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Calcium in PDB 5gth: Native Xfel Structure of Photosystem II (Dark Dataset)

Enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset)

All present enzymatic activity of Native Xfel Structure of Photosystem II (Dark Dataset):
1.10.3.9;

Protein crystallography data

The structure of Native Xfel Structure of Photosystem II (Dark Dataset), PDB code: 5gth was solved by 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 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.520, 231.230, 287.460, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 18.6

Other elements in 5gth:

The structure of Native Xfel Structure of Photosystem II (Dark Dataset) also contains other interesting chemical elements:

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

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 5gth

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Calcium binding site 1 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:45.8
occ:1.00
 CA1 A:OEX413 0.0 45.8 1.0
OD1 A:ASP170 2.4 46.3 1.0
O A:ALA344 2.4 34.1 1.0
O A:HOH505 2.5 40.4 1.0
O1 A:OEX413 2.6 43.3 1.0
O5 A:OEX413 2.6 31.5 1.0
O A:HOH614 2.6 45.2 1.0
O2 A:OEX413 2.6 26.4 1.0
OE1 A:GLU189 3.1 36.9 1.0
CG A:ASP170 3.2 30.7 1.0
C A:ALA344 3.5 42.4 1.0
MN2 A:OEX413 3.5 30.7 1.0
MN3 A:OEX413 3.5 28.0 1.0
OD2 A:ASP170 3.5 38.6 1.0
MN1 A:OEX413 3.6 27.9 1.0
OXT A:ALA344 3.7 31.1 1.0
MN4 A:OEX413 3.8 36.6 1.0
O A:HOH560 3.8 35.0 1.0
OE2 A:GLU189 3.8 36.3 1.0
O4 A:OEX413 3.9 22.4 1.0
CD A:GLU189 3.9 29.5 1.0
O3 A:OEX413 4.2 37.4 1.0
NH1 C:ARG357 4.2 23.8 1.0
CB A:ASP170 4.5 23.0 1.0
NH2 C:ARG357 4.5 24.8 1.0
OE1 A:GLN165 4.6 31.8 1.0
O A:HOH559 4.6 33.3 1.0
O A:HOH573 4.8 42.2 1.0
CA A:ALA344 4.8 51.4 1.0
OH A:TYR161 4.8 27.1 1.0
CZ C:ARG357 4.8 39.3 1.0
CG A:GLN165 5.0 32.7 1.0

Calcium binding site 2 out of 8 in 5gth

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Calcium binding site 2 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

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

b:62.5
occ:1.00
 O C:THR254 2.5 53.2 1.0
OD1 C:ASN155 2.7 77.1 1.0
O C:HIS251 2.8 52.0 1.0
OG1 C:THR158 2.8 53.2 1.0
OG1 C:THR159 2.9 53.8 1.0
O C:ASN155 2.9 58.4 1.0
O C:ILE252 3.2 55.7 1.0
N C:THR159 3.6 56.0 1.0
C C:THR254 3.7 54.6 1.0
CG C:ASN155 3.7 75.7 1.0
C C:ASN155 3.7 61.5 1.0
C C:ILE252 3.8 62.6 1.0
CB C:THR158 3.9 52.3 1.0
CA C:ASN155 3.9 65.8 1.0
C C:HIS251 4.0 52.6 1.0
CB C:THR159 4.0 56.4 1.0
C C:THR158 4.1 56.0 1.0
CA C:THR159 4.1 56.7 1.0
CA C:ILE252 4.1 49.6 1.0
N C:THR254 4.3 62.2 1.0
CB C:ASN155 4.4 67.9 1.0
CA C:THR158 4.5 53.5 1.0
N C:ILE252 4.5 57.9 1.0
O C:HOH614 4.6 50.9 1.0
CA C:THR254 4.6 56.0 1.0
N C:THR255 4.6 52.5 1.0
O C:THR158 4.6 55.8 1.0
ND2 C:ASN155 4.6 87.9 1.0
CA C:THR255 4.7 57.6 1.0
N C:LEU253 4.7 64.2 1.0
N C:THR158 4.9 48.3 1.0
C C:LEU253 4.9 60.2 1.0
N C:LYS156 5.0 49.6 1.0
O C:LYS154 5.0 72.0 1.0

Calcium binding site 3 out of 8 in 5gth

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Calcium binding site 3 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:87.7
occ:1.00
 OD1 O:ASN200 2.5 86.4 1.0
O O:HOH420 2.9 50.7 1.0
O O:THR138 2.9 77.7 1.0
O O:THR140 3.2 83.3 1.0
O O:VAL201 3.3 68.2 1.0
CG O:ASN200 3.4 79.9 1.0
C O:SER139 3.7 65.1 1.0
CA O:SER139 3.7 74.4 1.0
C O:THR138 3.7 67.3 1.0
O O:SER139 3.9 51.2 1.0
N O:VAL201 3.9 44.9 1.0
ND2 O:ASN200 3.9 92.2 1.0
C O:THR140 4.0 68.0 1.0
OD2 O:ASP141 4.1 0.6 1.0
N O:SER139 4.1 70.2 1.0
N O:THR140 4.2 71.1 1.0
C O:VAL201 4.2 61.2 1.0
CB O:ASP141 4.2 81.8 1.0
C O:ASN200 4.4 53.1 1.0
CA O:ASN200 4.5 51.8 1.0
CG O:ASP141 4.5 97.7 1.0
CB O:ASN200 4.5 62.2 1.0
CA O:VAL201 4.6 51.5 1.0
N O:ASP141 4.7 63.0 1.0
CA O:THR140 4.8 43.8 1.0
CA O:ASP141 4.9 70.0 1.0
CA O:THR138 5.0 65.5 1.0
CB O:VAL201 5.0 46.1 1.0

Calcium binding site 4 out of 8 in 5gth

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Calcium binding site 4 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Native Xfel Structure of Photosystem II (Dark Dataset) within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca201

b:93.7
occ:1.00
 OE2 V:GLU23 2.8 89.0 1.0
O F:HOH101 2.8 71.9 1.0
O F:HOH102 3.1 86.5 1.0
O A:ALA309 3.5 47.6 1.0
OXT F:ARG45 3.6 47.4 1.0
CD V:GLU23 3.7 90.8 1.0
O V:HOH370 3.8 66.7 1.0
O F:ARG45 3.9 57.6 1.0
C F:ARG45 4.1 46.3 1.0
O V:HOH331 4.2 46.8 1.0
OE1 V:GLU23 4.3 98.7 1.0
NH1 F:ARG45 4.4 39.0 1.0
CG V:GLU23 4.5 70.4 1.0
CG F:ARG45 4.6 33.7 1.0
C A:ALA309 4.6 50.5 1.0
CB V:LEU3 4.6 48.8 1.0
CZ F:ARG45 4.8 39.5 1.0
CD2 V:LEU3 4.9 54.0 1.0
CA A:ALA309 4.9 50.3 1.0

Calcium binding site 5 out of 8 in 5gth

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Calcium binding site 5 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

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

b:53.4
occ:1.00
 CA1 a:OEX413 0.0 53.4 1.0
OD1 a:ASP170 2.4 47.0 1.0
O a:ALA344 2.4 35.0 1.0
O a:HOH502 2.5 53.2 1.0
O1 a:OEX413 2.6 42.9 1.0
O a:HOH594 2.6 62.3 1.0
O5 a:OEX413 2.6 37.9 1.0
O2 a:OEX413 2.6 28.3 1.0
OE1 a:GLU189 3.1 41.7 1.0
CG a:ASP170 3.3 27.4 1.0
C a:ALA344 3.4 47.0 1.0
MN2 a:OEX413 3.5 33.6 1.0
O a:HOH509 3.5 61.8 1.0
MN3 a:OEX413 3.5 28.9 1.0
OXT a:ALA344 3.6 29.4 1.0
OD2 a:ASP170 3.6 47.9 1.0
MN1 a:OEX413 3.7 37.2 1.0
OE2 a:GLU189 3.8 28.1 1.0
CD a:GLU189 3.9 41.0 1.0
MN4 a:OEX413 3.9 34.9 1.0
NH1 c:ARG357 4.0 29.1 1.0
O4 a:OEX413 4.1 27.2 1.0
OE1 a:GLN165 4.2 35.9 1.0
O3 a:OEX413 4.2 45.3 1.0
O a:HOH506 4.3 39.6 1.0
NH2 c:ARG357 4.5 28.3 1.0
CB a:ASP170 4.6 27.4 1.0
OH a:TYR161 4.7 28.3 1.0
CA a:ALA344 4.8 54.7 1.0
CZ c:ARG357 4.8 42.6 1.0
CB a:GLN165 4.9 30.6 1.0
CG a:GLN165 4.9 33.9 1.0
O a:HOH565 5.0 26.1 1.0

Calcium binding site 6 out of 8 in 5gth

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Calcium binding site 6 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

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

b:68.4
occ:1.00
 O c:THR254 2.7 54.6 1.0
OG1 c:THR159 2.7 57.8 1.0
O c:ASN155 2.7 57.6 1.0
O c:HIS251 2.8 51.6 1.0
OD1 c:ASN155 2.8 77.6 1.0
OG1 c:THR158 2.9 53.8 1.0
O c:ILE252 3.1 57.0 1.0
N c:THR159 3.5 56.1 1.0
C c:ASN155 3.6 62.4 1.0
C c:ILE252 3.7 60.2 1.0
CG c:ASN155 3.7 74.7 1.0
CB c:THR159 3.8 57.9 1.0
CA c:ASN155 3.9 69.0 1.0
C c:THR254 3.9 58.0 1.0
CB c:THR158 3.9 51.5 1.0
CA c:THR159 3.9 55.7 1.0
C c:HIS251 3.9 55.0 1.0
C c:THR158 4.0 57.0 1.0
CA c:ILE252 4.0 53.0 1.0
O c:HOH631 4.3 63.1 1.0
N c:THR254 4.3 61.1 1.0
CA c:THR158 4.4 54.1 1.0
CB c:ASN155 4.4 64.8 1.0
N c:ILE252 4.5 52.1 1.0
O c:THR158 4.6 52.3 1.0
N c:LEU253 4.6 61.1 1.0
ND2 c:ASN155 4.7 90.3 1.0
CA c:THR254 4.7 58.3 1.0
N c:LYS156 4.8 54.0 1.0
N c:THR158 4.8 49.1 1.0
N c:THR255 4.8 51.9 1.0
C c:LEU253 4.9 59.3 1.0
CA c:THR255 4.9 60.5 1.0
O c:LYS154 5.0 69.5 1.0

Calcium binding site 7 out of 8 in 5gth

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Calcium binding site 7 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

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

b:66.8
occ:1.00
 O c:PHE22 2.3 77.0 1.0
OG c:SER30 2.4 0.1 1.0
OE1 c:GLU29 2.4 60.9 1.0
OD2 c:ASP27 2.5 50.9 1.0
O c:HOH709 2.5 65.0 1.0
O c:THR24 2.6 59.9 1.0
OD1 c:ASP27 2.7 49.8 1.0
CG c:ASP27 2.9 71.6 1.0
C c:PHE22 3.4 67.8 1.0
CB c:SER30 3.5 50.4 1.0
CD c:GLU29 3.6 70.1 1.0
C c:THR24 3.8 72.2 1.0
CA c:PHE22 4.0 76.5 1.0
CB c:PHE22 4.1 73.1 1.0
OE2 c:GLU29 4.1 85.1 1.0
O c:HOH606 4.1 51.9 1.0
O c:ALA23 4.1 88.0 1.0
N c:SER30 4.2 77.6 1.0
C c:ALA23 4.2 77.4 1.0
CA c:SER30 4.4 49.6 1.0
N c:ALA23 4.4 71.8 1.0
CB c:ASP27 4.4 52.6 1.0
N c:THR24 4.5 64.5 1.0
CA c:ASN25 4.5 72.2 1.0
N c:ASN25 4.6 72.4 1.0
CB c:GLU29 4.7 73.7 1.0
CG c:GLU29 4.7 61.1 1.0
CA c:ALA23 4.7 70.2 1.0
CA c:THR24 4.8 65.1 1.0
C c:ASN25 4.9 68.4 1.0

Calcium binding site 8 out of 8 in 5gth

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Calcium binding site 8 out of 8 in the Native Xfel Structure of Photosystem II (Dark Dataset)


Mono view


Stereo pair view

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

b:85.9
occ:1.00
 O o:THR138 2.4 86.8 1.0
O o:HOH489 2.6 87.1 1.0
O o:VAL201 2.6 66.5 1.0
OD1 o:ASN200 2.8 86.9 1.0
O o:HOH509 2.8 76.8 1.0
O o:HOH404 2.9 52.7 1.0
C o:THR138 3.5 83.2 1.0
C o:VAL201 3.8 60.1 1.0
CG o:ASN200 3.9 80.4 1.0
CA o:SER139 4.2 92.2 1.0
N o:SER139 4.3 88.5 1.0
ND2 o:ASN200 4.3 90.1 1.0
CA o:THR138 4.5 66.5 1.0
CA o:ALA202 4.5 59.2 1.0
N o:VAL201 4.6 47.9 1.0
N o:ALA202 4.6 61.1 1.0
O o:THR140 4.6 84.6 1.0
C o:SER139 4.7 82.8 1.0
CA o:VAL201 4.8 50.5 1.0
CB o:THR138 4.8 68.8 1.0
C o:ASN200 4.9 51.5 1.0

Reference:

M.Suga, F.Akita, M.Sugahara, M.Kubo, Y.Nakajima, T.Nakane, K.Yamashita, Y.Umena, M.Nakabayashi, T.Yamane, T.Nakano, M.Suzuki, T.Masuda, S.Inoue, T.Kimura, T.Nomura, S.Yonekura, L.J.Yu, T.Sakamoto, T.Motomura, J.H.Chen, Y.Kato, T.Noguchi, K.Tono, Y.Joti, T.Kameshima, T.Hatsui, E.Nango, R.Tanaka, H.Naitow, Y.Matsuura, A.Yamashita, M.Yamamoto, O.Nureki, M.Yabashi, T.Ishikawa, S.Iwata, J.R.Shen. Light-Induced Structural Changes and the Site of O=O Bond Formation in Psii Caught By Xfel. Nature V. 543 131 2017.
ISSN: ESSN 1476-4687
PubMed: 28219079
DOI: 10.1038/NATURE21400
Page generated: Sun Jul 14 19:42:16 2024

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