.0
O4 A:OEX602 4.1 32.7 0.3
O4 A:OEY601 4.1 31.6 0.7
MN4 A:OEY601 4.2 34.1 0.7
O A:HOH705 4.2 29.9 1.0
NH1 C:ARG357 4.3 33.7 0.3
NH1 C:ARG357 4.4 28.0 0.7
CB A:ASP170 4.4 28.3 0.7
OH A:TYR161 4.5 38.0 0.3
CB A:ASP170 4.5 30.2 0.3
OE1 A:GLN165 4.5 38.7 0.7
OH A:TYR161 4.6 24.7 0.7
OE1 A:GLN165 4.6 40.4 0.3
CA A:ALA344 4.7 33.2 0.3
CA A:ALA344 4.7 31.5 0.7
NH2 C:ARG357 4.7 33.7 0.3
O A:HOH755 4.8 34.9 0.7
NH2 C:ARG357 4.8 30.1 0.7
OE2 C:GLU354 4.8 32.2 0.3
O A:HOH755 4.8 32.5 0.3
OD1 A:ASP342 4.9 32.9 0.3
CG A:GLN165 4.9 39.2 0.3
OE1 C:GLU354 5.0 37.0 0.3
OE1 C:GLU354 5.0 32.5 0.7
OD1 A:ASP342 5.0 31.6 0.7

Calcium binding site 3 out of 4 in 8f4d

Go back to Calcium Binding Sites List in 8f4d
Calcium binding site 3 out of 4 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 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 Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:34.3
occ:0.65
 CA1 a:OEY601 0.0 34.3 0.7
CA1 a:OEX602 0.1 36.1 0.3
O a:HOH747 2.2 35.6 0.3
O a:HOH747 2.3 33.7 0.7
OD2 a:ASP170 2.4 33.9 0.7
O1 a:OEY601 2.4 29.4 0.7
OD2 a:ASP170 2.4 37.5 0.3
O5 a:OEY601 2.5 30.1 0.7
O1 a:OEX602 2.5 36.9 0.3
O a:HOH782 2.5 33.7 0.7
O a:HOH782 2.6 37.2 0.3
O2 a:OEX602 2.6 29.1 0.3
O2 a:OEY601 2.6 28.0 0.7
O a:ALA344 2.6 30.0 0.7
O5 a:OEX602 2.6 43.8 0.3
O a:ALA344 2.7 32.8 0.3
O6 a:OEY601 2.7 33.6 0.7
OE1 a:GLU189 3.0 36.5 0.3
OE1 a:GLU189 3.0 32.4 0.7
CG a:ASP170 3.2 32.0 0.7
CG a:ASP170 3.2 40.3 0.3
OE2 a:GLU189 3.4 33.3 0.3
MN1 a:OEX602 3.4 33.8 0.3
MN1 a:OEY601 3.4 35.4 0.7
MN2 a:OEX602 3.5 38.8 0.3
CD a:GLU189 3.5 32.9 0.3
MN2 a:OEY601 3.6 28.8 0.7
C a:ALA344 3.6 35.1 0.3
MN3 a:OEX602 3.6 35.0 0.3
C a:ALA344 3.6 34.0 0.7
OD1 a:ASP170 3.6 30.7 0.7
OD1 a:ASP170 3.6 39.6 0.3
MN3 a:OEY601 3.6 33.5 0.7
OXT a:ALA344 3.8 35.8 0.3
O3 a:OEX602 3.8 31.1 0.3
CD a:GLU189 3.9 33.3 0.7
OXT a:ALA344 3.9 31.4 0.7
OE2 a:GLU189 3.9 30.9 0.7
O3 a:OEY601 4.0 32.0 0.7
MN4 a:OEX602 4.1 35.4 0.3
MN4 a:OEY601 4.2 34.6 0.7
O4 a:OEX602 4.2 29.7 0.3
O a:HOH720 4.3 33.5 1.0
CB a:ASP170 4.3 37.1 0.3
CB a:ASP170 4.3 29.5 0.7
OH a:TYR161 4.4 35.9 0.3
OH a:TYR161 4.4 36.9 0.7
OE1 a:GLN165 4.5 28.2 0.3
NH1 c:ARG357 4.5 29.2 0.7
NH1 c:ARG357 4.5 27.5 0.3
O4 a:OEY601 4.6 33.5 0.7
O a:HOH714 4.6 39.2 0.3
O a:HOH710 4.6 36.5 1.0
O a:HOH714 4.8 28.8 0.7
NH2 c:ARG357 4.8 27.5 0.7
OE1 a:GLN165 4.8 30.3 0.7
O a:HOH770 4.9 44.0 1.0
NH2 c:ARG357 4.9 36.1 0.3
CG1 a:VAL185 4.9 36.9 0.3
CG1 a:VAL185 4.9 32.4 0.7
CA a:ALA344 4.9 34.0 0.7
CA a:ALA344 5.0 39.5 0.3

Calcium binding site 4 out of 4 in 8f4d

Go back to Calcium Binding Sites List in 8f4d
Calcium binding site 4 out of 4 in the Rt Xfel Structure of Photosystem II 50 Microseconds After the Third Illumination at 2.15 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 Photosystem II 50 Microseconds After the Third Illumination at 2.15 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca602

b:36.1
occ:0.35
 CA1 a:OEX602 0.0 36.1 0.3
CA1 a:OEY601 0.1 34.3 0.7
O a:HOH747 2.3 35.6 0.3
O1 a:OEY601 2.3 29.4 0.7
O5 a:OEY601 2.4 30.1 0.7
O a:HOH747 2.4 33.7 0.7
O1 a:OEX602 2.4 36.9 0.3
OD2 a:ASP170 2.5 33.9 0.7
O2 a:OEX602 2.5 29.1 0.3
OD2 a:ASP170 2.5 37.5 0.3
O2 a:OEY601 2.5 28.0 0.7
O5 a:OEX602 2.5 43.8 0.3
O a:HOH782 2.6 33.7 0.7
O6 a:OEY601 2.6 33.6 0.7
O a:HOH782 2.6 37.2 0.3
O a:ALA344 2.7 30.0 0.7
O a:ALA344 2.7 32.8 0.3
OE1 a:GLU189 3.0 36.5 0.3
OE1 a:GLU189 3.0 32.4 0.7
MN1 a:OEX602 3.3 33.8 0.3
OE2 a:GLU189 3.3 33.3 0.3
MN1 a:OEY601 3.3 35.4 0.7
CG a:ASP170 3.3 40.3 0.3
CG a:ASP170 3.3 32.0 0.7
MN2 a:OEX602 3.4 38.8 0.3
MN2 a:OEY601 3.4 28.8 0.7
MN3 a:OEX602 3.5 35.0 0.3
CD a:GLU189 3.5 32.9 0.3
MN3 a:OEY601 3.5 33.5 0.7
C a:ALA344 3.6 35.1 0.3
C a:ALA344 3.6 34.0 0.7
OD1 a:ASP170 3.6 30.7 0.7
OD1 a:ASP170 3.7 39.6 0.3
O3 a:OEX602 3.7 31.1 0.3
OXT a:ALA344 3.7 35.8 0.3
CD a:GLU189 3.8 33.3 0.7
O3 a:OEY601 3.8 32.0 0.7
OE2 a:GLU189 3.8 30.9 0.7
OXT a:ALA344 3.8 31.4 0.7
MN4 a:OEX602 4.1 35.4 0.3
MN4 a:OEY601 4.1 34.6 0.7
O4 a:OEX602 4.2 29.7 0.3
O a:HOH720 4.3 33.5 1.0
CB a:ASP170 4.4 37.1 0.3
CB a:ASP170 4.4 29.5 0.7
OH a:TYR161 4.5 35.9 0.3
O4 a:OEY601 4.5 33.5 0.7
NH1 c:ARG357 4.5 29.2 0.7
OH a:TYR161 4.5 36.9 0.7
O a:HOH714 4.6 39.2 0.3
OE1 a:GLN165 4.6 28.2 0.3
NH1 c:ARG357 4.6 27.5 0.3
O a:HOH710 4.6 36.5 1.0
O a:HOH714 4.7 28.8 0.7
NH2 c:ARG357 4.8 27.5 0.7
CG1 a:VAL185 4.9 36.9 0.3
CG1 a:VAL185 4.9 32.4 0.7
O a:HOH770 4.9 44.0 1.0
NH2 c:ARG357 4.9 36.1 0.3
OE1 a:GLN165 5.0 30.3 0.7
OE1 c:GLU354 5.0 37.5 0.3
CA a:ALA344 5.0 34.0 0.7
CG a:GLU189 5.0 35.9 0.3
CA a:ALA344 5.0 39.5 0.3
OD2 a:ASP342 5.0 39.2 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 04:31:26 2025

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