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Calcium in PDB 8iri: Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay, PDB code: 8iri was solved by H.Li, M.Suga, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.77, 231.76, 288.58, 90, 90, 90
R / Rfree (%) 14 / 17.7

Other elements in 8iri:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Magnesium (Mg) 80 atoms
Manganese (Mn) 16 atoms
Chlorine (Cl) 8 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay (pdb code 8iri). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay, PDB code: 8iri:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 8iri

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Calcium binding site 1 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:46.5
occ:0.51
 CA1 A:OEY401 0.0 46.5 0.5
CA1 A:OEX413 0.2 44.5 0.5
O A:HOH540 2.4 48.2 0.5
O A:HOH610 2.4 42.7 0.5
O5 A:OEX413 2.4 49.3 0.5
O A:HOH610 2.4 42.7 0.5
OD1 A:ASP170 2.5 43.0 0.5
O1 A:OEX413 2.5 42.8 0.5
OD1 A:ASP170 2.5 43.0 0.5
O A:HOH540 2.6 46.7 0.5
O1 A:OEY401 2.6 41.2 0.5
O2 A:OEX413 2.6 42.4 0.5
O6 A:OEY401 2.6 47.2 0.5
O A:ALA344 2.6 46.4 0.5
O5 A:OEY401 2.6 57.0 0.5
O A:ALA344 2.6 46.0 0.5
O2 A:OEY401 2.6 41.0 0.5
OE1 A:GLU189 2.9 48.4 0.5
OE1 A:GLU189 3.1 47.8 0.5
CG A:ASP170 3.3 40.2 0.5
CG A:ASP170 3.3 40.2 0.5
MN2 A:OEY401 3.4 43.2 0.5
MN1 A:OEX413 3.4 42.9 0.5
MN2 A:OEX413 3.4 43.8 0.5
MN3 A:OEX413 3.5 43.6 0.5
MN1 A:OEY401 3.5 46.0 0.5
MN3 A:OEY401 3.5 44.2 0.5
OE2 A:GLU189 3.5 52.8 0.5
C A:ALA344 3.6 43.7 0.5
C A:ALA344 3.6 43.6 0.5
CD A:GLU189 3.6 45.2 0.5
OD2 A:ASP170 3.6 43.4 0.5
O3 A:OEY401 3.7 44.9 0.5
OD2 A:ASP170 3.7 42.7 0.5
OE2 A:GLU189 3.8 50.1 0.5
OXT A:ALA344 3.8 47.8 0.5
OXT A:ALA344 3.8 47.7 0.5
CD A:GLU189 3.9 45.1 0.5
O4 A:OEX413 3.9 45.8 0.5
MN4 A:OEX413 3.9 47.0 0.5
O3 A:OEX413 3.9 44.8 0.5
MN4 A:OEY401 4.1 47.7 0.5
O A:HOH546 4.3 42.7 0.5
O A:HOH611 4.3 58.8 0.5
O4 A:OEY401 4.3 49.3 0.5
O A:HOH546 4.3 42.6 0.5
CB A:ASP170 4.4 42.2 0.5
CB A:ASP170 4.4 42.3 0.5
O A:HOH611 4.5 59.8 0.5
NH1 C:ARG357 4.5 41.0 0.5
OE1 A:GLN165 4.5 47.3 0.5
NH1 C:ARG357 4.5 41.0 0.5
O A:HOH520 4.5 41.5 0.5
NH2 C:ARG357 4.6 42.0 0.5
NH2 C:ARG357 4.7 42.0 0.5
OH A:TYR161 4.7 44.5 0.5
O A:HOH520 4.7 42.3 0.5
OH A:TYR161 4.7 44.5 0.5
OE1 A:GLN165 4.8 46.7 0.5
CA A:ALA344 4.8 46.6 0.5
CA A:ALA344 4.9 46.7 0.5
CG1 A:VAL185 4.9 41.5 0.5
CG1 A:VAL185 5.0 41.5 0.5
O A:HOH626 5.0 48.3 0.5

Calcium binding site 2 out of 11 in 8iri

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Calcium binding site 2 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:44.5
occ:0.49
 CA1 A:OEX413 0.0 44.5 0.5
CA1 A:OEY401 0.2 46.5 0.5
O A:HOH540 2.2 48.2 0.5
O A:HOH540 2.4 46.7 0.5
OD1 A:ASP170 2.4 43.0 0.5
OD1 A:ASP170 2.4 43.0 0.5
O A:ALA344 2.5 46.4 0.5
O A:ALA344 2.5 46.0 0.5
O A:HOH610 2.5 42.7 0.5
O A:HOH610 2.5 42.7 0.5
O1 A:OEX413 2.5 42.8 0.5
O5 A:OEX413 2.6 49.3 0.5
O1 A:OEY401 2.6 41.2 0.5
O2 A:OEX413 2.6 42.4 0.5
O2 A:OEY401 2.7 41.0 0.5
O6 A:OEY401 2.8 47.2 0.5
O5 A:OEY401 2.8 57.0 0.5
OE1 A:GLU189 2.9 48.4 0.5
OE1 A:GLU189 3.1 47.8 0.5
CG A:ASP170 3.3 40.2 0.5
CG A:ASP170 3.3 40.2 0.5
MN2 A:OEY401 3.4 43.2 0.5
C A:ALA344 3.5 43.7 0.5
C A:ALA344 3.5 43.6 0.5
MN2 A:OEX413 3.5 43.8 0.5
MN1 A:OEX413 3.6 42.9 0.5
MN1 A:OEY401 3.6 46.0 0.5
MN3 A:OEX413 3.6 43.6 0.5
MN3 A:OEY401 3.6 44.2 0.5
OE2 A:GLU189 3.6 52.8 0.5
CD A:GLU189 3.6 45.2 0.5
OD2 A:ASP170 3.7 43.4 0.5
OD2 A:ASP170 3.8 42.7 0.5
OXT A:ALA344 3.8 47.8 0.5
OXT A:ALA344 3.8 47.7 0.5
O3 A:OEY401 3.8 44.9 0.5
OE2 A:GLU189 3.9 50.1 0.5
CD A:GLU189 3.9 45.1 0.5
O4 A:OEX413 4.0 45.8 0.5
MN4 A:OEX413 4.1 47.0 0.5
O3 A:OEX413 4.1 44.8 0.5
MN4 A:OEY401 4.2 47.7 0.5
O A:HOH611 4.3 58.8 0.5
O A:HOH546 4.3 42.7 0.5
O A:HOH546 4.3 42.6 0.5
OE1 A:GLN165 4.3 47.3 0.5
CB A:ASP170 4.4 42.2 0.5
CB A:ASP170 4.4 42.3 0.5
NH1 C:ARG357 4.4 41.0 0.5
O A:HOH611 4.4 59.8 0.5
NH1 C:ARG357 4.4 41.0 0.5
O4 A:OEY401 4.4 49.3 0.5
OE1 A:GLN165 4.6 46.7 0.5
OH A:TYR161 4.6 44.5 0.5
OH A:TYR161 4.6 44.5 0.5
NH2 C:ARG357 4.6 42.0 0.5
NH2 C:ARG357 4.6 42.0 0.5
O A:HOH520 4.7 41.5 0.5
CA A:ALA344 4.7 46.6 0.5
CA A:ALA344 4.8 46.7 0.5
O A:HOH520 4.9 42.3 0.5

Calcium binding site 3 out of 11 in 8iri

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Calcium binding site 3 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca524

b:70.6
occ:1.00
 O C:THR254 2.7 62.1 1.0
OD1 C:ASN155 2.8 72.7 1.0
O C:HIS251 2.8 68.7 1.0
OG1 C:THR159 2.8 67.2 1.0
O C:ASN155 2.8 67.1 1.0
OG1 C:THR158 3.0 66.5 1.0
O C:ILE252 3.1 60.1 1.0
N C:THR159 3.6 63.9 1.0
C C:ILE252 3.7 69.1 1.0
C C:ASN155 3.8 68.0 1.0
CG C:ASN155 3.8 72.9 1.0
CB C:THR159 3.9 62.7 1.0
C C:THR254 3.9 68.1 1.0
C C:HIS251 3.9 64.1 1.0
CA C:THR159 4.0 59.4 1.0
CB C:THR158 4.0 63.6 1.0
CA C:ILE252 4.0 67.1 1.0
CA C:ASN155 4.0 68.2 1.0
C C:THR158 4.1 63.3 1.0
N C:THR254 4.4 75.0 1.0
N C:ILE252 4.5 71.8 1.0
CA C:THR158 4.5 64.1 1.0
O C:HOH622 4.5 64.1 1.0
CB C:ASN155 4.5 73.8 1.0
N C:LEU253 4.6 73.5 1.0
O C:THR158 4.7 67.1 1.0
ND2 C:ASN155 4.7 95.6 1.0
C C:LEU253 4.8 72.8 1.0
CA C:THR254 4.8 58.0 1.0
N C:THR255 4.8 67.6 1.0
N C:THR158 4.9 61.2 1.0
CA C:THR255 4.9 67.7 1.0
N C:LYS156 4.9 64.8 1.0

Calcium binding site 4 out of 11 in 8iri

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Calcium binding site 4 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca103

b:122.1
occ:1.00
 OXT F:ARG45 3.2 63.7 1.0
O F:ARG45 3.2 66.9 1.0
OE2 V:GLU23 3.5 112.9 1.0
OE1 V:GLU2 3.5 53.4 0.5
OE2 V:GLU2 3.6 58.6 0.5
C F:ARG45 3.7 64.6 1.0
CD V:GLU2 4.0 63.1 0.5
CD V:GLU23 4.4 98.0 1.0
OE1 V:GLU23 4.5 108.9 1.0
O A:ALA309 4.7 56.6 1.0
CB A:ALA309 4.9 51.7 1.0

Calcium binding site 5 out of 11 in 8iri

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Calcium binding site 5 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:100.8
occ:1.00
 O O:HOH405 2.3 72.2 1.0
ND2 O:ASN200 2.7 103.5 1.0
O O:THR138 2.8 89.3 1.0
O O:VAL201 2.9 86.0 1.0
OD2 O:ASP141 2.9 93.4 1.0
CA O:SER139 3.4 79.7 1.0
O O:THR140 3.4 76.0 1.0
CG O:ASN200 3.5 84.5 1.0
C O:THR138 3.6 82.3 1.0
C O:SER139 3.8 81.3 1.0
OD1 O:ASN200 3.8 103.2 1.0
N O:SER139 3.9 88.2 1.0
CG O:ASP141 3.9 104.2 1.0
C O:VAL201 4.0 69.0 1.0
N O:VAL201 4.1 66.6 1.0
O O:SER139 4.1 88.8 1.0
OD1 O:ASP141 4.3 121.3 1.0
N O:THR140 4.3 75.6 1.0
C O:THR140 4.3 92.1 1.0
C O:ASN200 4.4 63.3 1.0
CB O:ASN200 4.5 76.4 1.0
CA O:ASN200 4.5 64.5 1.0
CA O:VAL201 4.5 63.2 1.0
CB O:SER139 4.6 99.8 1.0
CA O:THR138 4.8 84.1 1.0
CB O:VAL201 4.9 72.3 1.0
CA O:THR140 5.0 82.8 1.0

Calcium binding site 6 out of 11 in 8iri

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Calcium binding site 6 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca401

b:52.5
occ:0.51
 CA1 a:OEY401 0.0 52.5 0.5
CA1 a:OEX413 0.1 52.3 0.5
O a:HOH519 2.3 54.7 0.5
O a:HOH519 2.4 52.5 0.5
OD1 a:ASP170 2.4 48.0 0.5
OD1 a:ASP170 2.4 48.0 0.5
O a:ALA344 2.5 52.0 0.5
O a:ALA344 2.5 51.9 0.5
O1 a:OEX413 2.5 49.9 0.5
O a:HOH615 2.5 52.5 0.5
O1 a:OEY401 2.6 50.9 0.5
O a:HOH615 2.6 51.2 0.5
O6 a:OEY401 2.6 59.5 0.5
O5 a:OEY401 2.6 51.0 0.5
O2 a:OEY401 2.6 53.1 0.5
O5 a:OEX413 2.6 51.1 0.5
O2 a:OEX413 2.7 48.1 0.5
OE1 a:GLU189 2.9 48.9 0.5
OE1 a:GLU189 3.1 49.4 0.5
MN2 a:OEY401 3.3 49.2 0.5
CG a:ASP170 3.3 47.4 0.5
MN2 a:OEX413 3.4 46.7 0.5
C a:ALA344 3.4 53.2 0.5
MN1 a:OEY401 3.4 47.8 0.5
CG a:ASP170 3.4 47.3 0.5
MN1 a:OEX413 3.4 48.3 0.5
C a:ALA344 3.4 53.0 0.5
MN3 a:OEX413 3.5 47.9 0.5
MN3 a:OEY401 3.6 46.9 0.5
CD a:GLU189 3.6 50.1 0.5
OE2 a:GLU189 3.7 54.7 0.5
OXT a:ALA344 3.7 51.0 0.5
OXT a:ALA344 3.7 51.2 0.5
OD2 a:ASP170 3.8 49.3 0.5
O3 a:OEY401 3.8 48.0 0.5
O3 a:OEX413 3.9 48.0 0.5
CD a:GLU189 3.9 49.1 0.5
OD2 a:ASP170 4.0 49.2 0.5
OE2 a:GLU189 4.0 53.4 0.5
MN4 a:OEX413 4.0 49.7 0.5
MN4 a:OEY401 4.0 48.5 0.5
O a:HOH610 4.2 69.8 0.5
O4 a:OEX413 4.3 49.9 0.5
O a:HOH517 4.3 50.1 0.5
NH1 c:ARG357 4.3 50.7 0.5
O a:HOH610 4.3 70.1 0.5
NH1 c:ARG357 4.4 50.5 0.5
O a:HOH517 4.4 50.7 0.5
O4 a:OEY401 4.4 50.8 0.5
CB a:ASP170 4.5 46.4 0.5
CB a:ASP170 4.5 46.4 0.5
OH a:TYR161 4.5 48.9 0.5
OE1 a:GLN165 4.6 52.6 0.5
OE1 a:GLN165 4.6 52.6 0.5
OH a:TYR161 4.7 49.1 0.5
CA a:ALA344 4.7 52.9 0.5
NH2 c:ARG357 4.7 46.5 0.5
O a:HOH549 4.7 46.6 0.5
NH2 c:ARG357 4.8 46.5 0.5
CA a:ALA344 4.8 53.0 0.5
O a:HOH549 4.8 47.5 0.5
OD1 a:ASP342 4.9 48.5 0.5
OD2 a:ASP342 5.0 51.7 0.5
OD1 a:ASP342 5.0 48.7 0.5

Calcium binding site 7 out of 11 in 8iri

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Calcium binding site 7 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca413

b:52.3
occ:0.49
 CA1 a:OEX413 0.0 52.3 0.5
CA1 a:OEY401 0.1 52.5 0.5
O a:HOH519 2.3 54.7 0.5
OD1 a:ASP170 2.3 48.0 0.5
OD1 a:ASP170 2.3 48.0 0.5
O a:HOH519 2.4 52.5 0.5
O a:ALA344 2.5 52.0 0.5
O a:ALA344 2.5 51.9 0.5
O a:HOH615 2.5 52.5 0.5
O a:HOH615 2.5 51.2 0.5
O1 a:OEX413 2.6 49.9 0.5
O5 a:OEY401 2.6 51.0 0.5
O6 a:OEY401 2.6 59.5 0.5
O1 a:OEY401 2.6 50.9 0.5
O5 a:OEX413 2.6 51.1 0.5
O2 a:OEY401 2.7 53.1 0.5
O2 a:OEX413 2.7 48.1 0.5
OE1 a:GLU189 2.9 48.9 0.5
OE1 a:GLU189 3.1 49.4 0.5
CG a:ASP170 3.3 47.4 0.5
MN2 a:OEY401 3.3 49.2 0.5
CG a:ASP170 3.4 47.3 0.5
MN2 a:OEX413 3.4 46.7 0.5
C a:ALA344 3.4 53.2 0.5
MN1 a:OEY401 3.5 47.8 0.5
C a:ALA344 3.5 53.0 0.5
MN1 a:OEX413 3.5 48.3 0.5
MN3 a:OEX413 3.5 47.9 0.5
MN3 a:OEY401 3.6 46.9 0.5
CD a:GLU189 3.7 50.1 0.5
OE2 a:GLU189 3.7 54.7 0.5
OXT a:ALA344 3.8 51.0 0.5
OXT a:ALA344 3.8 51.2 0.5
OD2 a:ASP170 3.8 49.3 0.5
O3 a:OEY401 3.9 48.0 0.5
OD2 a:ASP170 3.9 49.2 0.5
O3 a:OEX413 3.9 48.0 0.5
MN4 a:OEX413 4.0 49.7 0.5
CD a:GLU189 4.0 49.1 0.5
MN4 a:OEY401 4.0 48.5 0.5
OE2 a:GLU189 4.0 53.4 0.5
O4 a:OEX413 4.2 49.9 0.5
O a:HOH517 4.3 50.1 0.5
O a:HOH610 4.3 69.8 0.5
NH1 c:ARG357 4.3 50.7 0.5
NH1 c:ARG357 4.3 50.5 0.5
O a:HOH517 4.4 50.7 0.5
O a:HOH610 4.4 70.1 0.5
O4 a:OEY401 4.4 50.8 0.5
CB a:ASP170 4.4 46.4 0.5
CB a:ASP170 4.5 46.4 0.5
OH a:TYR161 4.5 48.9 0.5
OE1 a:GLN165 4.6 52.6 0.5
OE1 a:GLN165 4.6 52.6 0.5
OH a:TYR161 4.6 49.1 0.5
NH2 c:ARG357 4.7 46.5 0.5
O a:HOH549 4.7 46.6 0.5
CA a:ALA344 4.7 52.9 0.5
NH2 c:ARG357 4.8 46.5 0.5
O a:HOH549 4.8 47.5 0.5
CA a:ALA344 4.8 53.0 0.5
OD1 a:ASP342 4.9 48.5 0.5

Calcium binding site 8 out of 11 in 8iri

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Calcium binding site 8 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca523

b:73.1
occ:1.00
 O c:THR254 2.6 70.6 1.0
O c:HIS251 2.6 66.1 1.0
OG1 c:THR159 2.8 70.8 1.0
O c:ASN155 2.9 68.9 1.0
OG1 c:THR158 3.0 72.4 1.0
OD1 c:ASN155 3.1 94.5 1.0
O c:ILE252 3.2 81.5 1.0
CG c:ASN155 3.5 88.0 1.0
N c:THR159 3.6 67.5 1.0
C c:ILE252 3.7 75.9 1.0
C c:ASN155 3.7 69.1 1.0
C c:HIS251 3.8 78.8 1.0
CB c:THR158 3.8 65.7 1.0
C c:THR254 3.8 61.0 1.0
CB c:THR159 3.9 67.2 1.0
CA c:ASN155 3.9 75.2 1.0
ND2 c:ASN155 3.9 114.5 1.0
CA c:ILE252 4.0 66.6 1.0
CA c:THR159 4.0 70.8 1.0
C c:THR158 4.0 69.2 1.0
CB c:ASN155 4.3 78.2 1.0
N c:THR254 4.3 73.5 1.0
O c:HOH664 4.3 70.8 1.0
N c:ILE252 4.4 70.9 1.0
CA c:THR158 4.4 66.4 1.0
N c:LEU253 4.6 81.4 1.0
O c:THR158 4.6 70.7 1.0
CA c:THR254 4.7 67.8 1.0
N c:THR255 4.7 68.8 1.0
CA c:THR255 4.8 66.9 1.0
C c:LEU253 4.8 75.5 1.0
N c:THR158 4.9 65.4 1.0
CA c:HIS251 5.0 75.2 1.0
OG1 c:THR255 5.0 96.0 1.0
N c:LYS156 5.0 66.6 1.0
O c:LYS154 5.0 70.7 1.0

Calcium binding site 9 out of 11 in 8iri

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Calcium binding site 9 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca524

b:79.0
occ:1.00
 OE1 c:GLU29 2.4 78.9 1.0
OD2 c:ASP27 2.5 68.9 1.0
O c:PHE22 2.5 89.0 1.0
O c:THR24 2.6 76.0 1.0
O c:HOH717 2.6 75.4 1.0
OG c:SER30 2.6 86.0 1.0
OD1 c:ASP27 2.7 60.2 1.0
CG c:ASP27 2.9 77.4 1.0
CD c:GLU29 3.4 83.1 1.0
C c:PHE22 3.4 70.0 1.0
CB c:SER30 3.5 62.9 1.0
C c:THR24 3.8 68.5 1.0
OE2 c:GLU29 3.9 90.7 1.0
N c:SER30 4.0 61.7 1.0
CA c:PHE22 4.0 90.5 1.0
CB c:PHE22 4.0 77.0 1.0
CA c:SER30 4.2 70.0 1.0
O c:HOH623 4.3 72.4 1.0
C c:ALA23 4.4 86.2 1.0
N c:THR24 4.4 79.6 1.0
N c:ALA23 4.5 80.7 1.0
CB c:ASP27 4.5 78.7 1.0
CA c:ASN25 4.6 78.4 1.0
O c:ALA23 4.6 89.5 1.0
N c:ASN25 4.6 68.8 1.0
CG c:GLU29 4.7 76.3 1.0
CB c:GLU29 4.7 75.3 1.0
CA c:THR24 4.8 77.1 1.0
CA c:ALA23 4.8 87.1 1.0
C c:GLU29 4.8 66.7 1.0

Calcium binding site 10 out of 11 in 8iri

Go back to Calcium Binding Sites List in 8iri
Calcium binding site 10 out of 11 in the Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Xfel Structure of Cyanobacterial Photosystem II Following Two Flashes (2F) with A 5-Millisecond Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:119.2
occ:1.00
 O v:HOH312 2.7 90.7 1.0
OXT f:ARG45 3.1 74.7 1.0
OE2 v:GLU23 3.1 128.6 1.0
O f:ARG45 3.1 81.5 1.0
C f:ARG45 3.5 66.8 1.0
CD v:GLU23 4.1 124.4 1.0
O a:ALA309 4.2 61.2 1.0
OE1 v:GLU23 4.5 121.5 1.0
OE1 v:GLU2 4.8 110.5 1.0
CA a:ALA309 4.9 67.9 1.0
CB a:ALA309 5.0 58.5 1.0
CA f:ARG45 5.0 69.8 1.0
C a:ALA309 5.0 75.8 1.0

Reference:

H.Li, Y.Nakajima, E.Nango, S.Owada, D.Yamada, K.Hashimoto, F.Luo, R.Tanaka, F.Akita, K.Kato, J.M.Kang, Y.Saitoh, S.Kishi, H.Yu, N.Matsubara, H.Fujii, M.Sugahara, M.Suzuki, T.Masuda, T.Kimura, T.N.Thao, S.Yonekura, L.J.Yu, T.Tosha, K.Tono, Y.Joti, T.Hatsui, M.Yabashi, M.Kubo, S.Iwata, H.Isobe, K.Yamaguchi, M.Suga, J.R.Shen. Oxygen-Evolving Photosystem II Structures During S1-S2-S3 Transitions. Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-023-06987-5
Page generated: Thu Jul 10 05:24:02 2025

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