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Calcium in PDB 7cji: Photosystem II Structure in the S1 State

Enzymatic activity of Photosystem II Structure in the S1 State

All present enzymatic activity of Photosystem II Structure in the S1 State:
1.10.3.9;

Protein crystallography data

The structure of Photosystem II Structure in the S1 State, PDB code: 7cji was solved by H.Li, J.-R.Shen, M.Suga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.93 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.02, 231.7, 288.32, 90, 90, 90
R / Rfree (%) 16 / 20.8

Other elements in 7cji:

The structure of Photosystem II Structure in the S1 State also contains other interesting chemical elements:

Iron (Fe) 6 atoms
Chlorine (Cl) 4 atoms
Manganese (Mn) 8 atoms
Magnesium (Mg) 72 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Photosystem II Structure in the S1 State (pdb code 7cji). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Photosystem II Structure in the S1 State, PDB code: 7cji:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7cji

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Calcium binding site 1 out of 9 in the Photosystem II Structure in the S1 State


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:47.3
occ:1.00
 CA1 A:OEX412 0.0 47.3 1.0
OD1 A:ASP170 2.4 47.7 1.0
O A:ALA344 2.5 43.5 1.0
O A:HOH510 2.5 54.1 1.0
O A:HOH631 2.6 51.4 1.0
O1 A:OEX412 2.6 44.0 1.0
O5 A:OEX412 2.6 52.3 1.0
O2 A:OEX412 2.6 44.0 1.0
OE1 A:GLU189 3.0 49.3 1.0
CG A:ASP170 3.3 41.3 1.0
MN2 A:OEX412 3.4 50.8 1.0
C A:ALA344 3.4 44.8 1.0
MN3 A:OEX412 3.5 49.4 1.0
OD2 A:ASP170 3.6 50.1 1.0
MN1 A:OEX412 3.6 52.0 1.0
OE2 A:GLU189 3.7 48.0 1.0
CD A:GLU189 3.7 46.9 1.0
OXT A:ALA344 3.7 49.6 1.0
MN4 A:OEX412 3.9 53.1 1.0
O4 A:OEX412 4.0 45.3 1.0
O A:HOH568 4.2 58.7 1.0
O3 A:OEX412 4.2 56.4 1.0
NH1 C:ARG357 4.3 42.7 1.0
NH2 C:ARG357 4.4 42.1 1.0
CB A:ASP170 4.5 44.1 1.0
O A:HOH521 4.5 43.8 1.0
OE1 A:GLN165 4.7 47.5 1.0
OH A:TYR161 4.7 42.9 1.0
CA A:ALA344 4.7 48.0 1.0
O A:HOH574 4.8 48.7 1.0
CZ C:ARG357 4.9 53.7 1.0

Calcium binding site 2 out of 9 in 7cji

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Calcium binding site 2 out of 9 in the Photosystem II Structure in the S1 State


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca524

b:72.9
occ:1.00
 O C:THR254 2.6 68.6 1.0
O C:HIS251 2.7 67.5 1.0
OD1 C:ASN155 2.8 79.5 1.0
OG1 C:THR159 2.8 77.4 1.0
OG1 C:THR158 2.9 66.3 1.0
O C:ILE252 3.0 70.7 1.0
O C:ASN155 3.0 75.3 1.0
C C:ILE252 3.6 75.6 1.0
N C:THR159 3.7 70.0 1.0
C C:THR254 3.8 76.4 1.0
C C:HIS251 3.8 69.7 1.0
CA C:ILE252 3.9 70.8 1.0
CG C:ASN155 3.9 81.7 1.0
C C:ASN155 3.9 76.1 1.0
CB C:THR159 3.9 68.5 1.0
CB C:THR158 4.1 69.3 1.0
CA C:THR159 4.1 70.9 1.0
CA C:ASN155 4.1 77.4 1.0
C C:THR158 4.1 68.0 1.0
N C:THR254 4.3 84.7 1.0
N C:ILE252 4.4 69.0 1.0
O C:HOH625 4.5 66.3 1.0
N C:LEU253 4.6 84.2 1.0
CB C:ASN155 4.6 79.1 1.0
CA C:THR158 4.6 68.8 1.0
O C:THR158 4.6 68.1 1.0
CA C:THR254 4.7 76.2 1.0
N C:THR255 4.8 74.2 1.0
C C:LEU253 4.8 90.0 1.0
ND2 C:ASN155 4.9 82.8 1.0
CA C:THR255 4.9 72.5 1.0
N C:THR158 5.0 71.7 1.0

Calcium binding site 3 out of 9 in 7cji

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Calcium binding site 3 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:129.1
occ:1.00
 O V:HOH354 2.7 71.8 1.0
O F:HOH207 2.7 88.5 1.0
OXT F:ARG45 3.0 68.8 1.0
O F:ARG45 3.1 71.1 1.0
OE2 V:GLU23 3.4 106.5 1.0
O V:HOH366 3.5 73.5 1.0
C F:ARG45 3.5 68.3 1.0
O V:HOH374 3.6 77.5 1.0
CD V:GLU23 4.4 103.9 1.0
O F:HOH204 4.4 92.2 1.0
OE1 V:GLU23 4.6 110.8 1.0
O A:ALA309 4.7 66.7 1.0
O F:HOH205 4.9 89.1 1.0

Calcium binding site 4 out of 9 in 7cji

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Calcium binding site 4 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:116.7
occ:1.00
 O O:HOH402 2.7 64.6 1.0
OD1 O:ASN200 2.8 97.8 1.0
CG O:ASN200 3.3 99.3 1.0
O O:THR140 3.3 90.0 1.0
O O:THR138 3.4 85.6 1.0
ND2 O:ASN200 3.5 110.6 1.0
O O:SER139 3.7 83.3 1.0
O O:VAL201 3.7 88.3 1.0
C O:SER139 3.8 84.6 1.0
CA O:SER139 3.9 91.4 1.0
CB O:ASP141 4.0 89.9 1.0
C O:THR140 4.0 79.8 1.0
N O:VAL201 4.2 62.0 1.0
OD2 O:ASP141 4.2 113.7 1.0
CA O:ASN200 4.3 69.3 1.0
CB O:ASN200 4.3 83.8 1.0
C O:THR138 4.3 85.6 1.0
CG O:ASP141 4.3 107.1 1.0
N O:THR140 4.4 83.7 1.0
C O:ASN200 4.5 67.2 1.0
N O:SER139 4.6 86.6 1.0
N O:ASP141 4.6 70.9 1.0
C O:VAL201 4.7 77.4 1.0
CA O:ASP141 4.7 80.3 1.0
CA O:THR140 4.9 81.0 1.0
CA O:VAL201 4.9 69.2 1.0

Calcium binding site 5 out of 9 in 7cji

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Calcium binding site 5 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca413

b:55.9
occ:1.00
 CA1 a:OEX413 0.0 55.9 1.0
OD1 a:ASP170 2.3 47.7 1.0
O a:HOH520 2.5 53.6 1.0
O a:ALA344 2.5 53.0 1.0
O1 a:OEX413 2.6 54.6 1.0
O5 a:OEX413 2.6 55.2 1.0
O a:HOH623 2.6 51.5 1.0
O2 a:OEX413 2.6 46.6 1.0
OE1 a:GLU189 3.0 48.9 1.0
CG a:ASP170 3.2 45.6 1.0
MN2 a:OEX413 3.4 55.6 1.0
C a:ALA344 3.5 57.0 1.0
MN3 a:OEX413 3.5 51.9 1.0
OD2 a:ASP170 3.6 51.4 1.0
MN1 a:OEX413 3.6 51.6 1.0
OXT a:ALA344 3.7 55.4 1.0
CD a:GLU189 3.8 52.2 1.0
OE2 a:GLU189 3.8 55.4 1.0
MN4 a:OEX413 3.9 56.4 1.0
O4 a:OEX413 4.1 45.5 1.0
O a:HOH557 4.2 61.4 1.0
O3 a:OEX413 4.2 55.6 1.0
NH1 c:ARG357 4.2 47.4 1.0
CB a:ASP170 4.4 45.6 1.0
OE1 a:GLN165 4.5 53.8 1.0
O a:HOH532 4.5 46.5 1.0
NH2 c:ARG357 4.6 46.7 1.0
OH a:TYR161 4.6 46.5 1.0
O a:HOH583 4.8 48.8 1.0
CA a:ALA344 4.8 59.9 1.0
CZ c:ARG357 4.9 48.5 1.0

Calcium binding site 6 out of 9 in 7cji

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Calcium binding site 6 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca523

b:81.5
occ:1.00
 OG1 c:THR159 2.6 81.1 1.0
O c:HIS251 2.6 77.4 1.0
O c:THR254 2.7 70.6 1.0
O c:ASN155 2.9 78.2 1.0
OG1 c:THR158 2.9 82.8 1.0
O c:ILE252 3.0 77.4 1.0
OD1 c:ASN155 3.3 103.5 1.0
N c:THR159 3.5 78.7 1.0
C c:ILE252 3.6 80.2 1.0
CG c:ASN155 3.6 100.3 1.0
C c:ASN155 3.8 79.3 1.0
CB c:THR159 3.8 80.3 1.0
C c:HIS251 3.8 81.7 1.0
CA c:THR159 3.9 77.7 1.0
CB c:THR158 3.9 74.0 1.0
C c:THR254 3.9 75.7 1.0
C c:THR158 3.9 77.8 1.0
CA c:ILE252 3.9 71.6 1.0
CA c:ASN155 4.0 85.6 1.0
ND2 c:ASN155 4.0 105.8 1.0
N c:THR254 4.2 78.6 1.0
N c:ILE252 4.4 80.5 1.0
CB c:ASN155 4.4 90.5 1.0
O c:HOH733 4.4 87.1 1.0
CA c:THR158 4.4 75.9 1.0
N c:LEU253 4.5 83.7 1.0
O c:THR158 4.5 78.3 1.0
CA c:THR254 4.7 77.1 1.0
N c:THR158 4.9 75.2 1.0
N c:THR255 4.9 70.3 1.0
C c:LEU253 4.9 80.1 1.0
CA c:HIS251 5.0 79.9 1.0
CG2 c:THR159 5.0 71.8 1.0
N c:LYS156 5.0 75.1 1.0

Calcium binding site 7 out of 9 in 7cji

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Calcium binding site 7 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca524

b:90.2
occ:1.00
 OD2 c:ASP27 2.3 72.8 1.0
O c:THR24 2.4 81.5 1.0
OE1 c:GLU29 2.5 80.2 1.0
O c:PHE22 2.5 92.6 1.0
OG c:SER30 2.5 100.0 1.0
OD1 c:ASP27 2.8 74.5 1.0
CG c:ASP27 2.9 78.3 1.0
O c:HOH676 2.9 94.4 1.0
C c:PHE22 3.4 82.7 1.0
CB c:SER30 3.6 79.5 1.0
C c:THR24 3.7 82.0 1.0
CD c:GLU29 3.7 78.8 1.0
N c:SER30 4.0 71.0 1.0
CA c:PHE22 4.0 90.5 1.0
CB c:PHE22 4.2 92.2 1.0
N c:THR24 4.2 84.3 1.0
O c:HOH644 4.3 72.7 1.0
C c:ALA23 4.3 86.4 1.0
N c:ALA23 4.3 81.3 1.0
CA c:SER30 4.3 77.0 1.0
OE2 c:GLU29 4.3 88.9 1.0
CB c:ASP27 4.4 81.7 1.0
CA c:ASN25 4.5 82.0 1.0
N c:ASN25 4.6 81.0 1.0
CA c:THR24 4.6 83.5 1.0
CB c:GLU29 4.6 81.8 1.0
CA c:ALA23 4.6 83.3 1.0
O c:ALA23 4.7 91.1 1.0
CG c:GLU29 4.7 76.4 1.0
C c:GLU29 4.9 74.9 1.0

Calcium binding site 8 out of 9 in 7cji

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Calcium binding site 8 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:104.5
occ:1.00
 O o:THR138 2.5 90.8 1.0
O o:HOH424 2.6 77.3 1.0
OD1 o:ASN200 2.8 104.1 1.0
O o:VAL201 2.9 76.8 1.0
C o:THR138 3.7 91.1 1.0
CG o:ASN200 3.9 100.5 1.0
C o:VAL201 4.0 75.5 1.0
ND2 o:ASN200 4.2 106.2 1.0
CA o:ALA202 4.5 77.3 1.0
CA o:THR138 4.5 87.7 1.0
CB o:THR138 4.6 83.1 1.0
N o:ALA202 4.7 79.6 1.0
N o:SER139 4.7 98.8 1.0
CA o:SER139 4.8 107.6 1.0
N o:VAL201 4.9 64.1 1.0

Calcium binding site 9 out of 9 in 7cji

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Calcium binding site 9 out of 9 in the Photosystem II Structure in the S1 State


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Photosystem II Structure in the S1 State within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Ca201

b:117.3
occ:1.00
 O f:HOH205 2.7 90.8 1.0
OE2 v:GLU23 2.9 108.2 1.0
OXT f:ARG45 3.5 86.8 1.0
O a:ALA309 3.5 74.8 1.0
O f:ARG45 3.7 87.7 1.0
C f:ARG45 3.9 82.6 1.0
CD v:GLU23 4.1 108.6 1.0
NH1 f:ARG45 4.1 62.1 1.0
O v:HOH337 4.2 88.9 1.0
CG f:ARG45 4.4 69.5 1.0
C a:ALA309 4.5 73.2 1.0
CZ f:ARG45 4.6 72.9 1.0
CA a:ALA309 4.7 66.4 1.0
CG v:GLU23 4.8 101.6 1.0
CB v:LEU3 4.8 76.2 1.0
OE1 v:GLU23 5.0 111.4 1.0

Reference:

H.Li, Y.Nakajima, T.Nomura, M.Sugahara, S.Yonekura, S.K.Chan, T.Nakane, T.Yamane, Y.Umena, M.Suzuki, T.Masuda, T.Motomura, H.Naitow, Y.Matsuura, T.Kimura, K.Tono, S.Owada, Y.Joti, R.Tanaka, E.Nango, F.Akita, M.Kubo, S.Iwata, J.-R.Shen, M.Suga. Capturing Structural Changes of the S1 to S2 Transition of Photosystem II Using Time-Resolved Serial Femtosecond Crystallography Iucrj 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521002177
Page generated: Wed Jul 9 21:19:15 2025

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