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Calcium in PDB 8gn2: Crystal Structure of Ppbq-Bound Photosystem II Complex

Enzymatic activity of Crystal Structure of Ppbq-Bound Photosystem II Complex

All present enzymatic activity of Crystal Structure of Ppbq-Bound Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Ppbq-Bound Photosystem II Complex, PDB code: 8gn2 was solved by S.Kamada, Y.Nakajima, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.018, 229.579, 287.18, 90, 90, 90
R / Rfree (%) 15.3 / 18.1

Other elements in 8gn2:

The structure of Crystal Structure of Ppbq-Bound Photosystem II Complex 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 Crystal Structure of Ppbq-Bound Photosystem II Complex (pdb code 8gn2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Ppbq-Bound Photosystem II Complex, PDB code: 8gn2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 8gn2

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Calcium binding site 1 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:39.9
occ:1.00
 CA1 A:OEX401 0.0 39.9 1.0
OD2 A:ASP170 2.4 40.5 1.0
O A:ALA344 2.4 39.0 1.0
O A:HOH539 2.4 40.8 1.0
O2 A:OEX401 2.4 39.1 1.0
O1 A:OEX401 2.5 36.7 1.0
O A:HOH639 2.5 39.5 1.0
O5 A:OEX401 2.5 40.3 1.0
CG A:ASP170 3.1 40.2 1.0
MN2 A:OEX401 3.4 37.9 1.0
OD1 A:ASP170 3.4 42.3 1.0
C A:ALA344 3.4 39.6 1.0
OE1 A:GLU189 3.4 41.8 1.0
MN3 A:OEX401 3.5 37.8 1.0
MN1 A:OEX401 3.6 35.4 1.0
OXT A:ALA344 3.7 38.8 1.0
MN4 A:OEX401 3.8 41.6 1.0
O4 A:OEX401 3.9 42.1 1.0
O3 A:OEX401 4.0 35.9 1.0
OE2 A:GLU189 4.1 40.9 1.0
CD A:GLU189 4.1 40.7 1.0
O A:HOH530 4.2 52.3 1.0
NH1 C:ARG357 4.2 41.8 1.0
NH2 C:ARG357 4.3 42.5 1.0
CB A:ASP170 4.4 34.2 1.0
O A:HOH588 4.6 40.6 1.0
OE1 A:GLN165 4.7 39.0 1.0
OH A:TYR161 4.7 37.3 1.0
CA A:ALA344 4.7 44.0 1.0
CZ C:ARG357 4.8 45.6 1.0
O A:HOH505 4.8 36.4 1.0

Calcium binding site 2 out of 9 in 8gn2

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Calcium binding site 2 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:110.0
occ:1.00
 O B:HOH852 2.4 74.4 1.0
O B:HOH1057 2.5 71.1 1.0
OD1 B:ASN438 2.6 44.3 1.0
O M:HOH217 2.7 117.5 1.0
O B:HOH1024 2.7 68.3 1.0
O B:HOH899 2.8 51.8 1.0
CG B:ASN438 3.8 52.8 1.0
O B:HOH753 4.2 45.8 1.0
ND2 B:ASN438 4.5 50.8 1.0
O B:SER439 4.6 34.7 1.0
O B:HOH779 4.7 65.0 1.0
CA B:ASN438 4.8 41.5 1.0
CB B:ASN438 4.9 44.9 1.0
C B:ASN438 4.9 40.5 1.0
O B:HOH970 5.0 75.3 1.0

Calcium binding site 3 out of 9 in 8gn2

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Calcium binding site 3 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:77.1
occ:1.00
 OXT F:ARG45 2.4 46.5 1.0
O2 V:GOL201 2.5 84.0 1.0
O V:HOH352 2.5 62.4 1.0
O V:HOH304 2.5 100.0 1.0
O F:HOH214 2.6 72.0 1.0
O3 V:GOL201 2.6 56.5 1.0
O F:HOH215 2.9 74.1 1.0
O F:ARG45 2.9 50.1 1.0
C F:ARG45 3.1 51.3 1.0
C3 V:GOL201 3.3 69.1 1.0
C2 V:GOL201 3.4 76.8 1.0
O F:HOH209 3.9 56.6 1.0
C1 V:GOL201 4.3 74.0 1.0
OE2 V:GLU23 4.4 88.2 1.0
OE1 V:GLU2 4.4 47.3 0.5
OE1 V:GLU23 4.5 90.7 1.0
CA F:ARG45 4.6 44.1 1.0
O1 V:GOL201 4.7 75.8 1.0
O F:HOH212 4.7 58.4 1.0
OE2 V:GLU2 4.7 58.9 0.5
CD V:GLU23 4.8 85.5 1.0
O A:ALA309 4.9 45.2 1.0
CD V:GLU2 5.0 53.7 0.5

Calcium binding site 4 out of 9 in 8gn2

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Calcium binding site 4 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

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

b:70.8
occ:1.00
 O O:HOH510 2.3 75.9 1.0
O O:VAL201 2.3 64.6 1.0
O O:HOH457 2.3 61.0 1.0
O O:HOH450 2.4 54.4 1.0
OD1 O:ASN200 2.4 69.4 1.0
O O:THR138 2.4 62.7 1.0
O O:HOH551 2.4 80.5 1.0
C O:VAL201 3.5 60.2 1.0
CG O:ASN200 3.5 68.7 1.0
C O:THR138 3.6 64.7 1.0
ND2 O:ASN200 4.1 77.0 1.0
N O:VAL201 4.2 49.8 1.0
N O:ALA202 4.3 61.6 1.0
CA O:ALA202 4.3 59.4 1.0
CA O:THR138 4.4 68.0 1.0
CA O:VAL201 4.4 55.2 1.0
C O:ASN200 4.5 52.5 1.0
N O:SER139 4.5 62.6 1.0
CA O:SER139 4.6 67.9 1.0
CB O:THR138 4.6 69.3 1.0
OD1 O:ASP141 4.7 65.6 0.5
CB O:ASN200 4.8 59.7 1.0
O O:THR140 4.8 62.2 1.0
O O:ASN200 4.9 55.6 1.0
O O:HOH500 4.9 76.5 1.0
CA O:ASN200 5.0 58.3 1.0

Calcium binding site 5 out of 9 in 8gn2

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Calcium binding site 5 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca403

b:42.9
occ:1.00
 CA1 a:OEX403 0.0 42.9 1.0
O a:HOH555 2.4 42.6 1.0
O a:HOH616 2.4 44.4 1.0
OD2 a:ASP170 2.4 45.8 1.0
O a:ALA344 2.5 43.8 1.0
O1 a:OEX403 2.5 39.4 1.0
O2 a:OEX403 2.6 41.7 1.0
O5 a:OEX403 2.6 42.2 1.0
CG a:ASP170 3.2 43.1 1.0
MN2 a:OEX403 3.3 39.9 1.0
OE1 a:GLU189 3.3 42.7 1.0
OD1 a:ASP170 3.4 39.5 1.0
MN3 a:OEX403 3.4 40.7 1.0
C a:ALA344 3.4 46.2 1.0
MN1 a:OEX403 3.5 40.4 1.0
OXT a:ALA344 3.7 42.9 1.0
MN4 a:OEX403 3.8 41.9 1.0
O3 a:OEX403 3.8 39.4 1.0
O4 a:OEX403 3.9 38.4 1.0
O a:HOH527 4.0 52.1 1.0
OE2 a:GLU189 4.1 44.9 1.0
CD a:GLU189 4.1 44.6 1.0
NH1 c:ARG357 4.3 42.4 1.0
CB a:ASP170 4.5 36.4 1.0
NH2 c:ARG357 4.5 48.2 1.0
O a:HOH580 4.7 41.6 1.0
OE1 a:GLN165 4.7 42.2 1.0
OH a:TYR161 4.7 37.3 1.0
O a:HOH530 4.8 43.4 1.0
CA a:ALA344 4.8 46.9 1.0
CZ c:ARG357 4.9 50.2 1.0

Calcium binding site 6 out of 9 in 8gn2

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Calcium binding site 6 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca603

b:143.0
occ:1.00
 O b:HOH1016 2.4 112.5 1.0
OD1 b:ASN438 2.5 56.0 1.0
O b:HOH754 2.5 87.9 1.0
O b:HOH821 2.6 50.5 1.0
O m:HOH223 2.7 76.3 1.0
O m:HOH226 2.8 109.0 1.0
CG b:ASN438 3.6 48.7 1.0
O b:HOH717 3.9 53.2 1.0
O b:SER439 4.1 37.1 1.0
ND2 b:ASN438 4.3 46.8 1.0
C b:ASN438 4.6 39.5 1.0
CA b:ASN438 4.6 41.0 1.0
O b:ASN438 4.7 37.4 1.0
O b:HOH806 4.7 59.8 1.0
CB b:ASN438 4.7 42.9 1.0
OE2 m:GLU2 4.8 52.7 0.5
O b:HOH813 4.8 47.3 1.0

Calcium binding site 7 out of 9 in 8gn2

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Calcium binding site 7 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca502

b:61.1
occ:1.00
 OG c:SER30 2.3 65.1 1.0
O c:THR24 2.4 56.5 1.0
O c:PHE22 2.4 65.2 1.0
O c:HOH735 2.4 59.0 1.0
OD2 c:ASP27 2.4 60.8 1.0
OE1 c:GLU29 2.4 60.5 1.0
OD1 c:ASP27 2.6 59.3 1.0
CG c:ASP27 2.9 60.8 1.0
C c:PHE22 3.4 60.5 1.0
CB c:SER30 3.5 53.4 1.0
CD c:GLU29 3.6 59.1 1.0
C c:THR24 3.6 57.4 1.0
CA c:PHE22 4.1 63.6 1.0
N c:SER30 4.1 51.6 1.0
OE2 c:GLU29 4.2 64.6 1.0
O c:HOH620 4.2 60.3 1.0
N c:THR24 4.2 70.8 1.0
O c:HOH650 4.3 71.9 1.0
CB c:PHE22 4.3 61.5 1.0
C c:ALA23 4.3 69.9 1.0
CA c:SER30 4.3 52.3 1.0
N c:ALA23 4.4 53.9 1.0
CB c:ASP27 4.4 63.6 1.0
CA c:ASN25 4.4 65.2 1.0
N c:ASN25 4.5 63.2 1.0
CA c:THR24 4.5 62.4 1.0
CA c:ALA23 4.6 63.5 1.0
CB c:GLU29 4.7 62.2 1.0
CG c:GLU29 4.7 62.8 1.0
O c:ALA23 4.8 69.9 1.0
C c:ASN25 4.9 62.9 1.0
C c:GLU29 5.0 54.8 1.0

Calcium binding site 8 out of 9 in 8gn2

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Calcium binding site 8 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:86.9
occ:1.00
 OXT f:ARG45 2.5 56.6 1.0
O2 v:GOL1602 2.6 86.3 1.0
O v:HOH1774 2.6 76.3 1.0
O3 v:GOL1602 2.6 64.9 1.0
O v:HOH1787 2.6 70.6 1.0
O f:HOH205 2.7 69.8 1.0
O f:ARG45 2.9 64.7 1.0
O f:HOH208 3.0 81.0 1.0
C f:ARG45 3.1 57.0 1.0
C2 v:GOL1602 3.6 80.0 1.0
C3 v:GOL1602 3.6 75.2 1.0
O f:HOH201 3.7 71.2 1.0
O v:HOH1754 4.2 69.1 1.0
C1 v:GOL1602 4.3 77.1 1.0
OE2 v:GLU23 4.5 94.6 1.0
OE1 v:GLU23 4.6 92.8 1.0
CA f:ARG45 4.6 51.8 1.0
O a:ALA309 4.8 54.2 1.0
CD v:GLU23 4.9 92.6 1.0
O1 v:GOL1602 5.0 73.0 1.0

Calcium binding site 9 out of 9 in 8gn2

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Calcium binding site 9 out of 9 in the Crystal Structure of Ppbq-Bound Photosystem II Complex


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Ppbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca303

b:67.1
occ:1.00
 O o:VAL201 2.3 64.5 1.0
OD1 o:ASN200 2.3 64.4 1.0
O o:THR138 2.4 68.4 1.0
O o:HOH542 2.5 88.9 1.0
O o:HOH429 2.5 62.0 1.0
O o:HOH547 2.5 80.4 1.0
CG o:ASN200 3.5 70.0 1.0
C o:THR138 3.5 68.0 1.0
C o:VAL201 3.5 63.9 1.0
ND2 o:ASN200 4.0 81.6 1.0
N o:VAL201 4.2 56.1 1.0
N o:SER139 4.3 76.0 1.0
CA o:THR138 4.3 65.8 1.0
CA o:SER139 4.4 79.4 1.0
N o:ALA202 4.4 59.8 1.0
CA o:ALA202 4.4 61.1 1.0
CA o:VAL201 4.4 58.1 1.0
C o:ASN200 4.5 59.6 1.0
O o:HOH541 4.6 91.8 1.0
O o:HOH520 4.7 68.9 1.0
CB o:THR138 4.7 70.9 1.0
O o:THR140 4.7 53.6 1.0
CB o:ASN200 4.7 54.9 1.0
C o:SER139 4.8 75.7 1.0
O o:ASN200 4.9 62.1 1.0
CA o:ASN200 5.0 54.9 1.0

Reference:

S.Kamada, Y.Nakajima, J.R.Shen. Structural Insights Into the Action Mechanisms of Artificial Electron Acceptors in Photosystem II. J.Biol.Chem. V. 299 04839 2023.
ISSN: ESSN 1083-351X
PubMed: 37209822
DOI: 10.1016/J.JBC.2023.104839
Page generated: Thu Jul 10 04:55:14 2025

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