Calcium in PDB 8f4j: Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution

Enzymatic activity of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution

All present enzymatic activity of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution:
1.10.3.9;

Protein crystallography data

The structure of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution, PDB code: 8f4j 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) 19.74 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.339, 222.833, 309.192, 90, 90, 90
R / Rfree (%) 18.2 / 22.6

Other elements in 8f4j:

The structure of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Magnesium (Mg) 70 atoms
Manganese (Mn) 24 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution (pdb code 8f4j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution, PDB code: 8f4j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8f4j

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Calcium binding site 1 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:31.7
occ:0.40
 CA1 A:OEX601 0.0 31.7 0.4
CA1 A:OEY602 0.2 32.3 0.3
CA1 A:OEX601 0.3 28.6 0.2
O A:HOH747 2.2 27.6 0.2
O A:HOH747 2.2 33.9 0.3
O A:HOH747 2.2 30.5 0.4
O1 A:OEX601 2.2 25.9 0.2
O1 A:OEY602 2.2 29.4 0.3
O A:ALA344 2.3 33.1 0.3
O A:ALA344 2.3 28.2 0.2
O1 A:OEX601 2.3 25.8 0.4
OD2 A:ASP170 2.4 30.4 0.3
OD2 A:ASP170 2.4 27.5 0.2
O2 A:OEY602 2.5 26.2 0.3
OD2 A:ASP170 2.5 30.3 0.4
O A:ALA344 2.5 33.4 0.4
O2 A:OEX601 2.5 29.5 0.4
O2 A:OEX601 2.5 26.2 0.2
O5 A:OEX601 2.6 29.6 0.4
O A:HOH804 2.6 31.3 0.4
O A:HOH804 2.7 29.7 0.3
O6 A:OEY602 2.7 30.2 0.3
O A:HOH804 2.8 26.5 0.2
O5 A:OEY602 2.8 32.8 0.3
O5 A:OEX601 2.9 26.1 0.2
OE1 A:GLU189 3.0 32.8 0.4
OE1 A:GLU189 3.2 32.6 0.3
C A:ALA344 3.2 32.5 0.3
OE1 A:GLU189 3.2 27.8 0.2
C A:ALA344 3.2 28.5 0.2
MN2 A:OEY602 3.3 29.2 0.3
MN2 A:OEX601 3.3 22.4 0.2
CG A:ASP170 3.4 31.2 0.4
CG A:ASP170 3.4 26.7 0.2
MN1 A:OEX601 3.4 29.2 0.4
CG A:ASP170 3.4 30.3 0.3
MN1 A:OEX601 3.4 24.4 0.2
MN2 A:OEX601 3.5 29.8 0.4
C A:ALA344 3.5 30.4 0.4
MN1 A:OEY602 3.5 29.0 0.3
OE2 A:GLU189 3.5 27.0 0.2
OXT A:ALA344 3.5 28.0 0.3
OXT A:ALA344 3.6 27.0 0.2
MN3 A:OEX601 3.6 29.8 0.4
MN3 A:OEY602 3.6 28.9 0.3
OE2 A:GLU189 3.7 29.0 0.4
CD A:GLU189 3.7 27.2 0.2
CD A:GLU189 3.7 29.5 0.4
OXT A:ALA344 3.7 29.9 0.4
MN3 A:OEX601 3.7 24.8 0.2
OD1 A:ASP170 3.8 26.0 0.2
O3 A:OEX601 3.8 33.3 0.4
O A:HOH742 3.8 36.2 1.0
O3 A:OEY602 3.8 32.4 0.3
OD1 A:ASP170 3.8 32.8 0.4
O3 A:OEX601 3.9 28.4 0.2
OE2 A:GLU189 3.9 34.1 0.3
OD1 A:ASP170 3.9 29.6 0.3
CD A:GLU189 3.9 31.9 0.3
MN4 A:OEX601 4.0 33.0 0.4
MN4 A:OEX601 4.1 28.2 0.2
O4 A:OEX601 4.1 25.3 0.2
O4 A:OEY602 4.2 30.2 0.3
MN4 A:OEY602 4.2 30.6 0.3
NH1 C:ARG357 4.2 24.8 0.2
O A:HOH701 4.3 27.9 1.0
OE1 A:GLN165 4.4 32.7 0.3
NH1 C:ARG357 4.4 26.6 0.4
O4 A:OEX601 4.4 32.3 0.4
NH1 C:ARG357 4.4 25.7 0.3
CB A:ASP170 4.5 28.0 0.4
CA A:ALA344 4.5 33.3 0.3
CA A:ALA344 4.5 29.4 0.2
CB A:ASP170 4.5 25.1 0.3
OH A:TYR161 4.6 26.3 0.2
OE1 A:GLN165 4.6 32.9 0.4
CB A:ASP170 4.6 25.6 0.2
OH A:TYR161 4.7 29.8 0.3
OH A:TYR161 4.7 25.6 0.4
NH2 C:ARG357 4.7 26.2 0.4
NH2 C:ARG357 4.8 27.0 0.3
CA A:ALA344 4.8 31.7 0.4
O A:HOH737 4.8 30.3 0.4
O A:HOH737 4.8 33.9 0.3
OD1 A:ASP342 4.8 25.8 0.3
OE1 A:GLN165 4.9 27.1 0.2
NH2 C:ARG357 4.9 26.1 0.2
OD1 A:ASP342 4.9 25.7 0.2
O A:HOH737 5.0 26.5 0.2
OD2 A:ASP342 5.0 28.0 0.2
OE1 C:GLU354 5.0 30.4 0.3
O A:HOH817 5.0 40.3 1.0

Calcium binding site 2 out of 6 in 8f4j

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Calcium binding site 2 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:28.6
occ:0.25
 CA1 A:OEX601 0.0 28.6 0.2
CA1 A:OEY602 0.1 32.3 0.3
CA1 A:OEX601 0.3 31.7 0.4
O1 A:OEX601 2.3 25.9 0.2
O1 A:OEY602 2.3 29.4 0.3
O5 A:OEX601 2.3 29.6 0.4
OD2 A:ASP170 2.3 30.4 0.3
OD2 A:ASP170 2.4 27.5 0.2
O A:HOH747 2.4 27.6 0.2
O A:HOH747 2.4 33.9 0.3
O A:HOH804 2.4 31.3 0.4
O1 A:OEX601 2.4 25.8 0.4
O A:HOH747 2.4 30.5 0.4
OD2 A:ASP170 2.4 30.3 0.4
O2 A:OEY602 2.4 26.2 0.3
O A:HOH804 2.5 29.7 0.3
O2 A:OEX601 2.5 26.2 0.2
O2 A:OEX601 2.5 29.5 0.4
O6 A:OEY602 2.5 30.2 0.3
O5 A:OEY602 2.5 32.8 0.3
O A:HOH804 2.5 26.5 0.2
O A:ALA344 2.5 33.1 0.3
O A:ALA344 2.6 28.2 0.2
O5 A:OEX601 2.6 26.1 0.2
O A:ALA344 2.8 33.4 0.4
OE1 A:GLU189 3.0 32.8 0.4
OE1 A:GLU189 3.2 32.6 0.3
OE1 A:GLU189 3.2 27.8 0.2
CG A:ASP170 3.2 31.2 0.4
CG A:ASP170 3.3 26.7 0.2
CG A:ASP170 3.3 30.3 0.3
MN1 A:OEX601 3.3 24.4 0.2
MN1 A:OEX601 3.3 29.2 0.4
MN2 A:OEX601 3.4 22.4 0.2
MN1 A:OEY602 3.4 29.0 0.3
MN2 A:OEY602 3.4 29.2 0.3
MN3 A:OEX601 3.4 29.8 0.4
OE2 A:GLU189 3.4 27.0 0.2
MN3 A:OEY602 3.4 28.9 0.3
C A:ALA344 3.5 32.5 0.3
C A:ALA344 3.5 28.5 0.2
MN2 A:OEX601 3.5 29.8 0.4
MN3 A:OEX601 3.5 24.8 0.2
OD1 A:ASP170 3.6 26.0 0.2
OD1 A:ASP170 3.6 32.8 0.4
OE2 A:GLU189 3.6 29.0 0.4
CD A:GLU189 3.6 27.2 0.2
CD A:GLU189 3.7 29.5 0.4
O3 A:OEX601 3.7 33.3 0.4
O3 A:OEY602 3.7 32.4 0.3
OXT A:ALA344 3.7 28.0 0.3
OD1 A:ASP170 3.7 29.6 0.3
MN4 A:OEX601 3.7 33.0 0.4
C A:ALA344 3.7 30.4 0.4
OXT A:ALA344 3.7 27.0 0.2
O3 A:OEX601 3.8 28.4 0.2
MN4 A:OEX601 3.8 28.2 0.2
OE2 A:GLU189 3.9 34.1 0.3
MN4 A:OEY602 3.9 30.6 0.3
O4 A:OEX601 3.9 25.3 0.2
CD A:GLU189 3.9 31.9 0.3
OXT A:ALA344 3.9 29.9 0.4
O4 A:OEY602 4.0 30.2 0.3
O A:HOH742 4.0 36.2 1.0
O4 A:OEX601 4.2 32.3 0.4
O A:HOH701 4.2 27.9 1.0
CB A:ASP170 4.4 28.0 0.4
NH1 C:ARG357 4.4 24.8 0.2
CB A:ASP170 4.5 25.1 0.3
CB A:ASP170 4.5 25.6 0.2
O A:HOH737 4.5 30.3 0.4
O A:HOH737 4.5 33.9 0.3
NH1 C:ARG357 4.5 26.6 0.4
NH1 C:ARG357 4.6 25.7 0.3
OH A:TYR161 4.6 26.3 0.2
O A:HOH737 4.6 26.5 0.2
OE1 A:GLN165 4.7 32.7 0.3
OH A:TYR161 4.7 29.8 0.3
NH2 C:ARG357 4.7 26.2 0.4
OH A:TYR161 4.8 25.6 0.4
CA A:ALA344 4.8 33.3 0.3
NH2 C:ARG357 4.8 27.0 0.3
CA A:ALA344 4.8 29.4 0.2
NH2 C:ARG357 4.9 26.1 0.2
OE1 A:GLN165 4.9 32.9 0.4
OD1 A:ASP342 4.9 25.8 0.3
NE2 A:HIS332 4.9 29.0 0.2
OD1 A:ASP342 5.0 25.7 0.2
OD2 A:ASP342 5.0 28.0 0.2
CG1 A:VAL185 5.0 27.5 0.4
OD2 A:ASP342 5.0 28.1 0.3

Calcium binding site 3 out of 6 in 8f4j

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Calcium binding site 3 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:32.3
occ:0.35
 CA1 A:OEY602 0.0 32.3 0.3
CA1 A:OEX601 0.1 28.6 0.2
CA1 A:OEX601 0.2 31.7 0.4
O1 A:OEX601 2.3 25.9 0.2
O1 A:OEY602 2.3 29.4 0.3
O A:HOH747 2.3 27.6 0.2
O A:HOH747 2.3 33.9 0.3
O A:HOH747 2.3 30.5 0.4
OD2 A:ASP170 2.4 30.4 0.3
O1 A:OEX601 2.4 25.8 0.4
OD2 A:ASP170 2.4 27.5 0.2
O5 A:OEX601 2.4 29.6 0.4
O A:ALA344 2.4 33.1 0.3
OD2 A:ASP170 2.5 30.3 0.4
O A:ALA344 2.5 28.2 0.2
O2 A:OEY602 2.5 26.2 0.3
O A:HOH804 2.5 31.3 0.4
O2 A:OEX601 2.5 26.2 0.2
O2 A:OEX601 2.5 29.5 0.4
O A:HOH804 2.5 29.7 0.3
O6 A:OEY602 2.6 30.2 0.3
O A:HOH804 2.6 26.5 0.2
O5 A:OEY602 2.7 32.8 0.3
O A:ALA344 2.7 33.4 0.4
O5 A:OEX601 2.7 26.1 0.2
OE1 A:GLU189 2.9 32.8 0.4
OE1 A:GLU189 3.1 32.6 0.3
OE1 A:GLU189 3.2 27.8 0.2
CG A:ASP170 3.3 31.2 0.4
CG A:ASP170 3.3 26.7 0.2
CG A:ASP170 3.3 30.3 0.3
MN1 A:OEX601 3.3 24.4 0.2
MN1 A:OEX601 3.3 29.2 0.4
MN2 A:OEX601 3.3 22.4 0.2
MN2 A:OEY602 3.3 29.2 0.3
C A:ALA344 3.4 32.5 0.3
MN1 A:OEY602 3.4 29.0 0.3
C A:ALA344 3.4 28.5 0.2
OE2 A:GLU189 3.4 27.0 0.2
MN3 A:OEX601 3.5 29.8 0.4
MN2 A:OEX601 3.5 29.8 0.4
MN3 A:OEY602 3.5 28.9 0.3
OE2 A:GLU189 3.6 29.0 0.4
MN3 A:OEX601 3.6 24.8 0.2
CD A:GLU189 3.6 27.2 0.2
C A:ALA344 3.6 30.4 0.4
OXT A:ALA344 3.6 28.0 0.3
CD A:GLU189 3.7 29.5 0.4
OD1 A:ASP170 3.7 26.0 0.2
OXT A:ALA344 3.7 27.0 0.2
OD1 A:ASP170 3.7 32.8 0.4
O3 A:OEX601 3.8 33.3 0.4
O3 A:OEY602 3.8 32.4 0.3
O3 A:OEX601 3.8 28.4 0.2
OD1 A:ASP170 3.8 29.6 0.3
MN4 A:OEX601 3.9 33.0 0.4
OXT A:ALA344 3.9 29.9 0.4
MN4 A:OEX601 3.9 28.2 0.2
OE2 A:GLU189 3.9 34.1 0.3
CD A:GLU189 3.9 31.9 0.3
O A:HOH742 3.9 36.2 1.0
O4 A:OEX601 4.0 25.3 0.2
MN4 A:OEY602 4.1 30.6 0.3
O4 A:OEY602 4.1 30.2 0.3
O A:HOH701 4.2 27.9 1.0
O4 A:OEX601 4.3 32.3 0.4
NH1 C:ARG357 4.3 24.8 0.2
CB A:ASP170 4.4 28.0 0.4
CB A:ASP170 4.5 25.1 0.3
NH1 C:ARG357 4.5 26.6 0.4
NH1 C:ARG357 4.5 25.7 0.3
OE1 A:GLN165 4.5 32.7 0.3
CB A:ASP170 4.6 25.6 0.2
OH A:TYR161 4.6 26.3 0.2
O A:HOH737 4.6 30.3 0.4
O A:HOH737 4.7 33.9 0.3
CA A:ALA344 4.7 33.3 0.3
OH A:TYR161 4.7 29.8 0.3
CA A:ALA344 4.7 29.4 0.2
OH A:TYR161 4.7 25.6 0.4
NH2 C:ARG357 4.7 26.2 0.4
O A:HOH737 4.8 26.5 0.2
OE1 A:GLN165 4.8 32.9 0.4
NH2 C:ARG357 4.8 27.0 0.3
NH2 C:ARG357 4.9 26.1 0.2
OD1 A:ASP342 4.9 25.8 0.3
OD1 A:ASP342 4.9 25.7 0.2
OD2 A:ASP342 5.0 28.0 0.2
CA A:ALA344 5.0 31.7 0.4
OD2 A:ASP342 5.0 28.1 0.3

Calcium binding site 4 out of 6 in 8f4j

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Calcium binding site 4 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:32.4
occ:0.40
 CA1 a:OEX601 0.0 32.4 0.4
CA1 a:OEY602 0.1 30.8 0.3
CA1 a:OEX601 0.2 25.8 0.2
O a:HOH765 2.1 25.5 0.2
O a:HOH765 2.2 32.6 0.4
O a:HOH765 2.2 31.9 0.3
O1 a:OEY602 2.2 29.8 0.3
O1 a:OEX601 2.3 23.9 0.2
O1 a:OEX601 2.4 29.1 0.4
O a:ALA344 2.4 30.3 0.3
OD2 a:ASP170 2.4 29.7 0.3
OD2 a:ASP170 2.5 24.3 0.2
O a:HOH792 2.5 24.4 0.2
O2 a:OEX601 2.5 29.1 0.4
O a:ALA344 2.5 28.5 0.4
O2 a:OEY602 2.5 28.9 0.3
OD2 a:ASP170 2.5 29.1 0.4
O5 a:OEX601 2.5 31.9 0.4
O6 a:OEY602 2.6 34.4 0.3
O a:HOH792 2.6 23.8 0.4
O5 a:OEX601 2.6 26.0 0.2
O a:HOH792 2.6 29.9 0.3
O2 a:OEX601 2.7 24.6 0.2
O a:ALA344 2.7 26.1 0.2
O5 a:OEY602 2.7 31.8 0.3
OE1 a:GLU189 2.9 32.5 0.4
OE1 a:GLU189 2.9 27.5 0.2
OE2 a:GLU189 3.0 26.3 0.2
OE1 a:GLU189 3.0 31.4 0.3
CG a:ASP170 3.3 25.6 0.2
CD a:GLU189 3.3 26.8 0.2
CG a:ASP170 3.3 28.5 0.4
MN2 a:OEY602 3.3 28.7 0.3
C a:ALA344 3.4 29.7 0.3
MN1 a:OEX601 3.4 25.2 0.2
MN1 a:OEX601 3.4 29.1 0.4
CG a:ASP170 3.4 31.2 0.3
MN2 a:OEX601 3.4 30.0 0.4
MN1 a:OEY602 3.4 29.2 0.3
MN2 a:OEX601 3.5 21.5 0.2
C a:ALA344 3.5 29.8 0.4
MN3 a:OEX601 3.5 30.4 0.4
OE2 a:GLU189 3.5 27.4 0.4
C a:ALA344 3.6 25.9 0.2
CD a:GLU189 3.6 28.8 0.4
MN3 a:OEY602 3.6 31.8 0.3
MN3 a:OEX601 3.6 22.2 0.2
OD1 a:ASP170 3.7 32.2 0.4
OXT a:ALA344 3.7 30.4 0.3
OD1 a:ASP170 3.7 24.1 0.2
OXT a:ALA344 3.8 29.4 0.4
O3 a:OEX601 3.8 30.2 0.4
O3 a:OEY602 3.8 33.5 0.3
CD a:GLU189 3.9 31.6 0.3
OD1 a:ASP170 3.9 34.0 0.3
OXT a:ALA344 3.9 25.8 0.2
OE2 a:GLU189 3.9 31.1 0.3
O3 a:OEX601 3.9 25.7 0.2
MN4 a:OEX601 4.0 32.8 0.4
MN4 a:OEY602 4.1 34.9 0.3
OH a:TYR161 4.2 27.9 0.2
MN4 a:OEX601 4.3 23.9 0.2
O a:HOH701 4.3 28.5 1.0
NH1 c:ARG357 4.3 23.1 0.2
O a:HOH713 4.4 30.8 1.0
NH1 c:ARG357 4.4 27.2 0.3
O4 a:OEX601 4.4 26.5 0.4
CB a:ASP170 4.4 25.5 0.2
O4 a:OEX601 4.5 23.7 0.2
CB a:ASP170 4.5 26.9 0.4
O4 a:OEY602 4.5 30.7 0.3
NH1 c:ARG357 4.5 26.5 0.4
CB a:ASP170 4.5 26.3 0.3
OH a:TYR161 4.6 28.7 0.3
OH a:TYR161 4.6 30.1 0.4
OE1 a:GLN165 4.6 28.4 0.4
OE1 a:GLN165 4.7 30.9 0.3
CA a:ALA344 4.7 27.3 0.3
CA a:ALA344 4.7 26.5 0.2
O a:HOH750 4.7 35.1 1.0
OE1 a:GLN165 4.7 28.7 0.2
NH2 c:ARG357 4.7 30.8 0.3
NH2 c:ARG357 4.8 25.4 0.2
O a:HOH773 4.8 23.6 0.2
CG a:GLU189 4.8 28.8 0.2
NH2 c:ARG357 4.8 27.9 0.4
CA a:ALA344 4.8 28.0 0.4
O a:HOH773 4.9 31.2 0.3
O a:HOH773 4.9 28.1 0.4
OD2 a:ASP342 4.9 27.3 0.2
CG1 a:VAL185 5.0 27.8 0.2
OD1 a:ASP342 5.0 30.5 0.3

Calcium binding site 5 out of 6 in 8f4j

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Calcium binding site 5 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 5 of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca601

b:25.8
occ:0.25
 CA1 a:OEX601 0.0 25.8 0.2
CA1 a:OEY602 0.2 30.8 0.3
CA1 a:OEX601 0.2 32.4 0.4
O1 a:OEY602 2.2 29.8 0.3
O a:HOH765 2.3 25.5 0.2
O2 a:OEX601 2.3 29.1 0.4
OD2 a:ASP170 2.3 29.7 0.3
O1 a:OEX601 2.3 23.9 0.2
O2 a:OEY602 2.3 28.9 0.3
OD2 a:ASP170 2.3 24.3 0.2
O1 a:OEX601 2.4 29.1 0.4
O a:ALA344 2.4 30.3 0.3
O a:HOH765 2.4 32.6 0.4
OD2 a:ASP170 2.4 29.1 0.4
O a:HOH765 2.4 31.9 0.3
O5 a:OEX601 2.4 31.9 0.4
O2 a:OEX601 2.5 24.6 0.2
O5 a:OEX601 2.5 26.0 0.2
O a:ALA344 2.5 28.5 0.4
O a:HOH792 2.6 24.4 0.2
O5 a:OEY602 2.6 31.8 0.3
O6 a:OEY602 2.6 34.4 0.3
O a:ALA344 2.6 26.1 0.2
O a:HOH792 2.7 23.8 0.4
O a:HOH792 2.7 29.9 0.3
OE2 a:GLU189 3.1 26.3 0.2
OE1 a:GLU189 3.1 32.5 0.4
OE1 a:GLU189 3.1 27.5 0.2
CG a:ASP170 3.2 25.6 0.2
MN2 a:OEY602 3.2 28.7 0.3
CG a:ASP170 3.2 28.5 0.4
OE1 a:GLU189 3.2 31.4 0.3
CG a:ASP170 3.3 31.2 0.3
MN2 a:OEX601 3.3 30.0 0.4
MN3 a:OEX601 3.3 30.4 0.4
C a:ALA344 3.3 29.7 0.3
MN2 a:OEX601 3.3 21.5 0.2
MN1 a:OEX601 3.4 25.2 0.2
MN1 a:OEX601 3.4 29.1 0.4
MN1 a:OEY602 3.4 29.2 0.3
MN3 a:OEY602 3.4 31.8 0.3
MN3 a:OEX601 3.5 22.2 0.2
C a:ALA344 3.5 29.8 0.4
CD a:GLU189 3.5 26.8 0.2
C a:ALA344 3.5 25.9 0.2
OD1 a:ASP170 3.5 32.2 0.4
OD1 a:ASP170 3.6 24.1 0.2
OXT a:ALA344 3.6 30.4 0.3
OE2 a:GLU189 3.6 27.4 0.4
O3 a:OEX601 3.7 30.2 0.4
O3 a:OEY602 3.7 33.5 0.3
OXT a:ALA344 3.7 29.4 0.4
OD1 a:ASP170 3.7 34.0 0.3
CD a:GLU189 3.8 28.8 0.4
OXT a:ALA344 3.8 25.8 0.2
O3 a:OEX601 3.8 25.7 0.2
MN4 a:OEX601 3.9 32.8 0.4
MN4 a:OEY602 4.0 34.9 0.3
OE2 a:GLU189 4.0 31.1 0.3
CD a:GLU189 4.0 31.6 0.3
MN4 a:OEX601 4.1 23.9 0.2
NH1 c:ARG357 4.2 23.1 0.2
O4 a:OEX601 4.2 26.5 0.4
NH1 c:ARG357 4.2 27.2 0.3
O4 a:OEX601 4.3 23.7 0.2
O4 a:OEY602 4.3 30.7 0.3
OH a:TYR161 4.4 27.9 0.2
CB a:ASP170 4.4 25.5 0.2
NH1 c:ARG357 4.4 26.5 0.4
CB a:ASP170 4.4 26.9 0.4
CB a:ASP170 4.5 26.3 0.3
O a:HOH701 4.5 28.5 1.0
O a:HOH713 4.5 30.8 1.0
NH2 c:ARG357 4.5 30.8 0.3
NH2 c:ARG357 4.6 25.4 0.2
NH2 c:ARG357 4.6 27.9 0.4
CA a:ALA344 4.7 27.3 0.3
CA a:ALA344 4.7 26.5 0.2
O a:HOH773 4.7 23.6 0.2
OE1 a:GLN165 4.8 28.4 0.4
OH a:TYR161 4.8 28.7 0.3
OE1 a:GLN165 4.8 30.9 0.3
O a:HOH773 4.8 31.2 0.3
OH a:TYR161 4.8 30.1 0.4
CA a:ALA344 4.8 28.0 0.4
O a:HOH773 4.9 28.1 0.4
OE1 a:GLN165 4.9 28.7 0.2
CZ c:ARG357 4.9 25.1 0.2
CZ c:ARG357 4.9 29.8 0.3
O a:HOH750 4.9 35.1 1.0
OD1 a:ASP342 4.9 30.5 0.3
OD1 a:ASP342 4.9 26.2 0.2
OE1 c:GLU354 5.0 31.5 0.4
OD2 a:ASP342 5.0 27.3 0.2
CZ c:ARG357 5.0 27.9 0.4
OE2 a:GLU333 5.0 29.3 0.4
CG a:GLU189 5.0 28.8 0.2
OD1 a:ASP342 5.0 30.1 0.4

Calcium binding site 6 out of 6 in 8f4j

Go back to Calcium Binding Sites List in 8f4j
Calcium binding site 6 out of 6 in the Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination 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 6 of Rt Xfel Structure of Photosystem II 4000 Microseconds After the Third Illumination at 2.00 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca602

b:30.8
occ:0.35
 CA1 a:OEY602 0.0 30.8 0.3
CA1 a:OEX601 0.1 32.4 0.4
CA1 a:OEX601 0.2 25.8 0.2
O a:HOH765 2.2 25.5 0.2
O a:HOH765 2.3 32.6 0.4
O1 a:OEY602 2.3 29.8 0.3
O a:HOH765 2.3 31.9 0.3
OD2 a:ASP170 2.3 29.7 0.3
O1 a:OEX601 2.4 23.9 0.2
OD2 a:ASP170 2.4 24.3 0.2
O a:HOH792 2.4 24.4 0.2
O1 a:OEX601 2.4 29.1 0.4
O5 a:OEX601 2.5 31.9 0.4
O a:ALA344 2.5 30.3 0.3
O2 a:OEX601 2.5 29.1 0.4
OD2 a:ASP170 2.5 29.1 0.4
O2 a:OEY602 2.5 28.9 0.3
O5 a:OEX601 2.5 26.0 0.2
O a:HOH792 2.5 23.8 0.4
O a:HOH792 2.6 29.9 0.3
O6 a:OEY602 2.6 34.4 0.3
O a:ALA344 2.6 28.5 0.4
O5 a:OEY602 2.6 31.8 0.3
O2 a:OEX601 2.7 24.6 0.2
O a:ALA344 2.8 26.1 0.2
OE1 a:GLU189 2.9 32.5 0.4
OE2 a:GLU189 3.0 26.3 0.2
OE1 a:GLU189 3.0 27.5 0.2
OE1 a:GLU189 3.1 31.4 0.3
CG a:ASP170 3.2 25.6 0.2
CG a:ASP170 3.2 28.5 0.4
CG a:ASP170 3.3 31.2 0.3
MN2 a:OEY602 3.4 28.7 0.3
CD a:GLU189 3.4 26.8 0.2
MN1 a:OEX601 3.4 25.2 0.2
MN1 a:OEX601 3.4 29.1 0.4
MN1 a:OEY602 3.4 29.2 0.3
MN2 a:OEX601 3.4 30.0 0.4
MN3 a:OEX601 3.5 30.4 0.4
C a:ALA344 3.5 29.7 0.3
MN2 a:OEX601 3.5 21.5 0.2
MN3 a:OEY602 3.5 31.8 0.3
OD1 a:ASP170 3.6 32.2 0.4
OE2 a:GLU189 3.6 27.4 0.4
MN3 a:OEX601 3.6 22.2 0.2
C a:ALA344 3.6 29.8 0.4
OD1 a:ASP170 3.6 24.1 0.2
C a:ALA344 3.6 25.9 0.2
CD a:GLU189 3.7 28.8 0.4
OD1 a:ASP170 3.8 34.0 0.3
O3 a:OEX601 3.8 30.2 0.4
OXT a:ALA344 3.8 30.4 0.3
O3 a:OEY602 3.8 33.5 0.3
OXT a:ALA344 3.8 29.4 0.4
CD a:GLU189 3.9 31.6 0.3
MN4 a:OEX601 3.9 32.8 0.4
O3 a:OEX601 3.9 25.7 0.2
OE2 a:GLU189 3.9 31.1 0.3
OXT a:ALA344 3.9 25.8 0.2
MN4 a:OEY602 4.0 34.9 0.3
MN4 a:OEX601 4.2 23.9 0.2
OH a:TYR161 4.2 27.9 0.2
O4 a:OEX601 4.3 26.5 0.4
O a:HOH701 4.3 28.5 1.0
NH1 c:ARG357 4.3 23.1 0.2
CB a:ASP170 4.4 25.5 0.2
NH1 c:ARG357 4.4 27.2 0.3
O4 a:OEX601 4.4 23.7 0.2
O4 a:OEY602 4.4 30.7 0.3
CB a:ASP170 4.4 26.9 0.4
CB a:ASP170 4.5 26.3 0.3
O a:HOH713 4.5 30.8 1.0
NH1 c:ARG357 4.5 26.5 0.4
OH a:TYR161 4.6 28.7 0.3
OH a:TYR161 4.7 30.1 0.4
O a:HOH773 4.7 23.6 0.2
NH2 c:ARG357 4.7 30.8 0.3
NH2 c:ARG357 4.7 25.4 0.2
O a:HOH773 4.7 31.2 0.3
OE1 a:GLN165 4.7 28.4 0.4
OE1 a:GLN165 4.8 30.9 0.3
NH2 c:ARG357 4.8 27.9 0.4
CA a:ALA344 4.8 27.3 0.3
O a:HOH773 4.8 28.1 0.4
CA a:ALA344 4.8 26.5 0.2
OE1 a:GLN165 4.8 28.7 0.2
O a:HOH750 4.8 35.1 1.0
CG a:GLU189 4.9 28.8 0.2
CA a:ALA344 4.9 28.0 0.4
CG1 a:VAL185 4.9 27.8 0.2
CG1 a:VAL185 5.0 24.9 0.4
OD2 a:ASP342 5.0 27.3 0.2

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 08:47:50 2024

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