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Calcium in PDB 4ub8: Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

Enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser

All present enzymatic activity of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser:
1.10.3.9;

Protein crystallography data

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8 was solved by M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.90 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.807, 230.001, 288.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.5

Other elements in 4ub8:

The structure of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser (pdb code 4ub8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser, PDB code: 4ub8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4ub8

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Calcium binding site 1 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca418

b:32.5
occ:1.00
 CA1 A:OEX418 0.0 32.5 1.0
OD1 A:ASP170 2.3 34.4 1.0
O A:ALA344 2.4 31.4 1.0
O5 A:OEX418 2.4 16.7 1.0
O A:HOH569 2.4 41.7 1.0
O A:HOH570 2.6 25.3 1.0
O1 A:OEX418 2.6 28.1 1.0
O2 A:OEX418 2.7 23.6 1.0
OE1 A:GLU189 3.2 30.5 1.0
CG A:ASP170 3.2 22.8 1.0
MN2 A:OEX418 3.3 23.2 1.0
MN3 A:OEX418 3.4 22.1 1.0
MN1 A:OEX418 3.5 21.4 1.0
C A:ALA344 3.5 30.3 1.0
OD2 A:ASP170 3.5 24.8 1.0
MN4 A:OEX418 3.7 24.2 1.0
O4 A:OEX418 3.7 23.8 1.0
OXT A:ALA344 3.9 21.9 1.0
CD A:GLU189 4.0 16.9 1.0
O3 A:OEX418 4.0 21.0 1.0
OE2 A:GLU189 4.0 23.3 1.0
O A:HOH602 4.1 48.0 1.0
NH1 C:ARG357 4.3 26.1 1.0
CB A:ASP170 4.4 18.8 1.0
NH2 C:ARG357 4.4 21.2 1.0
O A:HOH571 4.6 27.0 1.0
OE1 A:GLN165 4.6 26.0 1.0
O A:HOH608 4.6 30.3 1.0
OH A:TYR161 4.7 21.1 1.0
CA A:ALA344 4.8 27.7 1.0
CZ C:ARG357 4.8 30.7 1.0

Calcium binding site 2 out of 9 in 4ub8

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Calcium binding site 2 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:79.1
occ:1.00
 O O:HOH564 2.6 55.7 1.0
OD1 B:ASN438 2.7 28.3 1.0
O B:HOH860 2.8 53.4 1.0
O B:HOH842 2.8 30.0 1.0
O B:HOH855 3.1 61.5 1.0
O O:HOH551 3.2 69.0 1.0
CG B:ASN438 3.9 35.0 1.0
OE2 B:GLU435 4.2 52.7 0.5
O B:HOH776 4.5 38.2 1.0
O B:SER439 4.6 18.1 1.0
ND2 B:ASN438 4.6 30.4 1.0
O B:HOH800 4.7 28.8 1.0
CA B:ASN438 4.8 27.4 1.0
OE2 O:GLU181 4.8 99.7 1.0
CB B:ASN438 5.0 26.0 1.0
C B:ASN438 5.0 30.3 1.0

Calcium binding site 3 out of 9 in 4ub8

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Calcium binding site 3 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:72.8
occ:1.00
 O V:HOH321 2.5 38.8 1.0
O F:HOH202 2.5 55.7 1.0
OXT F:ARG45 2.5 27.2 1.0
O F:HOH207 2.7 48.9 1.0
O F:HOH203 2.7 69.0 1.0
O2 F:GOL103 2.8 68.3 1.0
O3 F:GOL103 2.8 52.6 1.0
O F:ARG45 3.0 30.4 1.0
C F:ARG45 3.2 39.9 1.0
C3 F:GOL103 3.3 65.0 1.0
C2 F:GOL103 3.6 65.8 1.0
O F:HOH201 3.9 51.4 1.0
O V:HOH322 4.3 36.1 1.0
OE2 V:GLU23 4.4 66.1 1.0
OE1 V:GLU23 4.5 79.3 1.0
O F:HOH205 4.5 42.2 1.0
C1 F:GOL103 4.6 56.0 1.0
O1 F:GOL103 4.6 59.8 1.0
CA F:ARG45 4.7 33.5 1.0
CD V:GLU23 4.7 75.6 1.0

Calcium binding site 4 out of 9 in 4ub8

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Calcium binding site 4 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:57.0
occ:1.00
 O O:VAL201 2.3 51.8 1.0
O O:THR138 2.4 44.3 1.0
O O:HOH518 2.4 53.9 1.0
OD1 O:ASN200 2.5 49.5 1.0
O O:HOH419 2.7 52.3 1.0
O O:HOH519 2.8 44.0 1.0
O O:HOH427 2.9 47.7 1.0
C O:VAL201 3.5 44.5 1.0
C O:THR138 3.5 44.2 1.0
CG O:ASN200 3.6 53.4 1.0
ND2 O:ASN200 4.1 60.6 1.0
N O:VAL201 4.1 34.0 1.0
CA O:VAL201 4.3 38.6 1.0
CA O:THR138 4.4 52.2 1.0
N O:SER139 4.4 38.7 1.0
N O:ALA202 4.4 42.3 1.0
CA O:SER139 4.4 37.6 1.0
C O:ASN200 4.5 37.2 1.0
O O:THR140 4.5 46.7 1.0
CA O:ALA202 4.5 38.0 1.0
CB O:THR138 4.7 57.2 1.0
C O:SER139 4.8 39.9 1.0
CB O:ASN200 4.8 43.9 1.0
CB O:VAL201 4.9 43.5 1.0
CA O:ASN200 5.0 41.1 1.0

Calcium binding site 5 out of 9 in 4ub8

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Calcium binding site 5 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca415

b:37.4
occ:1.00
 CA1 a:OEX415 0.0 37.4 1.0
OD1 a:ASP170 2.3 39.1 1.0
O a:HOH525 2.4 46.4 1.0
O a:ALA344 2.4 29.1 1.0
O5 a:OEX415 2.5 20.2 1.0
O a:HOH526 2.6 36.8 1.0
O1 a:OEX415 2.6 24.0 1.0
O2 a:OEX415 2.7 22.9 1.0
O a:HOH560 3.1 45.6 1.0
OE1 a:GLU189 3.1 30.9 1.0
CG a:ASP170 3.3 30.3 1.0
MN2 a:OEX415 3.3 25.3 1.0
MN3 a:OEX415 3.3 25.0 1.0
MN1 a:OEX415 3.4 27.4 1.0
C a:ALA344 3.5 34.1 1.0
OD2 a:ASP170 3.6 25.0 1.0
MN4 a:OEX415 3.8 25.2 1.0
O4 a:OEX415 3.8 20.3 1.0
OXT a:ALA344 3.8 21.9 1.0
OE2 a:GLU189 3.9 31.2 1.0
CD a:GLU189 3.9 35.4 1.0
O3 a:OEX415 4.0 35.8 1.0
NH1 c:ARG357 4.3 26.6 1.0
CB a:ASP170 4.6 26.4 1.0
NH2 c:ARG357 4.6 24.5 1.0
OE1 a:GLN165 4.6 26.2 1.0
O a:HOH565 4.6 26.9 1.0
O a:HOH527 4.6 31.5 1.0
OH a:TYR161 4.7 24.0 1.0
CA a:ALA344 4.8 33.2 1.0
CZ c:ARG357 4.9 30.5 1.0
OE2 c:GLU354 5.0 24.0 1.0

Calcium binding site 6 out of 9 in 4ub8

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Calcium binding site 6 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca605

b:95.7
occ:1.00
 OD1 b:ASN438 2.5 31.5 1.0
O b:HOH747 2.5 33.9 1.0
O o:HOH533 2.6 61.1 1.0
O b:HOH763 2.8 73.4 1.0
CG b:ASN438 3.7 32.8 1.0
O m:HOH203 4.0 38.1 1.0
O b:HOH718 4.5 44.0 1.0
O b:SER439 4.5 23.0 1.0
O b:HOH722 4.5 39.1 1.0
CA b:ASN438 4.6 25.5 1.0
ND2 b:ASN438 4.6 29.9 1.0
CB b:ASN438 4.7 25.8 1.0
C b:ASN438 4.7 31.1 1.0
O b:ASN438 4.9 22.4 1.0

Calcium binding site 7 out of 9 in 4ub8

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Calcium binding site 7 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca502

b:44.9
occ:1.00
 OG c:SER30 2.4 46.8 1.0
O c:HOH768 2.4 38.9 1.0
O c:PHE22 2.4 52.9 1.0
OE1 c:GLU29 2.4 35.0 1.0
O c:THR24 2.4 43.3 1.0
OD2 c:ASP27 2.4 40.5 1.0
OD1 c:ASP27 2.7 35.0 1.0
CG c:ASP27 2.9 39.1 1.0
C c:PHE22 3.4 36.5 1.0
CB c:SER30 3.5 35.7 1.0
CD c:GLU29 3.6 44.7 1.0
C c:THR24 3.7 36.1 1.0
N c:SER30 4.1 45.5 1.0
O c:HOH786 4.2 44.1 1.0
OE2 c:GLU29 4.2 56.6 1.0
CA c:PHE22 4.2 41.1 1.0
N c:THR24 4.2 48.1 1.0
CB c:PHE22 4.4 38.5 1.0
CA c:SER30 4.4 37.5 1.0
N c:ALA23 4.4 37.1 1.0
C c:ALA23 4.4 50.0 1.0
CB c:ASP27 4.4 48.6 1.0
CA c:ASN25 4.5 48.7 1.0
N c:ASN25 4.5 48.5 1.0
CA c:THR24 4.6 44.8 1.0
CA c:ALA23 4.7 37.7 1.0
CB c:GLU29 4.7 39.7 1.0
CG c:GLU29 4.7 52.3 1.0
C c:ASN25 4.9 42.0 1.0
C c:GLU29 4.9 43.1 1.0
O c:ALA23 5.0 53.2 1.0

Calcium binding site 8 out of 9 in 4ub8

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Calcium binding site 8 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Ca103

b:72.1
occ:1.00
 O f:HOH207 2.5 65.8 1.0
OXT f:ARG45 2.5 34.4 1.0
O3 f:GOL104 2.6 45.6 1.0
O f:HOH205 2.7 61.1 1.0
O v:HOH311 2.7 50.4 1.0
O2 f:GOL104 2.9 61.6 1.0
O f:ARG45 2.9 40.3 1.0
C f:ARG45 3.1 38.9 1.0
O f:HOH204 3.2 59.3 1.0
C3 f:GOL104 3.7 55.4 1.0
O f:HOH203 3.7 47.1 1.0
C2 f:GOL104 3.8 59.9 1.0
O v:HOH312 4.2 51.7 1.0
O v:HOH378 4.3 80.3 1.0
OE1 v:GLU23 4.5 78.5 1.0
OE2 v:GLU23 4.5 66.0 1.0
CA f:ARG45 4.6 32.8 1.0
C1 f:GOL104 4.6 51.0 1.0
O a:ALA309 4.7 33.5 1.0
CB a:ALA309 4.9 34.6 1.0
CD v:GLU23 4.9 75.4 1.0
O1 f:GOL104 4.9 49.7 1.0

Calcium binding site 9 out of 9 in 4ub8

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Calcium binding site 9 out of 9 in the Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Native Structure of Photosystem II (Dataset-2) By A Femtosecond X-Ray Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:62.0
occ:1.00
 OD1 o:ASN200 2.3 49.3 1.0
O o:HOH506 2.5 52.1 1.0
O o:VAL201 2.5 48.9 1.0
O o:HOH491 2.6 45.3 1.0
O o:HOH511 2.6 72.7 1.0
O o:THR138 2.6 48.6 1.0
O o:HOH492 2.6 50.5 1.0
CG o:ASN200 3.4 53.4 1.0
C o:VAL201 3.6 47.6 1.0
C o:THR138 3.7 46.6 1.0
ND2 o:ASN200 3.9 58.5 1.0
N o:VAL201 4.2 37.9 1.0
CA o:THR138 4.5 44.0 1.0
N o:ALA202 4.5 45.4 1.0
CA o:VAL201 4.5 45.1 1.0
N o:SER139 4.5 53.8 1.0
CA o:ALA202 4.6 39.0 1.0
CA o:SER139 4.6 51.9 1.0
C o:ASN200 4.6 43.8 1.0
O o:THR140 4.7 39.0 1.0
CB o:ASN200 4.7 42.7 1.0
CB o:THR138 4.7 55.5 1.0
C o:SER139 4.9 56.6 1.0
CA o:ASN200 5.0 33.8 1.0

Reference:

M.Suga, F.Akita, K.Hirata, G.Ueno, H.Murakami, Y.Nakajima, T.Shimizu, K.Yamashita, M.Yamamoto, H.Ago, J.R.Shen. Native Structure of Photosystem II at 1.95A Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13991
Page generated: Wed Jul 9 02:16:38 2025

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