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Calcium in PDB 8gn0: Crystal Structure of Dcbq-Bound Photosystem II Complex

Enzymatic activity of Crystal Structure of Dcbq-Bound Photosystem II Complex

All present enzymatic activity of Crystal Structure of Dcbq-Bound Photosystem II Complex:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0 was solved by S.Kamada, Y.Nakajima, J.-R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.223, 228.205, 286.997, 90, 90, 90
R / Rfree (%) 15.2 / 18.5

Other elements in 8gn0:

The structure of Crystal Structure of Dcbq-Bound Photosystem II Complex also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 74 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dcbq-Bound Photosystem II Complex (pdb code 8gn0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Dcbq-Bound Photosystem II Complex, PDB code: 8gn0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 8gn0

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Calcium binding site 1 out of 7 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:52.6
occ:1.00
 CA1 A:OEX401 0.0 52.6 1.0
OD2 A:ASP170 2.4 51.4 1.0
O A:HOH536 2.4 56.3 1.0
O1 A:OEX401 2.4 42.0 1.0
O5 A:OEX401 2.5 48.7 1.0
O A:ALA344 2.5 51.7 1.0
O2 A:OEX401 2.5 51.0 1.0
O A:HOH615 2.6 50.1 1.0
CG A:ASP170 3.2 48.4 1.0
OE1 A:GLU189 3.3 54.9 1.0
MN2 A:OEX401 3.4 46.1 1.0
MN3 A:OEX401 3.4 45.2 1.0
C A:ALA344 3.5 53.5 1.0
OD1 A:ASP170 3.5 47.6 1.0
MN1 A:OEX401 3.5 43.9 1.0
OXT A:ALA344 3.8 48.2 1.0
MN4 A:OEX401 3.8 48.5 1.0
OE2 A:GLU189 3.9 45.8 1.0
O3 A:OEX401 3.9 44.6 1.0
O4 A:OEX401 3.9 47.6 1.0
CD A:GLU189 3.9 50.9 1.0
O A:HOH524 4.1 62.4 1.0
NH1 C:ARG357 4.4 50.5 1.0
NH2 C:ARG357 4.5 48.5 1.0
CB A:ASP170 4.5 45.2 1.0
O A:HOH522 4.5 47.4 1.0
OE1 A:GLN165 4.7 50.6 1.0
O A:HOH601 4.7 52.7 1.0
OH A:TYR161 4.7 46.7 1.0
CA A:ALA344 4.8 52.0 1.0
CZ C:ARG357 4.9 52.3 1.0

Calcium binding site 2 out of 7 in 8gn0

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Calcium binding site 2 out of 7 in the Crystal Structure of Dcbq-Bound Photosystem II Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:68.6
occ:1.00
 O B:HOH852 2.2 79.0 1.0
OD1 B:ASN438 2.4 54.8 1.0
O D:HOH2536 2.5 80.2 1.0
O B:HOH826 2.5 45.5 1.0
O D:HOH2524 2.5 115.1 1.0
O B:HOH916 2.6 85.9 1.0
CG B:ASN438 3.6 55.9 1.0
OE2 B:GLU435 4.3 107.4 1.0
O B:HOH816 4.4 79.2 1.0
CA B:ASN438 4.4 49.5 1.0
O B:SER439 4.4 43.7 1.0
ND2 B:ASN438 4.4 56.4 1.0
O D:DMS2317 4.4 109.7 1.0
CB B:ASN438 4.6 48.5 1.0
C B:ASN438 4.7 51.1 1.0
O B:ASN438 4.9 42.8 1.0
O B:THR434 5.0 46.3 1.0

Calcium binding site 3 out of 7 in 8gn0

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Calcium binding site 3 out of 7 in the Crystal Structure of Dcbq-Bound 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 of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:77.4
occ:1.00
 O O:HOH479 2.3 71.8 1.0
O O:HOH494 2.3 90.4 1.0
O O:THR138 2.3 72.2 1.0
O O:VAL201 2.3 72.9 1.0
O O:HOH497 2.3 67.7 1.0
OD1 O:ASN200 2.4 80.0 1.0
O O:HOH430 2.4 70.7 1.0
C O:VAL201 3.5 73.2 1.0
C O:THR138 3.5 75.6 1.0
CG O:ASN200 3.5 73.2 1.0
ND2 O:ASN200 4.0 74.5 1.0
N O:VAL201 4.2 61.4 1.0
CA O:THR138 4.3 76.2 1.0
N O:ALA202 4.4 71.5 1.0
CA O:VAL201 4.4 69.0 1.0
CA O:ALA202 4.4 68.9 1.0
N O:SER139 4.5 76.8 1.0
CB O:THR138 4.5 78.9 1.0
CA O:SER139 4.6 71.1 1.0
C O:ASN200 4.6 61.9 1.0
OD1 O:ASP141 4.8 104.1 1.0
CB O:ASN200 4.8 69.5 1.0
O O:THR140 4.9 73.7 1.0

Calcium binding site 4 out of 7 in 8gn0

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Calcium binding site 4 out of 7 in the Crystal Structure of Dcbq-Bound 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 of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca2604

b:52.7
occ:1.00
 CA1 a:OEX2604 0.0 52.7 1.0
O a:HOH2741 2.4 59.3 1.0
OD2 a:ASP170 2.4 53.1 1.0
O a:HOH2785 2.4 50.0 1.0
O a:ALA344 2.4 53.3 1.0
O5 a:OEX2604 2.5 46.6 1.0
O1 a:OEX2604 2.5 41.9 1.0
O2 a:OEX2604 2.5 43.9 1.0
OE1 a:GLU189 3.2 58.2 1.0
CG a:ASP170 3.2 50.6 1.0
MN2 a:OEX2604 3.3 46.5 1.0
MN3 a:OEX2604 3.3 45.8 1.0
MN1 a:OEX2604 3.4 46.7 1.0
C a:ALA344 3.5 52.6 1.0
OD1 a:ASP170 3.6 51.1 1.0
MN4 a:OEX2604 3.8 49.4 1.0
O3 a:OEX2604 3.8 44.9 1.0
OXT a:ALA344 3.8 47.5 1.0
O4 a:OEX2604 3.9 51.5 1.0
O a:HOH2701 3.9 66.2 1.0
CD a:GLU189 4.0 51.0 1.0
OE2 a:GLU189 4.0 47.4 1.0
NH1 c:ARG357 4.4 46.9 1.0
NH2 c:ARG357 4.5 45.8 1.0
CB a:ASP170 4.5 45.7 1.0
OE1 a:GLN165 4.7 50.9 1.0
OH a:TYR161 4.7 49.2 1.0
O a:HOH2790 4.7 51.8 1.0
CA a:ALA344 4.8 52.1 1.0
O a:HOH2735 4.8 51.1 1.0
CZ c:ARG357 4.9 51.6 1.0
OD2 a:ASP342 5.0 48.8 1.0
OE1 c:GLU354 5.0 51.6 1.0

Calcium binding site 5 out of 7 in 8gn0

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Calcium binding site 5 out of 7 in the Crystal Structure of Dcbq-Bound 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 of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca605

b:72.8
occ:1.00
 O b:HOH818 2.3 83.3 1.0
O o:HOH484 2.3 100.3 1.0
OD1 b:ASN438 2.4 58.6 1.0
O b:HOH792 2.5 50.1 1.0
O b:HOH875 2.6 78.9 1.0
CG b:ASN438 3.6 51.1 1.0
OE1 b:GLU435 4.3 102.1 1.0
CA b:ASN438 4.3 48.9 1.0
O b:HOH731 4.3 78.8 1.0
O b:SER439 4.4 47.0 1.0
O b:HOH784 4.4 63.5 1.0
ND2 b:ASN438 4.5 52.7 1.0
CB b:ASN438 4.5 44.7 1.0
C b:ASN438 4.6 49.5 1.0
O b:HOH887 4.6 70.6 1.0
O b:HOH728 4.9 68.2 1.0
O b:ASN438 4.9 47.5 1.0
O b:THR434 4.9 46.0 1.0
OE2 o:GLU181 4.9 101.1 1.0

Calcium binding site 6 out of 7 in 8gn0

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Calcium binding site 6 out of 7 in the Crystal Structure of Dcbq-Bound 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 of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca503

b:73.3
occ:1.00
 OE1 c:GLU29 2.3 78.8 1.0
OG c:SER30 2.3 78.5 1.0
O c:PHE22 2.4 76.6 1.0
O c:THR24 2.4 72.7 1.0
O c:HOH692 2.5 68.2 1.0
OD2 c:ASP27 2.5 69.8 1.0
OD1 c:ASP27 2.6 65.2 1.0
CG c:ASP27 2.9 69.5 1.0
CD c:GLU29 3.4 84.5 1.0
C c:PHE22 3.4 67.9 1.0
CB c:SER30 3.5 74.4 1.0
C c:THR24 3.6 71.5 1.0
OE2 c:GLU29 3.9 88.3 1.0
O c:HOH603 4.0 70.0 1.0
N c:SER30 4.1 66.8 1.0
CA c:PHE22 4.1 79.1 1.0
N c:THR24 4.2 77.9 1.0
O c:HOH630 4.2 85.1 1.0
CB c:PHE22 4.3 72.2 1.0
CA c:SER30 4.3 68.5 1.0
C c:ALA23 4.4 83.2 1.0
N c:ALA23 4.4 63.0 1.0
CB c:ASP27 4.4 66.6 1.0
CA c:ASN25 4.5 70.2 1.0
N c:ASN25 4.5 70.6 1.0
CA c:THR24 4.6 71.2 1.0
CG c:GLU29 4.6 82.3 1.0
CA c:ALA23 4.7 76.5 1.0
CB c:GLU29 4.8 75.2 1.0
O c:ALA23 4.8 86.6 1.0
C c:GLU29 4.9 71.1 1.0
C c:ASN25 5.0 70.1 1.0

Calcium binding site 7 out of 7 in 8gn0

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Calcium binding site 7 out of 7 in the Crystal Structure of Dcbq-Bound 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 of Dcbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca302

b:74.3
occ:1.00
 O o:THR138 2.2 78.6 1.0
OD1 o:ASN200 2.4 65.5 1.0
O o:HOH514 2.4 79.3 1.0
O o:VAL201 2.4 73.2 1.0
O o:HOH489 2.5 80.0 1.0
O o:HOH463 2.6 89.8 1.0
O o:HOH405 2.7 64.7 1.0
C o:THR138 3.4 80.0 1.0
CG o:ASN200 3.5 66.9 1.0
C o:VAL201 3.5 72.3 1.0
ND2 o:ASN200 3.9 70.4 1.0
N o:VAL201 4.3 58.7 1.0
CA o:THR138 4.3 79.5 1.0
CA o:ALA202 4.4 69.4 1.0
N o:SER139 4.4 85.7 1.0
N o:ALA202 4.4 65.5 1.0
CA o:SER139 4.4 89.0 1.0
O o:HOH542 4.5 92.1 1.0
CA o:VAL201 4.5 63.5 1.0
CB o:THR138 4.5 85.3 1.0
OD2 o:ASP141 4.6 99.0 1.0
C o:ASN200 4.6 68.6 1.0
CB o:ASN200 4.8 63.8 1.0
O o:THR140 4.8 71.8 1.0
C o:SER139 4.9 85.7 1.0
O o:HOH475 4.9 89.8 1.0

Reference:

S.Kamada, Y.Nakajima, J.R.Shen. Structural Insights Into the Action Mechanisms of Artificial Electron Acceptors in Photosystem II. J.Biol.Chem. V. 299 04839 2023.
ISSN: ESSN 1083-351X
PubMed: 37209822
DOI: 10.1016/J.JBC.2023.104839
Page generated: Fri Jul 19 09:14:34 2024

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