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Calcium in PDB 8gn1: Crystal Structure of Dbbq-Bound Photosystem II Complex

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

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

Protein crystallography data

The structure of Crystal Structure of Dbbq-Bound Photosystem II Complex, PDB code: 8gn1 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) 49.02 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.185, 228.462, 286.626, 90, 90, 90
R / Rfree (%) 15.7 / 19.1

Other elements in 8gn1:

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

Bromine (Br) 12 atoms
Manganese (Mn) 8 atoms
Chlorine (Cl) 4 atoms
Iron (Fe) 6 atoms
Magnesium (Mg) 72 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Dbbq-Bound Photosystem II Complex (pdb code 8gn1). 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 Dbbq-Bound Photosystem II Complex, PDB code: 8gn1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 8gn1

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Calcium binding site 1 out of 7 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:46.0
occ:1.00
 CA1 A:OEX401 0.0 46.0 1.0
OD2 A:ASP170 2.4 48.6 1.0
O1 A:OEX401 2.4 40.6 1.0
O A:ALA344 2.4 46.6 1.0
O A:HOH519 2.5 47.8 1.0
O2 A:OEX401 2.5 40.4 1.0
O5 A:OEX401 2.6 43.7 1.0
O A:HOH619 2.6 45.1 1.0
CG A:ASP170 3.2 46.0 1.0
OE1 A:GLU189 3.3 53.5 1.0
MN2 A:OEX401 3.4 42.4 1.0
MN3 A:OEX401 3.4 43.4 1.0
OD1 A:ASP170 3.4 48.1 1.0
C A:ALA344 3.4 48.9 1.0
MN1 A:OEX401 3.5 40.9 1.0
OXT A:ALA344 3.7 44.0 1.0
O4 A:OEX401 3.7 45.0 1.0
MN4 A:OEX401 3.8 48.3 1.0
OE2 A:GLU189 3.9 45.6 1.0
CD A:GLU189 4.0 46.5 1.0
O3 A:OEX401 4.0 39.5 1.0
O A:HOH556 4.3 57.0 1.0
NH1 C:ARG357 4.3 45.4 1.0
NH2 C:ARG357 4.4 45.6 1.0
CB A:ASP170 4.4 44.2 1.0
O A:HOH513 4.6 44.9 1.0
O A:HOH580 4.7 50.4 1.0
OE1 A:GLN165 4.8 44.0 1.0
OH A:TYR161 4.8 40.6 1.0
CA A:ALA344 4.8 48.2 1.0
CZ C:ARG357 4.8 48.2 1.0

Calcium binding site 2 out of 7 in 8gn1

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Calcium binding site 2 out of 7 in the Crystal Structure of Dbbq-Bound 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 of Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:64.9
occ:1.00
 OD1 B:ASN438 2.4 47.8 1.0
O B:HOH861 2.4 76.7 1.0
O D:HOH626 2.5 73.0 1.0
O D:HOH624 2.5 87.7 1.0
O B:HOH834 2.6 53.6 1.0
O B:HOH922 2.6 89.5 1.0
CG B:ASN438 3.6 51.3 1.0
OE2 B:GLU435 4.1 99.8 1.0
O B:HOH807 4.1 63.6 1.0
CA B:ASN438 4.4 47.6 1.0
ND2 B:ASN438 4.5 51.0 1.0
O B:SER439 4.5 38.1 1.0
CB B:ASN438 4.6 46.4 1.0
O D:DMS417 4.6 95.8 1.0
O B:HOH892 4.6 66.8 1.0
C B:ASN438 4.7 50.1 1.0
O B:THR434 5.0 44.2 1.0
O B:ASN438 5.0 42.1 1.0

Calcium binding site 3 out of 7 in 8gn1

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

b:72.7
occ:1.00
 O O:VAL201 2.2 71.0 1.0
O O:HOH478 2.3 80.6 1.0
O O:HOH429 2.3 70.5 1.0
O O:HOH481 2.4 67.6 1.0
O O:THR138 2.4 64.8 1.0
OD1 O:ASN200 2.4 72.3 1.0
O O:HOH463 2.4 61.1 1.0
C O:VAL201 3.4 65.9 1.0
CG O:ASN200 3.5 70.0 1.0
C O:THR138 3.5 67.4 1.0
ND2 O:ASN200 4.1 71.5 1.0
N O:VAL201 4.2 58.6 1.0
N O:ALA202 4.2 61.0 1.0
CA O:ALA202 4.3 60.0 1.0
CA O:THR138 4.3 72.5 1.0
CA O:VAL201 4.4 59.5 1.0
C O:ASN200 4.5 61.3 1.0
N O:SER139 4.5 65.4 1.0
O O:HOH539 4.6 86.8 1.0
CB O:THR138 4.6 74.2 1.0
CA O:SER139 4.6 71.3 1.0
OD1 O:ASP141 4.7 85.1 1.0
CB O:ASN200 4.8 68.5 1.0
O O:ASN200 4.8 66.1 1.0
O O:THR140 4.9 73.8 1.0
CB O:VAL201 4.9 63.9 1.0
CA O:ASN200 5.0 67.3 1.0

Calcium binding site 4 out of 7 in 8gn1

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Calcium binding site 4 out of 7 in the Crystal Structure of Dbbq-Bound 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 4 of Crystal Structure of Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca2104

b:48.7
occ:1.00
 CA1 a:OEX2104 0.0 48.7 1.0
O a:HOH2306 2.4 43.4 1.0
O a:ALA344 2.4 48.9 1.0
OD2 a:ASP170 2.4 50.2 1.0
O a:HOH2230 2.4 49.2 1.0
O1 a:OEX2104 2.4 38.3 1.0
O2 a:OEX2104 2.5 44.6 1.0
O5 a:OEX2104 2.6 52.2 1.0
OE1 a:GLU189 3.2 52.5 1.0
CG a:ASP170 3.2 52.2 1.0
MN2 a:OEX2104 3.3 45.2 1.0
C a:ALA344 3.4 52.3 1.0
MN3 a:OEX2104 3.4 43.3 1.0
MN1 a:OEX2104 3.5 43.6 1.0
OD1 a:ASP170 3.6 49.9 1.0
OXT a:ALA344 3.7 46.0 1.0
MN4 a:OEX2104 3.9 49.2 1.0
OE2 a:GLU189 3.9 47.0 1.0
CD a:GLU189 3.9 50.0 1.0
O a:HOH2206 3.9 59.5 1.0
O3 a:OEX2104 4.0 39.9 1.0
O4 a:OEX2104 4.0 43.6 1.0
NH1 c:ARG357 4.4 51.4 1.0
NH2 c:ARG357 4.4 51.8 1.0
CB a:ASP170 4.5 47.1 1.0
CA a:ALA344 4.7 49.8 1.0
OE1 a:GLN165 4.7 52.9 1.0
OH a:TYR161 4.7 45.2 1.0
O a:HOH2254 4.7 49.9 1.0
O a:HOH2229 4.7 48.2 1.0
CZ c:ARG357 4.9 52.3 1.0
OD2 a:ASP342 4.9 43.5 1.0
OE1 c:GLU354 5.0 48.8 1.0
OD1 a:ASP342 5.0 47.4 1.0

Calcium binding site 5 out of 7 in 8gn1

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Calcium binding site 5 out of 7 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca603

b:72.3
occ:1.00
 OD1 b:ASN438 2.4 49.3 1.0
O b:HOH841 2.4 88.2 1.0
O o:HOH2765 2.5 96.4 1.0
O b:HOH876 2.5 78.9 1.0
O b:HOH736 2.6 50.8 1.0
CG b:ASN438 3.6 45.8 1.0
OE1 b:GLU435 3.8 97.0 1.0
CA b:ASN438 4.4 43.1 1.0
O b:HOH742 4.4 76.9 1.0
O b:SER439 4.5 46.0 1.0
CB b:ASN438 4.5 42.1 1.0
ND2 b:ASN438 4.5 47.3 1.0
C b:ASN438 4.7 45.7 1.0
CD b:GLU435 4.7 87.1 1.0
O b:THR434 4.8 47.6 1.0
OE2 b:GLU435 4.9 92.3 1.0

Calcium binding site 6 out of 7 in 8gn1

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Calcium binding site 6 out of 7 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca502

b:66.3
occ:1.00
 OE1 c:GLU29 2.3 71.1 1.0
OG c:SER30 2.3 69.1 1.0
O c:THR24 2.4 60.7 1.0
O c:PHE22 2.4 65.2 1.0
OD2 c:ASP27 2.5 61.0 1.0
O c:HOH712 2.6 68.6 1.0
OD1 c:ASP27 2.7 58.6 1.0
CG c:ASP27 2.9 62.6 1.0
C c:PHE22 3.4 60.7 1.0
CD c:GLU29 3.5 72.6 1.0
CB c:SER30 3.5 62.1 1.0
C c:THR24 3.6 66.0 1.0
O c:HOH603 4.0 58.1 1.0
N c:SER30 4.0 59.4 1.0
OE2 c:GLU29 4.1 79.5 1.0
CA c:PHE22 4.2 66.8 1.0
N c:THR24 4.2 73.8 1.0
C c:ALA23 4.3 73.2 1.0
CA c:SER30 4.3 61.7 1.0
N c:ALA23 4.3 52.8 1.0
CB c:PHE22 4.4 64.9 1.0
CA c:ASN25 4.4 69.5 1.0
N c:ASN25 4.4 65.5 1.0
CB c:ASP27 4.5 66.1 1.0
CA c:THR24 4.5 68.2 1.0
CB c:GLU29 4.6 68.1 1.0
CA c:ALA23 4.6 67.2 1.0
CG c:GLU29 4.6 70.3 1.0
O c:ALA23 4.8 78.8 1.0
C c:GLU29 4.8 63.4 1.0
C c:ASN25 4.9 67.5 1.0

Calcium binding site 7 out of 7 in 8gn1

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Calcium binding site 7 out of 7 in the Crystal Structure of Dbbq-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 Dbbq-Bound Photosystem II Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca2602

b:71.8
occ:1.00
 O o:THR138 2.3 67.9 1.0
OD1 o:ASN200 2.3 66.8 1.0
O o:VAL201 2.4 71.1 1.0
O o:HOH2820 2.5 100.3 1.0
O o:HOH2716 2.5 71.0 1.0
O o:HOH2802 2.5 80.5 1.0
O o:HOH2704 2.7 60.0 1.0
CG o:ASN200 3.4 67.2 1.0
C o:THR138 3.5 74.0 1.0
C o:VAL201 3.5 65.2 1.0
ND2 o:ASN200 3.9 72.2 1.0
N o:VAL201 4.3 65.2 1.0
N o:SER139 4.4 79.6 1.0
N o:ALA202 4.4 61.5 1.0
CA o:THR138 4.4 77.5 1.0
CA o:ALA202 4.4 63.7 1.0
CA o:SER139 4.4 82.7 1.0
O o:HOH2788 4.5 92.9 1.0
CA o:VAL201 4.5 60.6 1.0
C o:ASN200 4.5 65.8 1.0
OD2 o:ASP141 4.6 93.6 1.0
CB o:THR138 4.6 77.0 1.0
CB o:ASN200 4.7 61.6 1.0
O o:THR140 4.8 65.7 1.0
O o:HOH2809 4.9 81.9 1.0
C o:SER139 4.9 80.6 1.0
CA o:ASN200 4.9 61.8 1.0
O o:ASN200 5.0 67.0 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 09:14:41 2024

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