Atomistry » Calcium » PDB 5g39-5gth » 5gth
Atomistry »
  Calcium »
    PDB 5g39-5gth »
      5gth »

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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Go back to Calcium Binding Sites List in 5gth
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy