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Calcium in PDB 8irc: Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation):
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation), PDB code: 8irc 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 (%) 14.1 / 17.6

Other elements in 8irc:

The structure of Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation) also contains other interesting chemical elements:

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

Calcium Binding Sites:

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

Calcium binding site 1 out of 9 in 8irc

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Calcium binding site 1 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:47.3
occ:1.00
 CA1 A:OEX413 0.0 47.3 1.0
O A:HOH535 2.4 47.4 1.0
OD1 A:ASP170 2.4 47.1 1.0
O A:ALA344 2.5 49.3 1.0
O A:HOH605 2.5 46.2 1.0
O1 A:OEX413 2.5 42.3 1.0
O5 A:OEX413 2.6 49.8 1.0
O2 A:OEX413 2.6 41.0 1.0
OE1 A:GLU189 2.9 48.6 1.0
CG A:ASP170 3.3 41.9 1.0
C A:ALA344 3.5 48.1 1.0
MN2 A:OEX413 3.5 45.6 1.0
MN1 A:OEX413 3.6 44.7 1.0
MN3 A:OEX413 3.6 45.8 1.0
OE2 A:GLU189 3.6 49.6 1.0
CD A:GLU189 3.6 45.3 1.0
OD2 A:ASP170 3.7 44.1 1.0
OXT A:ALA344 3.8 43.4 1.0
O4 A:OEX413 4.0 45.8 1.0
MN4 A:OEX413 4.1 48.8 1.0
O3 A:OEX413 4.1 46.8 1.0
O A:HOH541 4.3 45.1 1.0
CB A:ASP170 4.4 43.3 1.0
NH1 C:ARG357 4.4 41.0 1.0
O A:HOH606 4.4 69.9 1.0
OE1 A:GLN165 4.6 45.4 1.0
OH A:TYR161 4.6 42.4 1.0
NH2 C:ARG357 4.6 39.7 1.0
O A:HOH517 4.7 42.1 1.0
CA A:ALA344 4.8 46.2 1.0

Calcium binding site 2 out of 9 in 8irc

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Calcium binding site 2 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca524

b:73.1
occ:1.00
 O C:THR254 2.6 67.8 1.0
OG1 C:THR159 2.8 69.4 1.0
O C:HIS251 2.8 69.8 1.0
O C:ASN155 2.8 68.5 1.0
OD1 C:ASN155 2.9 75.3 1.0
OG1 C:THR158 2.9 70.7 1.0
O C:ILE252 3.0 67.8 1.0
N C:THR159 3.6 63.6 1.0
C C:ILE252 3.7 70.0 1.0
CG C:ASN155 3.7 81.3 1.0
C C:ASN155 3.8 70.7 1.0
C C:THR254 3.9 71.8 1.0
CB C:THR159 3.9 61.6 1.0
C C:HIS251 3.9 69.7 1.0
CB C:THR158 4.0 67.3 1.0
CA C:THR159 4.0 64.8 1.0
CA C:ILE252 4.0 71.4 1.0
CA C:ASN155 4.0 75.4 1.0
C C:THR158 4.1 66.8 1.0
N C:THR254 4.4 77.7 1.0
N C:ILE252 4.5 73.2 1.0
O C:HOH634 4.5 61.6 1.0
CB C:ASN155 4.5 76.6 1.0
CA C:THR158 4.5 65.3 1.0
ND2 C:ASN155 4.6 84.4 1.0
N C:LEU253 4.6 74.5 1.0
O C:THR158 4.6 66.5 1.0
N C:THR255 4.8 75.1 1.0
CA C:THR254 4.8 69.2 1.0
C C:LEU253 4.8 77.4 1.0
CA C:THR255 4.9 71.1 1.0
N C:THR158 4.9 64.3 1.0
N C:LYS156 5.0 68.3 1.0

Calcium binding site 3 out of 9 in 8irc

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Calcium binding site 3 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca104

b:127.3
occ:1.00
 O F:ARG45 3.3 65.6 1.0
OXT F:ARG45 3.4 61.3 1.0
OE1 V:GLU2 3.4 58.9 0.5
OE2 V:GLU2 3.5 67.7 0.5
OE2 V:GLU23 3.5 96.0 1.0
C F:ARG45 3.8 67.8 1.0
CD V:GLU2 3.8 63.6 0.5
CD V:GLU23 4.3 87.5 1.0
OE1 V:GLU23 4.4 94.1 1.0
O A:ALA309 4.6 54.7 1.0

Calcium binding site 4 out of 9 in 8irc

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Calcium binding site 4 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


Mono view


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:102.5
occ:1.00
 O O:HOH405 2.4 71.8 1.0
ND2 O:ASN200 2.8 95.8 1.0
O O:VAL201 2.9 83.5 1.0
O O:THR138 2.9 92.9 1.0
OD2 O:ASP141 3.0 91.3 1.0
O O:THR140 3.3 79.7 1.0
CG O:ASN200 3.4 88.7 1.0
CA O:SER139 3.5 86.6 1.0
C O:THR138 3.7 90.5 1.0
OD1 O:ASN200 3.7 93.1 1.0
C O:SER139 3.7 84.0 1.0
C O:VAL201 4.0 65.6 1.0
N O:VAL201 4.0 65.5 1.0
N O:SER139 4.0 83.9 1.0
CG O:ASP141 4.0 95.5 1.0
O O:SER139 4.1 87.2 1.0
C O:THR140 4.2 88.5 1.0
N O:THR140 4.2 84.3 1.0
C O:ASN200 4.3 72.6 1.0
OD1 O:ASP141 4.4 106.4 1.0
CA O:ASN200 4.4 72.0 1.0
CB O:ASN200 4.4 77.4 1.0
CA O:VAL201 4.5 63.2 1.0
CB O:SER139 4.8 92.4 1.0
CB O:VAL201 4.8 73.3 1.0
CA O:THR138 4.8 89.0 1.0
CA O:THR140 4.9 84.5 1.0
O O:ASN200 5.0 73.3 1.0

Calcium binding site 5 out of 9 in 8irc

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Calcium binding site 5 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca413

b:55.4
occ:1.00
 CA1 a:OEX413 0.0 55.4 1.0
OD1 a:ASP170 2.3 50.9 1.0
O a:HOH518 2.4 56.1 1.0
O a:ALA344 2.5 54.3 1.0
O a:HOH611 2.5 54.7 1.0
O1 a:OEX413 2.6 53.1 1.0
O5 a:OEX413 2.6 52.2 1.0
O2 a:OEX413 2.7 47.1 1.0
OE1 a:GLU189 2.9 50.3 1.0
CG a:ASP170 3.3 48.5 1.0
MN2 a:OEX413 3.4 50.2 1.0
C a:ALA344 3.5 53.2 1.0
MN1 a:OEX413 3.5 50.2 1.0
MN3 a:OEX413 3.5 48.8 1.0
CD a:GLU189 3.7 51.1 1.0
OE2 a:GLU189 3.7 52.5 1.0
OXT a:ALA344 3.8 54.7 1.0
OD2 a:ASP170 3.8 53.4 1.0
O3 a:OEX413 3.9 50.1 1.0
MN4 a:OEX413 4.0 48.3 1.0
O4 a:OEX413 4.2 48.6 1.0
O a:HOH514 4.3 47.2 1.0
O a:HOH607 4.3 79.3 1.0
NH1 c:ARG357 4.3 46.1 1.0
CB a:ASP170 4.4 46.1 1.0
OH a:TYR161 4.5 50.5 1.0
OE1 a:GLN165 4.6 53.9 1.0
NH2 c:ARG357 4.7 43.1 1.0
O a:HOH548 4.7 47.5 1.0
CA a:ALA344 4.8 54.5 1.0

Calcium binding site 6 out of 9 in 8irc

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Calcium binding site 6 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca524

b:77.6
occ:1.00
 O c:THR254 2.5 72.7 1.0
O c:HIS251 2.7 74.7 1.0
OG1 c:THR159 2.7 73.3 1.0
O c:ASN155 2.9 73.2 1.0
OG1 c:THR158 2.9 74.9 1.0
O c:ILE252 3.1 75.5 1.0
OD1 c:ASN155 3.3 95.5 1.0
CG c:ASN155 3.5 84.7 1.0
N c:THR159 3.7 71.6 1.0
C c:ILE252 3.7 75.7 1.0
C c:ASN155 3.8 74.9 1.0
C c:THR254 3.8 69.4 1.0
ND2 c:ASN155 3.8 91.2 1.0
CB c:THR158 3.8 65.3 1.0
C c:HIS251 3.8 75.4 1.0
CB c:THR159 3.9 75.1 1.0
CA c:ASN155 3.9 80.3 1.0
CA c:ILE252 4.0 68.9 1.0
C c:THR158 4.0 71.2 1.0
CA c:THR159 4.0 73.3 1.0
N c:THR254 4.2 81.4 1.0
CB c:ASN155 4.3 84.6 1.0
O c:HOH666 4.4 73.4 1.0
N c:ILE252 4.4 69.5 1.0
CA c:THR158 4.4 62.9 1.0
O c:THR158 4.5 73.0 1.0
N c:LEU253 4.6 75.3 1.0
CA c:THR254 4.7 72.4 1.0
N c:THR255 4.7 73.5 1.0
CA c:THR255 4.8 77.8 1.0
N c:THR158 4.8 63.0 1.0
C c:LEU253 4.9 77.7 1.0
OG1 c:THR255 4.9 88.7 1.0
N c:LYS156 5.0 70.7 1.0
O c:LYS154 5.0 71.3 1.0

Calcium binding site 7 out of 9 in 8irc

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Calcium binding site 7 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca525

b:79.1
occ:1.00
 OE1 c:GLU29 2.4 78.6 1.0
O c:PHE22 2.5 85.4 1.0
OD2 c:ASP27 2.5 73.9 1.0
OG c:SER30 2.5 81.5 1.0
O c:THR24 2.6 76.1 1.0
O c:HOH712 2.7 80.9 1.0
OD1 c:ASP27 2.8 61.2 1.0
CG c:ASP27 3.0 72.3 1.0
C c:PHE22 3.4 82.5 1.0
CD c:GLU29 3.5 80.7 1.0
CB c:SER30 3.6 70.4 1.0
C c:THR24 3.8 75.2 1.0
CB c:PHE22 4.0 86.8 1.0
CA c:PHE22 4.0 86.8 1.0
N c:SER30 4.0 68.2 1.0
OE2 c:GLU29 4.1 84.9 1.0
O c:HOH625 4.3 69.0 1.0
CA c:SER30 4.3 67.4 1.0
N c:THR24 4.4 78.1 1.0
C c:ALA23 4.4 86.9 1.0
N c:ALA23 4.5 82.1 1.0
CB c:ASP27 4.5 78.1 1.0
CA c:ASN25 4.6 82.1 1.0
N c:ASN25 4.7 74.8 1.0
CB c:GLU29 4.7 80.5 1.0
O c:ALA23 4.7 84.0 1.0
CG c:GLU29 4.7 84.2 1.0
CA c:THR24 4.7 75.8 1.0
CA c:ALA23 4.8 90.2 1.0
C c:GLU29 4.9 71.1 1.0

Calcium binding site 8 out of 9 in 8irc

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Calcium binding site 8 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca102

b:125.9
occ:1.00
 O v:HOH323 2.7 91.1 1.0
OE2 v:GLU23 3.0 120.3 1.0
OXT f:ARG45 3.1 78.4 1.0
O f:ARG45 3.3 78.2 1.0
C f:ARG45 3.6 76.8 1.0
O a:ALA309 4.0 68.3 1.0
CD v:GLU23 4.0 113.0 1.0
OE1 v:GLU23 4.4 118.9 1.0
C a:ALA309 4.8 68.6 1.0
CA a:ALA309 4.8 71.2 1.0
OE1 v:GLU2 4.9 106.3 1.0
CB a:ALA309 4.9 66.4 1.0
CG f:ARG45 5.0 69.7 1.0

Calcium binding site 9 out of 9 in 8irc

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Calcium binding site 9 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Following One Flash (1F) with A 5-Millisecond Delay (Single Conformation)


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 One Flash (1F) with A 5-Millisecond Delay (Single Conformation) within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:108.4
occ:1.00
 O o:HOH401 2.4 76.3 1.0
O o:THR138 2.5 84.3 1.0
OD1 o:ASN200 2.9 89.0 1.0
O o:VAL201 3.0 77.1 1.0
C o:THR138 3.8 88.4 1.0
CG o:ASN200 3.9 83.3 1.0
ND2 o:ASN200 4.1 91.5 1.0
C o:VAL201 4.1 73.8 1.0
CA o:ALA202 4.5 72.4 1.0
CB o:THR138 4.6 85.0 1.0
CA o:THR138 4.6 82.8 1.0
N o:SER139 4.7 96.7 1.0
N o:ALA202 4.8 77.7 1.0
CA o:SER139 4.8 98.8 1.0
OG1 o:THR138 4.8 94.4 1.0
CB o:ALA202 4.9 75.4 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: Fri Jul 19 09:46:53 2024

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