Calcium in PDB 5zzn: Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus

Enzymatic activity of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus

All present enzymatic activity of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus:
1.10.3.9;

Protein crystallography data

The structure of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn was solved by Y.Nakajima, Y.Umena, R.Nagao, K.Endo, K.Kobayashi, F.Akita, M.Suga, H.Wada, T.Noguchi, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.250, 228.430, 287.120, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.7

Other elements in 5zzn:

The structure of Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus also contains other interesting chemical elements:

Magnesium (Mg) 74 atoms
Manganese (Mn) 8 atoms
Iron (Fe) 6 atoms
Chlorine (Cl) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus (pdb code 5zzn). 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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus, PDB code: 5zzn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 5zzn

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Calcium binding site 1 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:39.7
occ:1.00
 CA1 A:OEX401 0.0 39.7 1.0
O A:HOH535 2.3 34.5 1.0
O1 A:OEX401 2.4 30.1 1.0
O2 A:OEX401 2.4 31.3 1.0
OD2 A:ASP170 2.4 36.6 1.0
O A:HOH593 2.4 42.8 1.0
O A:ALA344 2.5 35.3 1.0
O5 A:OEX401 2.5 33.0 1.0
OE1 A:GLU189 3.2 37.7 1.0
CG A:ASP170 3.2 32.4 1.0
MN2 A:OEX401 3.3 30.0 1.0
MN1 A:OEX401 3.4 30.2 1.0
MN3 A:OEX401 3.4 34.2 1.0
C A:ALA344 3.5 32.0 1.0
OD1 A:ASP170 3.5 32.5 1.0
O4 A:OEX401 3.8 34.5 1.0
OXT A:ALA344 3.8 35.3 1.0
MN4 A:OEX401 3.9 40.7 1.0
CD A:GLU189 4.0 33.7 1.0
O3 A:OEX401 4.1 28.2 1.0
OE2 A:GLU189 4.1 34.1 1.0
O A:HOH569 4.2 53.5 1.0
NH1 C:ARG357 4.3 37.8 1.0
CB A:ASP170 4.5 32.1 1.0
NH2 C:ARG357 4.5 46.0 1.0
OE1 A:GLN165 4.6 36.1 1.0
CA A:ALA344 4.7 38.5 1.0
O A:HOH531 4.7 38.8 1.0
OH A:TYR161 4.7 32.3 1.0
O A:HOH579 4.8 36.1 1.0
CZ C:ARG357 5.0 37.6 1.0
OD1 A:ASP342 5.0 32.6 1.0

Calcium binding site 2 out of 9 in 5zzn

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Calcium binding site 2 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:60.9
occ:1.00
 O B:HOH852 2.3 71.0 1.0
O B:HOH893 2.4 58.4 1.0
OD1 B:ASN438 2.4 37.6 1.0
O O:HOH508 2.4 71.8 1.0
O B:HOH781 2.6 39.8 1.0
CG B:ASN438 3.6 41.2 1.0
OE2 B:GLU435 3.9 73.3 1.0
O B:HOH731 4.2 45.5 1.0
CA B:ASN438 4.3 37.0 1.0
O B:SER439 4.4 31.2 1.0
ND2 B:ASN438 4.5 40.8 1.0
CB B:ASN438 4.5 37.0 1.0
C B:ASN438 4.6 37.0 1.0
O B:HOH798 4.7 56.0 1.0
O B:THR434 4.7 37.6 1.0
CD B:GLU435 4.8 72.2 1.0
O B:ASN438 4.9 35.4 1.0
OE1 B:GLU435 4.9 87.8 1.0

Calcium binding site 3 out of 9 in 5zzn

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Calcium binding site 3 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Ca301

b:58.0
occ:1.00
 O O:HOH465 2.1 45.4 1.0
O O:HOH492 2.2 57.8 1.0
O O:VAL201 2.3 58.2 1.0
O O:HOH531 2.4 65.5 1.0
OD1 O:ASN200 2.5 57.2 1.0
O O:THR138 2.5 45.5 1.0
C O:VAL201 3.4 49.6 1.0
CG O:ASN200 3.5 58.9 1.0
C O:THR138 3.6 47.2 1.0
ND2 O:ASN200 4.0 58.1 1.0
N O:VAL201 4.2 47.4 1.0
N O:ALA202 4.3 44.4 1.0
CA O:ALA202 4.3 49.5 1.0
CA O:VAL201 4.4 48.0 1.0
N O:SER139 4.5 50.7 1.0
CA O:SER139 4.5 50.8 1.0
CA O:THR138 4.5 54.2 1.0
C O:ASN200 4.5 46.5 1.0
CB O:THR138 4.6 51.6 1.0
OD2 O:ASP141 4.7 77.0 1.0
O O:THR140 4.7 48.6 1.0
CB O:ASN200 4.8 53.4 1.0
O O:ASN200 4.9 40.4 1.0

Calcium binding site 4 out of 9 in 5zzn

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Calcium binding site 4 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Ca209

b:93.2
occ:1.00
 O F:HOH204 2.2 58.6 1.0
O V:HOH365 2.3 68.4 1.0
O V:HOH325 2.4 72.4 1.0
O V:HOH387 2.6 63.7 1.0
O A:HOH525 2.8 52.8 1.0
OE2 V:GLU2 2.8 67.5 1.0
OE1 V:GLU2 3.0 65.4 1.0
CD V:GLU2 3.3 58.5 1.0
O F:ARG45 4.0 44.8 1.0
O V:DMS204 4.2 90.6 1.0
OXT F:ARG45 4.4 51.5 1.0
OE2 V:GLU23 4.5 62.9 1.0
C F:ARG45 4.7 49.8 1.0
O E:HOH211 4.7 30.9 0.5
CB A:ALA309 4.8 38.8 1.0
CG V:GLU2 4.8 51.8 1.0
O V:DMS205 4.9 89.4 1.0
O A:ALA309 5.0 35.4 1.0
OE1 V:GLU23 5.0 82.0 1.0

Calcium binding site 5 out of 9 in 5zzn

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Calcium binding site 5 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Ca402

b:39.8
occ:1.00
 CA1 a:OEX402 0.0 39.8 1.0
O a:HOH559 2.3 38.0 1.0
O1 a:OEX402 2.4 30.8 1.0
O5 a:OEX402 2.5 34.6 1.0
O2 a:OEX402 2.5 33.8 1.0
O a:HOH592 2.5 35.7 1.0
OD2 a:ASP170 2.5 41.7 1.0
O a:ALA344 2.5 43.0 1.0
OE1 a:GLU189 3.0 38.2 1.0
MN2 a:OEX402 3.3 33.1 1.0
CG a:ASP170 3.3 38.8 1.0
MN1 a:OEX402 3.4 31.9 1.0
MN3 a:OEX402 3.4 34.2 1.0
C a:ALA344 3.4 47.0 1.0
OD1 a:ASP170 3.6 43.8 1.0
OXT a:ALA344 3.8 42.9 1.0
MN4 a:OEX402 3.9 41.4 1.0
O a:HOH518 3.9 53.0 1.0
O3 a:OEX402 3.9 28.6 1.0
CD a:GLU189 3.9 39.7 1.0
O4 a:OEX402 4.1 36.0 1.0
OE2 a:GLU189 4.1 31.0 1.0
NH1 c:ARG357 4.5 42.4 1.0
CB a:ASP170 4.6 38.2 1.0
OE1 a:GLN165 4.6 43.1 1.0
O a:HOH530 4.6 39.1 1.0
NH2 c:ARG357 4.7 37.5 1.0
OH a:TYR161 4.7 37.9 1.0
CA a:ALA344 4.7 42.9 1.0
O a:HOH590 4.8 36.2 1.0
OD1 a:ASP342 4.9 30.8 1.0

Calcium binding site 6 out of 9 in 5zzn

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Calcium binding site 6 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Ca604

b:63.9
occ:1.00
 O b:HOH809 2.2 63.3 1.0
O b:HOH857 2.3 67.5 1.0
O o:HOH471 2.4 60.8 1.0
O b:HOH897 2.4 61.6 1.0
OD1 b:ASN438 2.5 44.0 1.0
O b:HOH770 2.6 38.0 1.0
CG b:ASN438 3.7 37.9 1.0
OE2 b:GLU435 4.0 84.6 1.0
ND2 b:ASN438 4.5 42.5 1.0
CA b:ASN438 4.6 34.9 1.0
O b:SER439 4.6 34.7 1.0
CB b:ASN438 4.7 35.8 1.0
O b:HOH789 4.7 58.1 1.0
C b:ASN438 4.9 33.3 1.0
CD b:GLU435 4.9 67.3 1.0
OE2 o:GLU181 4.9 78.1 1.0
O b:THR434 4.9 37.7 1.0

Calcium binding site 7 out of 9 in 5zzn

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Calcium binding site 7 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Ca501

b:62.4
occ:1.00
 OE1 c:GLU29 2.4 50.9 1.0
OG c:SER30 2.4 60.4 1.0
O c:THR24 2.4 56.3 1.0
OD1 c:ASP27 2.5 51.0 1.0
O c:PHE22 2.6 60.8 1.0
O c:HOH750 2.6 52.4 1.0
OD2 c:ASP27 2.8 52.5 1.0
CG c:ASP27 3.0 53.4 1.0
C c:PHE22 3.5 57.4 1.0
CD c:GLU29 3.5 56.5 1.0
CB c:SER30 3.5 51.7 1.0
C c:THR24 3.7 58.7 1.0
O c:HOH615 4.1 43.9 1.0
N c:SER30 4.1 47.5 1.0
OE2 c:GLU29 4.2 63.2 1.0
N c:ALA23 4.2 55.2 1.0
N c:THR24 4.3 69.4 1.0
CA c:PHE22 4.3 60.7 1.0
CA c:SER30 4.4 48.9 1.0
C c:ALA23 4.4 62.5 1.0
CA c:ALA23 4.4 63.3 1.0
CB c:ASP27 4.5 54.7 1.0
N c:ASN25 4.6 53.0 1.0
CA c:ASN25 4.6 58.3 1.0
CA c:THR24 4.6 60.8 1.0
CB c:PHE22 4.6 62.3 1.0
CG c:GLU29 4.7 61.0 1.0
CB c:GLU29 4.8 50.4 1.0
C c:GLU29 5.0 47.5 1.0

Calcium binding site 8 out of 9 in 5zzn

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Calcium binding site 8 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


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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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Ca302

b:58.3
occ:1.00
 O o:HOH512 2.1 56.2 1.0
O o:VAL201 2.4 54.6 1.0
O o:THR138 2.4 61.5 1.0
OD1 o:ASN200 2.5 52.8 1.0
O o:HOH480 2.5 63.2 1.0
O o:HOH451 2.5 59.8 1.0
O o:HOH401 2.7 51.7 1.0
C o:VAL201 3.5 53.3 1.0
CG o:ASN200 3.5 57.0 1.0
C o:THR138 3.5 64.2 1.0
ND2 o:ASN200 3.9 53.5 1.0
N o:VAL201 4.2 54.5 1.0
CA o:SER139 4.3 61.5 1.0
N o:SER139 4.3 66.0 1.0
N o:ALA202 4.4 52.0 1.0
CA o:ALA202 4.4 53.1 1.0
CA o:THR138 4.4 55.6 1.0
CA o:VAL201 4.5 46.6 1.0
C o:ASN200 4.6 51.5 1.0
CB o:THR138 4.6 52.4 1.0
O o:THR140 4.6 55.6 1.0
OD1 o:ASP141 4.8 69.8 1.0
C o:SER139 4.9 56.2 1.0
CB o:ASN200 4.9 46.2 1.0
O o:ASN200 5.0 48.6 1.0

Calcium binding site 9 out of 9 in 5zzn

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Calcium binding site 9 out of 9 in the Crystal Structure of Photosystem II From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus


Mono view


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 From An Sqdg-Deficient Mutant of Thermosynechococcus Elongatus within 5.0Å range:
probe atom residue distance (Å) B Occ
v:Ca209

b:90.4
occ:1.00
 O v:HOH313 1.8 74.0 1.0
O f:HOH204 2.6 61.1 1.0
OE2 v:GLU2 2.8 60.7 1.0
O v:HOH357 3.0 72.5 1.0
OE1 v:GLU2 3.1 63.3 1.0
CD v:GLU2 3.4 62.4 1.0
O v:DMS204 4.1 96.3 1.0
OE1 v:GLU23 4.2 92.4 1.0
OXT f:ARG45 4.2 63.5 1.0
O f:ARG45 4.5 46.2 1.0
OE2 v:GLU23 4.5 74.5 1.0
CD v:GLU23 4.8 85.2 1.0
C f:ARG45 4.8 54.2 1.0
O a:ALA309 4.9 48.9 1.0
CG v:GLU2 4.9 55.1 1.0
CB a:ALA309 4.9 50.4 1.0
C1 v:DMS204 4.9 89.8 1.0

Reference:

Y.Nakajima, Y.Umena, R.Nagao, K.Endo, K.Kobayashi, F.Akita, M.Suga, H.Wada, T.Noguchi, J.R.Shen. Thylakoid Membrane Lipid Sulfoquinovosyl-Diacylglycerol (Sqdg) Is Required For Full Functioning of Photosystem II Inthermosynechococcus Elongatus. J. Biol. Chem. V. 293 14786 2018.
ISSN: ESSN 1083-351X
PubMed: 30076221
DOI: 10.1074/JBC.RA118.004304
Page generated: Sat Dec 12 05:56:24 2020

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