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Calcium in PDB 3wu2: Crystal Structure Analysis of Photosystem II Complex

Protein crystallography data

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 3wu2 was solved by Y.Umena, K.Kawakami, J.R.Shen, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.190, 228.510, 286.400, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 19.4

Other elements in 3wu2:

The structure of Crystal Structure Analysis of Photosystem II Complex 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 Crystal Structure Analysis of Photosystem II Complex (pdb code 3wu2). 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 Analysis of Photosystem II Complex, PDB code: 3wu2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 3wu2

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Calcium binding site 1 out of 9 in the Crystal Structure Analysis of 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 1 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.2
occ:1.00
 CA1 A:OEX401 0.0 25.2 1.0
O A:HOH569 2.3 26.4 1.0
O1 A:OEX401 2.4 21.8 1.0
OD2 A:ASP170 2.4 25.3 1.0
O5 A:OEX401 2.4 23.5 1.0
O A:HOH544 2.5 27.3 1.0
O2 A:OEX401 2.5 25.9 1.0
O A:ALA344 2.6 29.0 1.0
CG A:ASP170 3.1 24.5 1.0
OE1 A:GLU189 3.3 27.3 1.0
OD1 A:ASP170 3.3 25.6 1.0
MN2 A:OEX401 3.4 23.1 1.0
MN3 A:OEX401 3.4 23.4 1.0
C A:ALA344 3.5 26.3 1.0
MN1 A:OEX401 3.5 22.3 1.0
OXT A:ALA344 3.8 25.2 1.0
MN4 A:OEX401 3.8 27.0 1.0
O4 A:OEX401 3.9 28.5 1.0
O A:HOH597 4.0 38.0 1.0
O3 A:OEX401 4.1 23.1 1.0
CD A:GLU189 4.1 24.6 1.0
OE2 A:GLU189 4.1 25.3 1.0
NH1 C:ARG357 4.2 27.6 1.0
CB A:ASP170 4.4 23.4 1.0
NH2 C:ARG357 4.4 24.0 1.0
O A:HOH624 4.6 27.6 1.0
OH A:TYR161 4.7 23.4 1.0
O A:HOH564 4.8 25.4 1.0
CZ C:ARG357 4.8 31.9 1.0
OE1 A:GLN165 4.8 24.7 1.0
CA A:ALA344 4.8 25.4 1.0

Calcium binding site 2 out of 9 in 3wu2

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Calcium binding site 2 out of 9 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:81.2
occ:1.00
 O B:HOH829 2.6 36.8 1.0
OD1 B:ASN438 2.7 31.6 1.0
O B:HOH904 2.8 47.0 1.0
O D:HOH656 3.0 61.1 1.0
O B:HOH984 3.4 58.0 1.0
CG B:ASN438 3.9 32.1 1.0
OE2 B:GLU435 4.4 50.6 0.5
O B:SER439 4.5 22.7 1.0
O B:HOH816 4.5 31.1 1.0
O B:HOH849 4.6 39.4 1.0
CA B:ASN438 4.7 26.0 1.0
ND2 B:ASN438 4.7 33.2 1.0
C B:ASN438 4.8 24.8 1.0
CB B:ASN438 4.9 27.7 1.0
O B:ASN438 5.0 23.5 1.0

Calcium binding site 3 out of 9 in 3wu2

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Calcium binding site 3 out of 9 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca103

b:56.0
occ:1.00
 O V:HOH411 2.3 40.7 1.0
O F:HOH211 2.4 59.0 1.0
O F:HOH209 2.4 48.5 1.0
O2 A:GOL423 2.5 43.6 1.0
O3 A:GOL423 2.5 39.7 1.0
OXT F:ARG45 2.6 30.2 1.0
O F:HOH208 2.6 59.2 1.0
O F:ARG45 2.9 28.2 1.0
C F:ARG45 3.2 31.5 1.0
C3 A:GOL423 3.3 43.3 1.0
C2 A:GOL423 3.4 45.0 1.0
O F:HOH206 4.0 46.1 1.0
O V:HOH357 4.0 43.0 1.0
C1 A:GOL423 4.1 45.6 1.0
OE1 V:GLU23 4.3 59.0 1.0
OE2 V:GLU23 4.4 59.2 1.0
CD V:GLU23 4.6 54.6 1.0
O F:HOH203 4.7 42.5 1.0
CA F:ARG45 4.7 31.6 1.0
O1 A:GOL423 4.9 53.0 1.0
O A:ALA309 4.9 33.4 1.0

Calcium binding site 4 out of 9 in 3wu2

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Calcium binding site 4 out of 9 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

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

b:49.3
occ:1.00
 O O:HOH419 2.2 39.4 1.0
O O:VAL201 2.3 40.7 1.0
O O:HOH535 2.4 49.0 1.0
O O:HOH518 2.5 51.5 1.0
OD1 O:ASN200 2.5 49.2 1.0
O O:THR138 2.6 43.4 1.0
C O:VAL201 3.5 35.7 1.0
CG O:ASN200 3.6 52.2 1.0
C O:THR138 3.6 44.6 1.0
ND2 O:ASN200 4.1 57.4 1.0
N O:VAL201 4.2 35.8 1.0
N O:ALA202 4.3 39.1 1.0
CA O:ALA202 4.3 38.6 1.0
CA O:VAL201 4.4 34.4 1.0
CA O:THR138 4.4 43.8 1.0
C O:ASN200 4.5 33.9 1.0
N O:SER139 4.5 42.7 1.0
CA O:SER139 4.5 42.0 1.0
CB O:THR138 4.6 41.5 1.0
O O:THR140 4.7 37.3 1.0
O O:HOH499 4.7 49.5 1.0
O O:ASN200 4.8 36.2 1.0
CB O:ASN200 4.9 40.4 1.0
CB O:VAL201 4.9 37.7 1.0
C O:SER139 5.0 43.0 1.0

Calcium binding site 5 out of 9 in 3wu2

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Calcium binding site 5 out of 9 in the Crystal Structure Analysis of 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 Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca404

b:27.7
occ:1.00
 CA1 a:OEX404 0.0 27.7 1.0
OD2 a:ASP170 2.4 27.4 1.0
O a:HOH515 2.4 28.9 1.0
O a:HOH585 2.4 28.8 1.0
O a:ALA344 2.4 30.3 1.0
O1 a:OEX404 2.4 22.8 1.0
O2 a:OEX404 2.5 27.6 1.0
O5 a:OEX404 2.6 28.2 1.0
CG a:ASP170 3.2 27.3 1.0
OE1 a:GLU189 3.3 30.1 1.0
MN2 a:OEX404 3.3 26.4 1.0
MN3 a:OEX404 3.4 25.1 1.0
C a:ALA344 3.4 33.8 1.0
OD1 a:ASP170 3.4 27.7 1.0
MN1 a:OEX404 3.5 25.9 1.0
OXT a:ALA344 3.7 33.3 1.0
O3 a:OEX404 3.8 26.8 1.0
MN4 a:OEX404 3.8 29.5 1.0
CD a:GLU189 4.0 27.7 1.0
OE2 a:GLU189 4.0 24.2 1.0
O a:HOH609 4.1 33.4 1.0
O4 a:OEX404 4.1 27.2 1.0
NH1 c:ARG357 4.3 33.2 1.0
NH2 c:ARG357 4.5 33.2 1.0
CB a:ASP170 4.5 25.2 1.0
OE1 a:GLN165 4.6 25.3 1.0
OH a:TYR161 4.7 24.7 1.0
O a:HOH567 4.7 27.0 1.0
O a:HOH543 4.8 30.5 1.0
CA a:ALA344 4.8 32.8 1.0
CZ c:ARG357 4.9 31.2 1.0
OD1 a:ASP342 5.0 24.6 1.0

Calcium binding site 6 out of 9 in 3wu2

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Calcium binding site 6 out of 9 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

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

b:82.9
occ:1.00
 O b:HOH974 2.4 68.7 1.0
O b:HOH863 2.4 39.6 0.5
O b:HOH964 2.5 60.3 1.0
OD1 b:ASN438 2.6 37.6 1.0
O b:HOH872 2.7 36.6 1.0
CG b:ASN438 3.8 32.1 1.0
O b:HOH863 4.1 29.9 0.5
O b:HOH817 4.4 47.0 1.0
ND2 b:ASN438 4.6 29.8 1.0
CA b:ASN438 4.6 26.3 1.0
O b:HOH815 4.7 37.4 1.0
O b:SER439 4.7 22.8 1.0
CB b:ASN438 4.8 26.3 1.0
C b:ASN438 4.9 24.6 1.0

Calcium binding site 7 out of 9 in 3wu2

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Calcium binding site 7 out of 9 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca901

b:46.1
occ:1.00
 O c:THR24 2.3 45.3 1.0
O c:HOH1034 2.4 47.9 1.0
OE1 c:GLU29 2.4 46.1 1.0
OG c:SER30 2.4 43.1 1.0
OD2 c:ASP27 2.4 40.7 1.0
O c:PHE22 2.4 43.9 1.0
OD1 c:ASP27 2.6 37.0 1.0
CG c:ASP27 2.9 39.1 1.0
C c:PHE22 3.5 44.5 1.0
CB c:SER30 3.5 38.1 1.0
C c:THR24 3.6 40.7 1.0
CD c:GLU29 3.6 44.2 1.0
N c:SER30 4.1 35.2 1.0
O c:HOH1198 4.1 50.2 1.0
CA c:PHE22 4.2 46.4 1.0
OE2 c:GLU29 4.2 44.7 1.0
O c:HOH1185 4.2 42.4 1.0
N c:THR24 4.3 50.8 1.0
CB c:PHE22 4.3 47.1 1.0
CA c:SER30 4.3 36.3 1.0
CA c:ASN25 4.3 41.6 1.0
C c:ALA23 4.3 49.5 1.0
N c:ASN25 4.4 38.5 1.0
CB c:ASP27 4.4 43.8 1.0
N c:ALA23 4.5 43.7 1.0
CA c:THR24 4.6 44.4 1.0
O c:HOH1140 4.7 53.8 1.0
O c:ALA23 4.7 54.1 1.0
CA c:ALA23 4.8 47.1 1.0
C c:ASN25 4.8 44.1 1.0
CG c:GLU29 4.8 48.0 1.0
CB c:GLU29 4.9 42.3 1.0
C c:GLU29 4.9 36.6 1.0

Calcium binding site 8 out of 9 in 3wu2

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Calcium binding site 8 out of 9 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

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

b:56.5
occ:1.00
 O f:HOH209 2.2 52.7 1.0
O3 f:GOL104 2.4 46.2 1.0
OXT f:ARG45 2.5 35.1 1.0
O v:HOH303 2.6 50.4 1.0
O2 f:GOL104 2.6 51.8 1.0
O f:HOH208 2.6 58.6 1.0
O f:HOH210 2.6 60.5 1.0
O f:ARG45 2.9 42.2 1.0
C f:ARG45 3.1 37.9 1.0
C3 f:GOL104 3.5 46.2 1.0
C2 f:GOL104 3.6 51.9 1.0
O f:HOH213 3.8 47.1 1.0
OE2 v:GLU23 4.0 65.2 1.0
O v:HOH384 4.2 54.0 1.0
C1 f:GOL104 4.4 54.4 1.0
CA f:ARG45 4.6 35.6 1.0
O a:ALA309 4.8 37.4 1.0
CD v:GLU23 4.9 64.6 1.0

Calcium binding site 9 out of 9 in 3wu2

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Calcium binding site 9 out of 9 in the Crystal Structure Analysis of Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:51.7
occ:1.00
 O o:VAL201 2.2 42.3 1.0
O o:HOH562 2.3 59.9 1.0
OD1 o:ASN200 2.4 44.6 1.0
O o:HOH515 2.4 43.0 1.0
O o:THR138 2.5 46.1 1.0
O o:HOH563 2.6 64.0 1.0
O o:HOH514 2.6 55.6 1.0
C o:VAL201 3.4 39.9 1.0
CG o:ASN200 3.5 52.0 1.0
C o:THR138 3.5 49.2 1.0
ND2 o:ASN200 4.0 48.9 1.0
N o:VAL201 4.2 44.5 1.0
N o:ALA202 4.2 37.5 1.0
CA o:ALA202 4.3 40.8 1.0
N o:SER139 4.3 50.0 1.0
CA o:VAL201 4.3 36.3 1.0
CA o:THR138 4.4 45.6 1.0
CA o:SER139 4.4 47.7 1.0
C o:ASN200 4.4 42.5 1.0
O o:THR140 4.6 43.9 1.0
CB o:THR138 4.7 45.0 1.0
OD1 o:ASP141 4.7 49.2 0.5
CB o:ASN200 4.8 40.0 1.0
O o:ASN200 4.8 45.5 1.0
C o:SER139 4.9 48.2 1.0
CA o:ASN200 4.9 40.3 1.0
O o:HOH530 5.0 45.1 1.0
CB o:VAL201 5.0 41.2 1.0

Reference:

Y.Umena, K.Kawakami, J.-R.Shen, N.Kamiya. Crystal Structure of Oxygen-Evolving Photosystem II at A Resolution of 1.9 A Nature V. 473 55 2011.
ISSN: ISSN 0028-0836
PubMed: 21499260
DOI: 10.1038/NATURE09913
Page generated: Sat Jul 13 21:26:03 2024

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