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Calcium in PDB 5b66: Crystal Structure Analysis of Photosystem II Complex

Enzymatic activity of Crystal Structure Analysis of Photosystem II Complex

All present enzymatic activity of Crystal Structure Analysis of Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b66 was solved by A.Tanaka, Y.Fukushima, N.Kamiya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.465, 228.176, 286.422, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 20.1

Other elements in 5b66:

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 5b66). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure Analysis of Photosystem II Complex, PDB code: 5b66:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5b66

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Calcium binding site 1 out of 8 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:Ca420

b:24.8
occ:1.00
 CA1 A:OEX420 0.0 24.8 1.0
O A:HOH617 2.4 24.2 1.0
O A:HOH540 2.4 26.6 1.0
OD2 A:ASP170 2.4 24.5 1.0
O1 A:OEX420 2.4 21.5 1.0
O5 A:OEX420 2.5 24.4 1.0
O2 A:OEX420 2.5 24.4 1.0
O A:ALA344 2.5 27.5 1.0
OE1 A:GLU189 3.0 26.1 1.0
CG A:ASP170 3.2 24.5 1.0
MN2 A:OEX420 3.3 22.7 1.0
OD1 A:ASP170 3.4 23.4 1.0
MN3 A:OEX420 3.4 23.1 1.0
C A:ALA344 3.5 24.0 1.0
MN1 A:OEX420 3.5 21.9 1.0
MN4 A:OEX420 3.8 24.5 1.0
OXT A:ALA344 3.8 23.5 1.0
CD A:GLU189 3.9 21.7 1.0
O4 A:OEX420 3.9 23.9 1.0
OE2 A:GLU189 4.0 21.5 1.0
O3 A:OEX420 4.0 22.7 1.0
O A:HOH573 4.1 29.1 1.0
NH1 C:ARG357 4.2 21.1 1.0
CB A:ASP170 4.4 25.2 1.0
NH2 C:ARG357 4.5 21.0 1.0
O A:HOH515 4.5 22.0 1.0
O A:HOH591 4.5 26.9 1.0
CA A:ALA344 4.7 23.7 1.0
OH A:TYR161 4.7 21.7 1.0
OE1 A:GLN165 4.8 24.1 1.0
CZ C:ARG357 4.8 24.1 1.0

Calcium binding site 2 out of 8 in 5b66

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Calcium binding site 2 out of 8 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:Ca624

b:43.6
occ:1.00
 O B:HOH865 2.2 52.6 1.0
OD1 B:ASN438 2.4 34.2 1.0
O B:HOH1017 2.4 46.8 0.7
O B:HOH963 2.4 46.7 1.0
O B:HOH853 2.4 26.2 1.0
O B:HOH954 2.4 59.2 1.0
CG B:ASN438 3.6 32.4 1.0
OE2 B:GLU435 3.9 49.2 0.7
O B:HOH1017 4.2 19.7 0.3
O B:HOH709 4.3 40.0 1.0
CA B:ASN438 4.4 25.7 1.0
O M:HOH205 4.5 52.3 1.0
ND2 B:ASN438 4.5 32.7 1.0
CB B:ASN438 4.5 29.0 1.0
O B:SER439 4.5 24.4 1.0
O D:HOH663 4.6 53.4 1.0
O B:HOH894 4.6 48.1 1.0
C B:ASN438 4.7 25.6 1.0
OE1 B:GLU435 4.7 47.1 0.7
CD B:GLU435 4.7 42.7 0.7
O B:THR434 4.8 26.1 1.0
C1 D:DMS415 4.8 58.7 1.0
O B:HOH885 4.9 42.7 1.0
O B:ASN438 5.0 23.8 1.0
O O:HOH656 5.0 68.9 1.0

Calcium binding site 3 out of 8 in 5b66

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Calcium binding site 3 out of 8 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 3 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:47.0
occ:1.00
 O O:HOH583 2.2 50.7 1.0
O O:VAL201 2.3 39.0 1.0
O O:HOH489 2.3 43.9 1.0
O O:HOH462 2.3 47.3 1.0
OD1 O:ASN200 2.4 44.5 1.0
O O:THR138 2.4 38.9 1.0
O O:HOH536 2.5 48.9 1.0
C O:VAL201 3.4 36.4 1.0
CG O:ASN200 3.5 50.4 1.0
C O:THR138 3.5 43.3 1.0
ND2 O:ASN200 4.0 51.4 1.0
N O:VAL201 4.1 34.8 1.0
CA O:VAL201 4.3 33.4 1.0
N O:ALA202 4.3 39.2 1.0
CA O:THR138 4.4 43.8 1.0
CA O:ALA202 4.4 40.0 1.0
C O:ASN200 4.4 34.9 1.0
N O:SER139 4.5 40.4 1.0
CA O:SER139 4.5 40.5 1.0
CB O:THR138 4.6 45.7 1.0
OD1 O:ASP141 4.7 58.4 1.0
O O:THR140 4.7 38.0 1.0
O O:ASN200 4.8 35.0 1.0
CB O:ASN200 4.8 40.8 1.0
O O:HOH541 4.8 39.9 1.0
CB O:VAL201 4.8 34.1 1.0
O O:HOH661 4.9 68.2 1.0
CA O:ASN200 4.9 39.1 1.0
O O:HOH537 5.0 54.4 1.0

Calcium binding site 4 out of 8 in 5b66

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Calcium binding site 4 out of 8 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
V:Ca203

b:63.7
occ:1.00
 O V:HOH342 2.2 49.4 1.0
O V:HOH458 2.4 56.1 1.0
O A:HOH517 2.4 40.4 1.0
O V:HOH339 2.6 56.0 1.0
O V:HOH415 2.6 48.5 1.0
OE1 V:GLU2 2.7 49.5 1.0
OE2 V:GLU2 2.8 50.9 1.0
CD V:GLU2 3.1 46.7 1.0
O F:ARG45 4.1 31.7 1.0
OE1 V:GLU23 4.4 46.7 1.0
OXT F:ARG45 4.4 34.3 1.0
O F:DMS102 4.4 64.6 1.0
O A:ALA309 4.6 32.8 1.0
CG V:GLU2 4.7 42.0 1.0
C F:ARG45 4.7 34.0 1.0
O E:HOH237 4.8 24.5 0.5
CB A:ALA309 4.8 27.6 1.0
C1 V:DMS206 4.8 61.0 1.0
OE2 V:GLU23 4.9 50.2 1.0

Calcium binding site 5 out of 8 in 5b66

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Calcium binding site 5 out of 8 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 5 of Crystal Structure Analysis of Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca419

b:26.3
occ:1.00
 CA1 a:OEX419 0.0 26.3 1.0
OD2 a:ASP170 2.4 25.8 1.0
O a:HOH557 2.4 26.7 1.0
O5 a:OEX419 2.5 26.6 1.0
O a:HOH638 2.5 24.1 1.0
O a:ALA344 2.6 28.9 1.0
O2 a:OEX419 2.6 24.1 1.0
O1 a:OEX419 2.6 21.9 1.0
OE1 a:GLU189 3.0 25.5 1.0
CG a:ASP170 3.2 26.9 1.0
MN2 a:OEX419 3.3 24.2 1.0
MN3 a:OEX419 3.4 24.2 1.0
MN1 a:OEX419 3.5 23.8 1.0
OD1 a:ASP170 3.5 22.2 1.0
C a:ALA344 3.5 27.3 1.0
MN4 a:OEX419 3.7 25.4 1.0
OXT a:ALA344 3.8 28.4 1.0
O3 a:OEX419 3.9 24.1 1.0
CD a:GLU189 3.9 27.2 1.0
OE2 a:GLU189 4.0 23.6 1.0
O4 a:OEX419 4.0 25.4 1.0
O a:HOH543 4.1 31.8 1.0
NH1 c:ARG357 4.4 24.9 1.0
CB a:ASP170 4.5 22.6 1.0
O a:HOH571 4.5 24.1 1.0
NH2 c:ARG357 4.5 22.4 1.0
O a:HOH532 4.6 25.2 1.0
OH a:TYR161 4.7 22.5 1.0
OE1 a:GLN165 4.7 24.4 1.0
CA a:ALA344 4.8 26.8 1.0
CZ c:ARG357 4.9 22.9 1.0
OD1 a:ASP342 5.0 20.7 1.0

Calcium binding site 6 out of 8 in 5b66

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Calcium binding site 6 out of 8 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:Ca626

b:42.7
occ:1.00
 O b:HOH752 2.3 48.8 1.0
OD1 b:ASN438 2.4 34.9 1.0
O b:HOH1004 2.4 47.4 1.0
O b:HOH995 2.4 55.7 1.0
O b:HOH804 2.5 27.0 1.0
CG b:ASN438 3.6 29.8 1.0
O b:HOH771 4.2 52.7 1.0
CA b:ASN438 4.3 25.0 1.0
O b:HOH807 4.4 53.4 1.0
ND2 b:ASN438 4.5 32.2 1.0
CB b:ASN438 4.5 27.3 1.0
O d:HOH672 4.5 65.0 1.0
O b:SER439 4.5 26.2 1.0
O b:HOH868 4.5 30.9 0.5
O b:HOH1089 4.6 28.8 0.5
C b:ASN438 4.6 25.1 1.0
O b:HOH1089 4.7 32.9 0.5
O m:HOH212 4.7 52.5 1.0
OE1 b:GLU435 4.8 60.5 1.0
O d:HOH636 4.8 59.2 1.0
O b:THR434 4.8 26.5 1.0
OE2 b:GLU435 4.8 54.4 1.0
O b:ASN438 5.0 24.4 1.0

Calcium binding site 7 out of 8 in 5b66

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Calcium binding site 7 out of 8 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:Ca522

b:41.1
occ:1.00
 OE1 c:GLU29 1.9 41.4 1.0
O c:THR24 2.3 38.8 1.0
OG c:SER30 2.3 37.8 1.0
O c:PHE22 2.4 46.7 1.0
O c:HOH766 2.4 41.7 1.0
OD1 c:ASP27 2.5 41.0 1.0
OD2 c:ASP27 2.5 35.2 1.0
CG c:ASP27 2.8 39.3 1.0
CD c:GLU29 3.1 43.5 1.0
CB c:SER30 3.4 40.0 1.0
C c:THR24 3.5 40.2 1.0
C c:PHE22 3.5 45.3 1.0
CG c:GLU29 3.9 45.9 1.0
OE2 c:GLU29 4.0 45.3 1.0
N c:SER30 4.1 35.5 1.0
O c:HOH611 4.1 36.8 1.0
N c:THR24 4.1 45.0 1.0
CA c:SER30 4.2 36.5 1.0
C c:ALA23 4.3 46.1 1.0
CA c:ASN25 4.3 35.8 1.0
CA c:PHE22 4.3 47.1 1.0
N c:ASN25 4.4 36.6 1.0
CB c:ASP27 4.4 39.3 1.0
N c:ALA23 4.4 45.6 1.0
CA c:THR24 4.5 43.0 1.0
CB c:PHE22 4.6 46.4 1.0
CA c:ALA23 4.6 44.0 1.0
O c:HOH785 4.7 57.7 1.0
C c:ASN25 4.7 36.0 1.0
O c:ALA23 4.7 42.5 1.0
C c:GLU29 5.0 35.2 1.0

Calcium binding site 8 out of 8 in 5b66

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Calcium binding site 8 out of 8 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
o:Ca301

b:48.4
occ:1.00
 O o:HOH558 2.2 51.2 1.0
O o:VAL201 2.3 38.3 1.0
O o:HOH508 2.4 50.8 1.0
OD1 o:ASN200 2.4 38.1 1.0
O o:HOH406 2.5 39.4 1.0
O o:THR138 2.5 48.1 1.0
O o:HOH468 2.7 49.0 1.0
C o:VAL201 3.5 40.8 1.0
CG o:ASN200 3.5 43.0 1.0
C o:THR138 3.5 50.3 1.0
ND2 o:ASN200 4.0 41.8 1.0
N o:VAL201 4.2 38.6 1.0
N o:ALA202 4.3 37.7 1.0
CA o:VAL201 4.4 36.8 1.0
N o:SER139 4.4 50.4 1.0
CA o:THR138 4.4 47.4 1.0
CA o:ALA202 4.4 42.6 1.0
C o:ASN200 4.5 41.0 1.0
CA o:SER139 4.5 50.3 1.0
O o:HOH434 4.5 56.2 1.0
O o:THR140 4.6 41.0 1.0
CB o:THR138 4.7 48.5 1.0
OD1 o:ASP141 4.7 63.4 1.0
O o:HOH517 4.8 45.3 1.0
CB o:ASN200 4.8 37.6 1.0
O o:ASN200 4.8 44.0 1.0
C o:SER139 4.9 45.1 1.0
O o:HOH561 4.9 53.6 1.0
CA o:ASN200 4.9 40.2 1.0

Reference:

A.Tanaka, Y.Fukushima, N.Kamiya. Two Different Structures of the Oxygen-Evolving Complex in the Same Polypeptide Frameworks of Photosystem II J. Am. Chem. Soc. V. 139 1718 2017.
ISSN: ESSN 1520-5126
PubMed: 28102667
DOI: 10.1021/JACS.6B09666
Page generated: Sun Jul 14 16:49:59 2024

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