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Calcium in PDB 8ir5: Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

Enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions

All present enzymatic activity of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions:
1.10.3.9;

Protein crystallography data

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions, PDB code: 8ir5 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) 19.98 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 125.75, 231.6, 288.28, 90, 90, 90
R / Rfree (%) 14.5 / 17.5

Other elements in 8ir5:

The structure of Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions 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 Under Dark Conditions (pdb code 8ir5). 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 Under Dark Conditions, PDB code: 8ir5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8ir5

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Calcium binding site 1 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:50.7
occ:1.00
 CA1 A:OEX413 0.0 50.7 1.0
O A:HOH513 2.4 48.8 1.0
OD1 A:ASP170 2.4 46.2 1.0
O A:HOH621 2.4 48.5 1.0
O A:ALA344 2.5 51.2 1.0
O5 A:OEX413 2.5 46.6 1.0
O1 A:OEX413 2.6 41.8 1.0
O2 A:OEX413 2.6 43.2 1.0
OE1 A:GLU189 3.0 52.2 1.0
CG A:ASP170 3.3 43.5 1.0
MN2 A:OEX413 3.4 45.9 1.0
C A:ALA344 3.5 48.2 1.0
MN1 A:OEX413 3.5 44.7 1.0
MN3 A:OEX413 3.5 44.6 1.0
OD2 A:ASP170 3.6 42.4 1.0
OE2 A:GLU189 3.6 47.2 1.0
CD A:GLU189 3.7 45.5 1.0
OXT A:ALA344 3.8 46.2 1.0
MN4 A:OEX413 3.8 48.6 1.0
O4 A:OEX413 4.0 42.6 1.0
O3 A:OEX413 4.0 46.4 1.0
O A:HOH590 4.1 59.8 1.0
NH1 C:ARG357 4.3 44.2 1.0
O A:HOH529 4.5 46.0 1.0
CB A:ASP170 4.5 42.4 1.0
NH2 C:ARG357 4.6 45.1 1.0
OE1 A:GLN165 4.6 46.8 1.0
O A:HOH542 4.6 42.0 1.0
OH A:TYR161 4.7 45.4 1.0
CA A:ALA344 4.8 46.8 1.0
CZ C:ARG357 4.9 51.7 1.0

Calcium binding site 2 out of 9 in 8ir5

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Calcium binding site 2 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca524

b:73.4
occ:1.00
 O C:THR254 2.7 65.1 1.0
O C:ASN155 2.7 68.0 1.0
O C:HIS251 2.7 70.2 1.0
OD1 C:ASN155 2.8 74.2 1.0
OG1 C:THR159 2.8 66.8 1.0
OG1 C:THR158 2.9 68.8 1.0
O C:ILE252 3.1 66.6 1.0
N C:THR159 3.5 65.5 1.0
C C:ASN155 3.6 70.1 1.0
CG C:ASN155 3.7 77.9 1.0
C C:ILE252 3.7 69.6 1.0
CB C:THR159 3.9 63.0 1.0
C C:HIS251 3.9 66.1 1.0
C C:THR254 3.9 65.6 1.0
CB C:THR158 3.9 63.0 1.0
CA C:ASN155 3.9 72.4 1.0
CA C:THR159 3.9 64.0 1.0
C C:THR158 4.0 64.1 1.0
CA C:ILE252 4.0 66.5 1.0
N C:THR254 4.4 76.9 1.0
CB C:ASN155 4.4 75.4 1.0
CA C:THR158 4.4 61.2 1.0
O C:HOH640 4.5 63.9 1.0
N C:ILE252 4.5 70.6 1.0
ND2 C:ASN155 4.6 84.2 1.0
O C:THR158 4.6 64.7 1.0
N C:LEU253 4.7 72.5 1.0
CA C:THR254 4.8 66.0 1.0
N C:THR255 4.8 76.7 1.0
N C:THR158 4.8 63.6 1.0
N C:LYS156 4.9 70.5 1.0
C C:LEU253 4.9 80.7 1.0
CA C:THR255 4.9 72.0 1.0
O C:LYS154 4.9 72.7 1.0

Calcium binding site 3 out of 9 in 8ir5

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Calcium binding site 3 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca104

b:127.2
occ:1.00
 O F:ARG45 3.2 64.1 1.0
OXT F:ARG45 3.3 62.4 1.0
OE1 V:GLU2 3.4 59.6 0.5
OE2 V:GLU2 3.5 66.4 0.5
OE2 V:GLU23 3.5 95.9 1.0
C F:ARG45 3.7 66.1 1.0
CD V:GLU2 3.9 65.1 0.5
CD V:GLU23 4.4 90.8 1.0
OE1 V:GLU23 4.4 97.1 1.0
O A:ALA309 4.5 55.2 1.0
CB A:ALA309 4.8 54.7 1.0
O F:HOH206 4.9 81.4 1.0

Calcium binding site 4 out of 9 in 8ir5

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Calcium binding site 4 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:100.8
occ:1.00
 O O:HOH410 2.4 78.0 1.0
ND2 O:ASN200 2.5 94.7 1.0
O O:VAL201 2.8 82.7 1.0
O O:THR138 2.9 85.4 1.0
OD2 O:ASP141 3.0 90.9 1.0
CG O:ASN200 3.2 86.9 1.0
O O:THR140 3.4 79.1 1.0
OD1 O:ASN200 3.5 91.1 1.0
CA O:SER139 3.7 86.0 1.0
C O:THR138 3.7 85.1 1.0
C O:SER139 3.9 82.3 1.0
C O:VAL201 3.9 72.2 1.0
N O:VAL201 3.9 66.0 1.0
CG O:ASP141 4.0 96.6 1.0
N O:SER139 4.1 88.0 1.0
O O:SER139 4.2 88.1 1.0
C O:ASN200 4.2 70.9 1.0
C O:THR140 4.3 89.5 1.0
N O:THR140 4.3 86.7 1.0
CB O:ASN200 4.3 77.5 1.0
CA O:ASN200 4.4 72.6 1.0
OD1 O:ASP141 4.4 100.8 1.0
CA O:VAL201 4.4 70.9 1.0
CB O:VAL201 4.8 73.5 1.0
CA O:THR138 4.9 85.0 1.0
O O:ASN200 4.9 72.1 1.0
CB O:SER139 4.9 92.6 1.0
CA O:THR140 5.0 87.2 1.0

Calcium binding site 5 out of 9 in 8ir5

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Calcium binding site 5 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca413

b:55.0
occ:1.00
 CA1 a:OEX413 0.0 55.0 1.0
OD1 a:ASP170 2.3 49.7 1.0
O a:HOH520 2.4 57.5 1.0
O a:ALA344 2.5 53.0 1.0
O a:HOH622 2.6 54.3 1.0
O1 a:OEX413 2.6 49.7 1.0
O5 a:OEX413 2.6 50.1 1.0
O2 a:OEX413 2.6 50.2 1.0
OE1 a:GLU189 3.0 51.2 1.0
CG a:ASP170 3.2 48.6 1.0
MN2 a:OEX413 3.4 51.6 1.0
MN3 a:OEX413 3.4 50.7 1.0
C a:ALA344 3.5 55.9 1.0
MN1 a:OEX413 3.5 49.4 1.0
OD2 a:ASP170 3.6 49.0 1.0
MN4 a:OEX413 3.8 49.7 1.0
OXT a:ALA344 3.8 53.5 1.0
O3 a:OEX413 3.8 48.0 1.0
CD a:GLU189 3.8 49.9 1.0
OE2 a:GLU189 3.9 54.0 1.0
O4 a:OEX413 4.1 50.6 1.0
O a:HOH590 4.2 62.5 1.0
NH1 c:ARG357 4.2 52.9 1.0
CB a:ASP170 4.4 47.6 1.0
O a:HOH516 4.4 53.4 1.0
NH2 c:ARG357 4.5 46.1 1.0
O a:HOH569 4.6 48.7 1.0
OH a:TYR161 4.6 50.1 1.0
OE1 a:GLN165 4.6 56.0 1.0
CA a:ALA344 4.8 55.9 1.0
CZ c:ARG357 4.9 53.5 1.0
OD1 a:ASP342 5.0 50.0 1.0

Calcium binding site 6 out of 9 in 8ir5

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Calcium binding site 6 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca523

b:75.1
occ:1.00
 O c:THR254 2.6 72.5 1.0
O c:HIS251 2.7 69.3 1.0
OG1 c:THR159 2.7 73.0 1.0
O c:ASN155 2.9 79.5 1.0
OG1 c:THR158 2.9 73.6 1.0
O c:ILE252 3.1 76.7 1.0
OD1 c:ASN155 3.4 100.2 1.0
N c:THR159 3.5 71.2 1.0
CG c:ASN155 3.6 91.3 1.0
C c:ILE252 3.6 74.6 1.0
C c:ASN155 3.7 75.3 1.0
ND2 c:ASN155 3.8 95.5 1.0
C c:HIS251 3.8 73.9 1.0
CB c:THR159 3.8 72.1 1.0
CB c:THR158 3.8 67.2 1.0
C c:THR254 3.9 69.5 1.0
CA c:THR159 3.9 70.8 1.0
C c:THR158 3.9 72.4 1.0
CA c:ILE252 3.9 68.8 1.0
CA c:ASN155 3.9 81.1 1.0
N c:ILE252 4.4 70.9 1.0
N c:THR254 4.4 78.1 1.0
CB c:ASN155 4.4 87.1 1.0
O c:HOH692 4.4 71.7 1.0
CA c:THR158 4.4 65.3 1.0
O c:THR158 4.5 71.7 1.0
N c:LEU253 4.6 78.9 1.0
N c:THR255 4.8 68.6 1.0
CA c:THR254 4.8 69.1 1.0
N c:THR158 4.8 64.2 1.0
CA c:THR255 4.9 74.6 1.0
C c:LEU253 4.9 79.8 1.0
N c:LYS156 4.9 68.7 1.0
CG2 c:THR159 5.0 58.2 1.0
CA c:HIS251 5.0 76.5 1.0

Calcium binding site 7 out of 9 in 8ir5

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Calcium binding site 7 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca524

b:76.4
occ:1.00
 OE1 c:GLU29 2.4 82.3 1.0
OD2 c:ASP27 2.5 71.8 1.0
O c:THR24 2.5 75.1 1.0
O c:PHE22 2.5 80.9 1.0
OG c:SER30 2.5 82.6 1.0
O c:HOH721 2.5 82.5 1.0
OD1 c:ASP27 2.7 66.1 1.0
CG c:ASP27 2.9 71.3 1.0
C c:PHE22 3.5 80.7 1.0
CB c:SER30 3.5 74.6 1.0
CD c:GLU29 3.6 78.0 1.0
C c:THR24 3.7 73.6 1.0
CA c:PHE22 4.0 82.9 1.0
N c:SER30 4.0 68.3 1.0
CB c:PHE22 4.0 83.8 1.0
OE2 c:GLU29 4.1 90.7 1.0
O c:HOH624 4.2 71.4 1.0
CA c:SER30 4.3 72.6 1.0
N c:THR24 4.3 79.2 1.0
C c:ALA23 4.4 86.0 1.0
CB c:ASP27 4.5 75.1 1.0
N c:ALA23 4.5 83.2 1.0
CA c:ASN25 4.5 80.6 1.0
N c:ASN25 4.6 74.9 1.0
CA c:THR24 4.6 75.7 1.0
CB c:GLU29 4.7 80.2 1.0
O c:ALA23 4.7 84.1 1.0
CG c:GLU29 4.7 84.9 1.0
CA c:ALA23 4.8 89.5 1.0
C c:GLU29 4.9 67.2 1.0

Calcium binding site 8 out of 9 in 8ir5

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Calcium binding site 8 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:125.7
occ:1.00
 O v:HOH316 2.5 93.7 1.0
OE2 v:GLU23 3.0 115.7 1.0
OXT f:ARG45 3.1 79.8 1.0
O f:ARG45 3.2 79.7 1.0
C f:ARG45 3.5 78.2 1.0
CD v:GLU23 4.1 110.6 1.0
O a:ALA309 4.2 65.4 1.0
OE1 v:GLU23 4.4 116.3 1.0
OE1 v:GLU2 4.8 106.4 1.0
CB a:ALA309 4.9 63.8 1.0
CA a:ALA309 4.9 68.1 1.0
C a:ALA309 5.0 67.3 1.0
CA f:ARG45 5.0 76.3 1.0

Calcium binding site 9 out of 9 in 8ir5

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Calcium binding site 9 out of 9 in the Xfel Structure of Cyanobacterial Photosystem II Under Dark Conditions


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 Under Dark Conditions within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:103.1
occ:1.00
 O o:HOH401 2.3 78.5 1.0
O o:THR138 2.4 88.3 1.0
O o:VAL201 2.8 75.1 1.0
OD1 o:ASN200 2.9 86.6 1.0
C o:THR138 3.7 86.0 1.0
CG o:ASN200 3.9 81.0 1.0
C o:VAL201 4.0 71.3 1.0
ND2 o:ASN200 4.2 88.7 1.0
CA o:ALA202 4.4 74.8 1.0
CA o:THR138 4.5 84.0 1.0
CB o:THR138 4.5 84.8 1.0
N o:SER139 4.6 91.3 1.0
N o:ALA202 4.6 75.9 1.0
CA o:SER139 4.7 93.7 1.0
CB o:ALA202 4.9 77.1 1.0
OG1 o:THR138 4.9 93.5 1.0
N o:VAL201 5.0 64.5 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 09:41:06 2024

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