Calcium in PDB 7yq2: Crystal Structure of Photosystem II Expressing PSBA2 Gene Only

Enzymatic activity of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only

All present enzymatic activity of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only, PDB code: 7yq2 was solved by Y.Nakajima, M.Suga, J.R.Shen, 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 (°) 122.135, 228.172, 286.685, 90, 90, 90
R / Rfree (%) 15.1 / 18.4

Other elements in 7yq2:

The structure of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only (pdb code 7yq2). 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 of Photosystem II Expressing PSBA2 Gene Only, PDB code: 7yq2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7yq2

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Calcium binding site 1 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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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 Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:31.2
occ:1.00
 CA1 A:OEX401 0.0 31.2 1.0
OD2 A:ASP170 2.4 30.1 1.0
O A:HOH533 2.4 33.0 1.0
O A:HOH633 2.5 26.8 1.0
O1 A:OEX401 2.5 25.8 1.0
O A:ALA344 2.5 29.1 1.0
O5 A:OEX401 2.5 28.4 1.0
O2 A:OEX401 2.6 31.5 1.0
OE1 A:GLU189 3.1 29.8 1.0
CG A:ASP170 3.1 28.2 1.0
MN2 A:OEX401 3.3 29.2 1.0
OD1 A:ASP170 3.4 30.3 1.0
MN3 A:OEX401 3.4 28.3 1.0
C A:ALA344 3.5 33.3 1.0
MN1 A:OEX401 3.5 27.4 1.0
MN4 A:OEX401 3.8 30.8 1.0
CD A:GLU189 3.9 31.9 1.0
O4 A:OEX401 3.9 30.9 1.0
OE2 A:GLU189 4.0 28.4 1.0
O3 A:OEX401 4.0 28.9 1.0
O A:HOH528 4.1 37.7 1.0
NH1 C:ARG357 4.3 27.2 1.0
CB A:ASP170 4.4 24.4 1.0
NH2 C:ARG357 4.5 34.6 1.0
O A:HOH596 4.5 30.3 1.0
O A:HOH530 4.6 29.9 1.0
OH A:TYR161 4.6 28.9 1.0
CA A:ALA344 4.8 29.1 1.0
OE1 A:GLN165 4.8 30.6 1.0
CZ C:ARG357 4.9 32.6 1.0
OD1 A:ASP342 5.0 27.4 1.0

Calcium binding site 2 out of 9 in 7yq2

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Calcium binding site 2 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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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 Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:51.6
occ:1.00
 O B:HOH977 2.4 57.9 1.0
O B:HOH914 2.4 60.6 1.0
OD1 B:ASN438 2.4 37.5 1.0
O B:HOH1034 2.5 77.3 1.0
O B:HOH772 2.5 34.6 1.0
O B:HOH983 2.5 81.8 1.0
CG B:ASN438 3.6 42.2 1.0
OE1 B:GLU435 3.8 83.0 1.0
O M:HOH215 4.3 86.1 1.0
O B:HOH755 4.3 50.8 1.0
CA B:ASN438 4.4 34.2 1.0
O B:SER439 4.4 28.4 1.0
O B:HOH879 4.5 56.4 1.0
ND2 B:ASN438 4.5 40.9 1.0
CB B:ASN438 4.6 37.3 1.0
C B:ASN438 4.6 31.6 1.0
C2 D:DMS415 4.7 99.5 1.0
O B:THR434 4.7 30.4 1.0
O B:HOH854 4.8 54.7 1.0
CD B:GLU435 4.8 76.5 1.0
O D:HOH661 4.9 77.7 1.0
O B:ASN438 5.0 30.7 1.0
O B:HOH838 5.0 48.3 1.0
O D:HOH666 5.0 60.0 1.0

Calcium binding site 3 out of 9 in 7yq2

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Calcium binding site 3 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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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 of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:56.5
occ:1.00
 O O:HOH501 2.3 64.3 1.0
O O:HOH454 2.3 48.5 1.0
O O:VAL201 2.3 52.7 1.0
O O:THR138 2.3 48.5 1.0
O O:HOH496 2.3 63.8 1.0
OD1 O:ASN200 2.4 58.1 1.0
O O:HOH514 2.4 68.5 1.0
C O:VAL201 3.4 52.2 1.0
CG O:ASN200 3.5 58.0 1.0
C O:THR138 3.5 52.3 1.0
ND2 O:ASN200 4.1 60.2 1.0
N O:VAL201 4.2 42.4 1.0
N O:ALA202 4.3 49.6 1.0
CA O:THR138 4.3 57.1 1.0
CA O:ALA202 4.3 51.1 1.0
CA O:VAL201 4.4 46.7 1.0
C O:ASN200 4.5 48.6 1.0
CB O:THR138 4.5 55.4 1.0
N O:SER139 4.5 48.8 1.0
O O:HOH609 4.5 42.1 0.5
CA O:SER139 4.7 53.9 1.0
O O:HOH557 4.7 60.2 1.0
O O:HOH609 4.7 47.1 0.5
OD1 O:ASP141 4.7 74.1 1.0
CB O:ASN200 4.8 53.2 1.0
O O:ASN200 4.8 48.2 1.0
O O:THR140 4.8 52.4 1.0
CA O:ASN200 4.9 51.7 1.0
CB O:VAL201 4.9 52.8 1.0

Calcium binding site 4 out of 9 in 7yq2

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Calcium binding site 4 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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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 Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca202

b:89.1
occ:1.00
 O A:HOH526 2.7 47.0 1.0
O V:HOH387 2.9 65.3 1.0
O F:HOH205 2.9 65.6 1.0
OE2 V:GLU2 3.0 46.0 0.5
OE1 V:GLU2 3.1 45.6 0.5
OE1 V:GLU23 3.3 91.2 1.0
CD V:GLU2 3.4 50.4 0.5
C1 V:DMS212 3.6 96.3 1.0
C2 V:DMS201 3.8 88.6 1.0
CD V:GLU23 4.2 85.3 1.0
OE2 V:GLU23 4.4 88.1 1.0
O F:ARG45 4.5 43.1 1.0
OXT F:ARG45 4.6 44.0 1.0
O A:ALA309 4.8 39.1 1.0
CG V:GLU2 4.9 56.4 0.5
S V:DMS201 5.0 79.6 1.0

Calcium binding site 5 out of 9 in 7yq2

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Calcium binding site 5 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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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 of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca404

b:33.0
occ:1.00
 CA1 a:OEX404 0.0 33.0 1.0
OD2 a:ASP170 2.4 36.0 1.0
O a:ALA344 2.4 30.4 1.0
O a:HOH562 2.4 34.2 1.0
O a:HOH624 2.4 33.8 1.0
O1 a:OEX404 2.5 29.3 1.0
O5 a:OEX404 2.5 32.9 1.0
O2 a:OEX404 2.6 30.9 1.0
OE1 a:GLU189 3.1 32.6 1.0
CG a:ASP170 3.2 32.3 1.0
MN2 a:OEX404 3.3 33.4 1.0
C a:ALA344 3.4 33.2 1.0
MN3 a:OEX404 3.4 31.2 1.0
OD1 a:ASP170 3.5 28.1 1.0
MN1 a:OEX404 3.5 32.2 1.0
MN4 a:OEX404 3.9 32.4 1.0
CD a:GLU189 3.9 34.1 1.0
O3 a:OEX404 3.9 34.0 1.0
OE2 a:GLU189 4.0 29.7 1.0
O4 a:OEX404 4.0 32.7 1.0
O a:HOH593 4.1 41.3 1.0
NH1 c:ARG357 4.4 31.7 1.0
CB a:ASP170 4.4 30.1 1.0
O a:HOH550 4.5 29.0 1.0
NH2 c:ARG357 4.5 32.3 1.0
O a:HOH530 4.6 28.6 1.0
OH a:TYR161 4.6 28.8 1.0
CA a:ALA344 4.7 36.9 1.0
OE1 a:GLN165 4.8 33.2 1.0
CZ c:ARG357 5.0 35.0 1.0
OD1 a:ASP342 5.0 33.2 1.0

Calcium binding site 6 out of 9 in 7yq2

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Calcium binding site 6 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca604

b:53.0
occ:1.00
 O b:HOH733 2.4 63.0 1.0
OD1 b:ASN438 2.4 42.1 1.0
O o:HOH500 2.4 87.0 1.0
O b:HOH984 2.4 54.5 1.0
O b:HOH741 2.5 37.4 1.0
CG b:ASN438 3.6 39.2 1.0
OE1 b:GLU435 3.9 64.7 0.6
O b:HOH824 4.3 71.4 1.0
CA b:ASN438 4.3 33.1 1.0
O b:SER439 4.4 33.2 1.0
ND2 b:ASN438 4.5 39.3 1.0
CB b:ASN438 4.5 38.0 1.0
O o:HOH580 4.6 54.0 1.0
C b:ASN438 4.6 36.8 1.0
O b:THR434 4.7 33.8 1.0
O b:HOH962 4.7 61.1 1.0
O b:HOH908 4.8 52.5 1.0
CD b:GLU435 4.9 50.5 0.6
O b:HOH775 4.9 44.4 1.0
O b:ASN438 5.0 30.5 1.0

Calcium binding site 7 out of 9 in 7yq2

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Calcium binding site 7 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca901

b:52.7
occ:1.00
 O c:THR24 2.3 46.7 1.0
O c:PHE22 2.4 55.8 1.0
OE1 c:GLU29 2.4 53.8 1.0
OG c:SER30 2.4 50.3 1.0
OD2 c:ASP27 2.4 44.2 1.0
O c:HOH1162 2.5 51.5 1.0
OD1 c:ASP27 2.5 46.3 1.0
CG c:ASP27 2.8 46.6 1.0
C c:PHE22 3.4 50.1 1.0
C c:THR24 3.5 46.2 1.0
CB c:SER30 3.5 45.2 1.0
CD c:GLU29 3.6 52.4 1.0
O c:HOH1003 4.0 46.0 1.0
N c:SER30 4.0 47.4 1.0
N c:THR24 4.1 58.9 1.0
CA c:PHE22 4.1 60.2 1.0
OE2 c:GLU29 4.2 59.3 1.0
CA c:SER30 4.3 44.9 1.0
CA c:ASN25 4.3 47.8 1.0
CB c:PHE22 4.3 52.1 1.0
N c:ASN25 4.3 47.0 1.0
C c:ALA23 4.3 59.6 1.0
CB c:ASP27 4.4 45.6 1.0
N c:ALA23 4.4 46.5 1.0
CA c:THR24 4.4 52.9 1.0
O c:HOH1042 4.5 59.9 1.0
CB c:GLU29 4.6 49.6 1.0
CA c:ALA23 4.7 53.5 1.0
CG c:GLU29 4.7 57.0 1.0
C c:ASN25 4.8 48.5 1.0
C c:GLU29 4.9 45.8 1.0
O c:ALA23 4.9 50.0 1.0
N c:ARG26 5.0 48.9 1.0

Calcium binding site 8 out of 9 in 7yq2

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Calcium binding site 8 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca301

b:55.8
occ:1.00
 O o:THR138 2.3 52.9 1.0
OD1 o:ASN200 2.3 49.8 1.0
O o:HOH550 2.4 71.7 1.0
O o:VAL201 2.4 52.5 1.0
O o:HOH455 2.4 56.3 1.0
O o:HOH412 2.4 66.4 1.0
O o:HOH432 2.5 48.0 1.0
CG o:ASN200 3.4 51.8 1.0
C o:THR138 3.5 53.1 1.0
C o:VAL201 3.5 51.4 1.0
ND2 o:ASN200 4.0 58.8 1.0
N o:VAL201 4.2 49.0 1.0
CA o:THR138 4.4 54.2 1.0
N o:ALA202 4.4 49.6 1.0
N o:SER139 4.4 57.5 1.0
CA o:ALA202 4.4 50.2 1.0
CA o:SER139 4.4 59.0 1.0
CA o:VAL201 4.5 47.5 1.0
OD1 o:ASP141 4.5 68.6 1.0
C o:ASN200 4.5 51.2 1.0
O o:HOH467 4.5 76.2 1.0
O o:HOH594 4.6 68.6 1.0
CB o:THR138 4.6 58.2 1.0
O o:THR140 4.7 58.6 1.0
CB o:ASN200 4.7 45.2 1.0
O o:HOH420 4.8 61.7 1.0
C o:SER139 4.9 59.8 1.0
CA o:ASN200 4.9 45.8 1.0
O o:ASN200 5.0 51.8 1.0

Calcium binding site 9 out of 9 in 7yq2

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Calcium binding site 9 out of 9 in the Crystal Structure of Photosystem II Expressing PSBA2 Gene Only


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Photosystem II Expressing PSBA2 Gene Only within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Ca201

b:104.4
occ:1.00
 OE2 v:GLU2 3.2 51.4 0.6
OE1 v:GLU2 3.2 49.5 0.6
OE1 v:GLU23 3.4 96.4 1.0
CD v:GLU2 3.6 53.7 0.6
O a:HOH640 3.7 59.5 1.0
O v:DMS207 4.1 114.6 1.0
CD v:GLU23 4.3 92.0 1.0
OE2 v:GLU23 4.4 92.2 1.0
O f:ARG45 4.5 52.8 1.0
OXT f:ARG45 4.5 46.0 1.0
O a:ALA309 4.8 43.8 1.0
C f:ARG45 5.0 50.3 1.0

Reference:

Y.Nakajima, N.Ugai-Amo, N.Tone, A.Nakagawa, M.Iwai, M.Ikeuchi, M.Sugiura, M.Suga, J.R.Shen. Crystal Structures of Photosystem II From A Cyanobacterium Expressing Psba 2 in Comparison to Psba 3 Reveal Differences in the D1 Subunit. J.Biol.Chem. V. 298 02668 2022.
ISSN: ESSN 1083-351X
PubMed: 36334624
DOI: 10.1016/J.JBC.2022.102668
Page generated: Tue Apr 4 19:18:04 2023

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