Magnesium in PDB 8xr6: Cryo-Em Structure of Cryptophyte Photosystem II

Enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem II

All present enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem II:
1.10.3.9;

Other elements in 8xr6:

The structure of Cryo-Em Structure of Cryptophyte Photosystem II also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 2 atoms
Iron (Fe) 6 atoms
Manganese (Mn) 8 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 224 in 8xr6

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Magnesium binding site 1 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg405

b:19.5
occ:1.00
MG a:CLA405 0.0 19.5 1.0
NA a:CLA405 1.9 19.5 1.0
ND a:CLA405 1.9 19.5 1.0
NB a:CLA405 2.0 19.5 1.0
NC a:CLA405 2.0 19.5 1.0
C4D a:CLA405 2.9 19.5 1.0
C4A a:CLA405 2.9 19.5 1.0
NE2 a:HIS198 2.9 19.9 1.0
C1C a:CLA405 3.0 19.5 1.0
C1B a:CLA405 3.0 19.5 1.0
C1A a:CLA405 3.1 19.5 1.0
C4B a:CLA405 3.1 19.5 1.0
C4C a:CLA405 3.1 19.5 1.0
C1D a:CLA405 3.2 19.5 1.0
CHB a:CLA405 3.3 19.5 1.0
CHC a:CLA405 3.4 19.5 1.0
CHA a:CLA405 3.4 19.5 1.0
CHD a:CLA405 3.6 19.5 1.0
CE a:MET183 3.6 19.6 1.0
CE1 a:HIS198 3.8 19.9 1.0
CD2 a:HIS198 3.9 19.9 1.0
CAB d:CLA404 4.1 19.9 1.0
C3D a:CLA405 4.2 19.5 1.0
C2B a:CLA405 4.2 19.5 1.0
C3B a:CLA405 4.2 19.5 1.0
C3A a:CLA405 4.3 19.5 1.0
C2D a:CLA405 4.3 19.5 1.0
C2C a:CLA405 4.3 19.5 1.0
C3C a:CLA405 4.3 19.5 1.0
C2A a:CLA405 4.3 19.5 1.0
CHC d:CLA404 4.6 19.9 1.0
SD a:MET183 4.7 19.6 1.0
C3B d:CLA404 4.8 19.9 1.0
CBB d:CLA404 4.8 19.9 1.0
CBD a:CLA405 4.9 19.5 1.0
CAA a:CLA405 4.9 19.5 1.0
ND1 a:HIS198 5.0 19.9 1.0
C4B d:CLA404 5.0 19.9 1.0

Magnesium binding site 2 out of 224 in 8xr6

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Magnesium binding site 2 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg406

b:20.6
occ:1.00
MG a:CLA406 0.0 20.6 1.0
NA a:CLA406 1.9 20.6 1.0
NB a:CLA406 1.9 20.6 1.0
ND a:CLA406 1.9 20.6 1.0
NC a:CLA406 2.0 20.6 1.0
C4D a:CLA406 2.9 20.6 1.0
C4A a:CLA406 2.9 20.6 1.0
O a:HOH518 3.0 50.0 1.0
C1C a:CLA406 3.0 20.6 1.0
C1B a:CLA406 3.0 20.6 1.0
C1A a:CLA406 3.0 20.6 1.0
C4B a:CLA406 3.1 20.6 1.0
C4C a:CLA406 3.1 20.6 1.0
C1D a:CLA406 3.2 20.6 1.0
CHB a:CLA406 3.3 20.6 1.0
CHC a:CLA406 3.4 20.6 1.0
CHA a:CLA406 3.4 20.6 1.0
CHD a:CLA406 3.6 20.6 1.0
CBB d:PHO403 3.6 21.0 1.0
C3D a:CLA406 4.2 20.6 1.0
C2B a:CLA406 4.2 20.6 1.0
C3B a:CLA406 4.2 20.6 1.0
C2C a:CLA406 4.3 20.6 1.0
C2D a:CLA406 4.3 20.6 1.0
C3A a:CLA406 4.3 20.6 1.0
C2A a:CLA406 4.3 20.6 1.0
C3C a:CLA406 4.3 20.6 1.0
CE2 a:PHE206 4.3 19.2 1.0
O a:HOH515 4.3 50.0 1.0
CBA a:CLA406 4.5 20.6 1.0
CD2 a:PHE206 4.8 19.2 1.0
CAB d:PHO403 4.8 21.0 1.0
CAA a:CLA406 4.9 20.6 1.0
CBD a:CLA406 4.9 20.6 1.0
C1 d:CLA404 4.9 19.9 1.0

Magnesium binding site 3 out of 224 in 8xr6

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Magnesium binding site 3 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg408

b:23.7
occ:1.00
MG a:CLA408 0.0 23.7 1.0
NA a:CLA408 1.9 23.7 1.0
ND a:CLA408 1.9 23.7 1.0
NB a:CLA408 2.0 23.7 1.0
NC a:CLA408 2.0 23.7 1.0
NE2 a:HIS118 2.9 20.4 1.0
C4D a:CLA408 2.9 23.7 1.0
C4A a:CLA408 2.9 23.7 1.0
C1C a:CLA408 3.0 23.7 1.0
C1B a:CLA408 3.0 23.7 1.0
C1A a:CLA408 3.0 23.7 1.0
C4B a:CLA408 3.1 23.7 1.0
C4C a:CLA408 3.1 23.7 1.0
C1D a:CLA408 3.2 23.7 1.0
CHB a:CLA408 3.3 23.7 1.0
CHA a:CLA408 3.4 23.7 1.0
CHC a:CLA408 3.4 23.7 1.0
CHD a:CLA408 3.5 23.7 1.0
CE1 a:HIS118 3.7 20.4 1.0
CG2 i:VAL12 3.8 24.2 1.0
CD2 a:HIS118 3.9 20.4 1.0
CG1 i:VAL8 3.9 25.7 1.0
C3D a:CLA408 4.2 23.7 1.0
C3B a:CLA408 4.2 23.7 1.0
C2B a:CLA408 4.2 23.7 1.0
C2D a:CLA408 4.3 23.7 1.0
C3A a:CLA408 4.3 23.7 1.0
C2C a:CLA408 4.3 23.7 1.0
C2A a:CLA408 4.3 23.7 1.0
C3C a:CLA408 4.3 23.7 1.0
CBA a:CLA408 4.6 23.7 1.0
ND1 a:HIS118 4.9 20.4 1.0
CBD a:CLA408 4.9 23.7 1.0
CG a:HIS118 5.0 20.4 1.0

Magnesium binding site 4 out of 224 in 8xr6

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Magnesium binding site 4 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg412

b:19.6
occ:1.00
MG a:CLA412 0.0 19.6 1.0
NA a:CLA412 1.9 19.6 1.0
ND a:CLA412 1.9 19.6 1.0
NB a:CLA412 2.0 19.6 1.0
NC a:CLA412 2.0 19.6 1.0
C4A a:CLA412 2.9 19.6 1.0
C4D a:CLA412 2.9 19.6 1.0
C1C a:CLA412 3.0 19.6 1.0
C1A a:CLA412 3.0 19.6 1.0
C1B a:CLA412 3.0 19.6 1.0
C4B a:CLA412 3.1 19.6 1.0
C4C a:CLA412 3.1 19.6 1.0
C1D a:CLA412 3.2 19.6 1.0
CHB a:CLA412 3.3 19.6 1.0
CHC a:CLA412 3.4 19.6 1.0
CHA a:CLA412 3.4 19.6 1.0
CHD a:CLA412 3.5 19.6 1.0
CBB a:PHO407 4.0 19.1 1.0
C3D a:CLA412 4.2 19.6 1.0
C2C a:CLA412 4.2 19.6 1.0
C2B a:CLA412 4.2 19.6 1.0
C3B a:CLA412 4.2 19.6 1.0
C3A a:CLA412 4.3 19.6 1.0
C3C a:CLA412 4.3 19.6 1.0
C2A a:CLA412 4.3 19.6 1.0
C2D a:CLA412 4.3 19.6 1.0
O a:HOH519 4.3 50.0 1.0
CBA a:CLA412 4.4 19.6 1.0
CAA a:CLA412 4.8 19.6 1.0
CG2 a:THR179 4.9 19.4 1.0
CBD a:CLA412 4.9 19.6 1.0

Magnesium binding site 5 out of 224 in 8xr6

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Magnesium binding site 5 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:19.5
occ:1.00
MG A:CLA405 0.0 19.5 1.0
NA A:CLA405 1.9 19.5 1.0
ND A:CLA405 1.9 19.5 1.0
NB A:CLA405 2.0 19.5 1.0
NC A:CLA405 2.0 19.5 1.0
C4D A:CLA405 2.9 19.5 1.0
C4A A:CLA405 2.9 19.5 1.0
NE2 A:HIS198 2.9 19.9 1.0
C1C A:CLA405 3.0 19.5 1.0
C1B A:CLA405 3.0 19.5 1.0
C1A A:CLA405 3.1 19.5 1.0
C4B A:CLA405 3.1 19.5 1.0
C4C A:CLA405 3.1 19.5 1.0
C1D A:CLA405 3.2 19.5 1.0
CHB A:CLA405 3.3 19.5 1.0
CHC A:CLA405 3.4 19.5 1.0
CHA A:CLA405 3.4 19.5 1.0
CHD A:CLA405 3.6 19.5 1.0
CE A:MET183 3.6 19.6 1.0
CE1 A:HIS198 3.8 19.9 1.0
CD2 A:HIS198 3.9 19.9 1.0
CAB D:CLA404 4.1 19.9 1.0
C3D A:CLA405 4.2 19.5 1.0
C2B A:CLA405 4.2 19.5 1.0
C3B A:CLA405 4.2 19.5 1.0
C3A A:CLA405 4.3 19.5 1.0
C2D A:CLA405 4.3 19.5 1.0
C2C A:CLA405 4.3 19.5 1.0
C3C A:CLA405 4.3 19.5 1.0
C2A A:CLA405 4.3 19.5 1.0
CHC D:CLA404 4.6 19.9 1.0
SD A:MET183 4.7 19.6 1.0
C3B D:CLA404 4.8 19.9 1.0
CBB D:CLA404 4.8 19.9 1.0
CBD A:CLA405 4.9 19.5 1.0
CAA A:CLA405 4.9 19.5 1.0
ND1 A:HIS198 5.0 19.9 1.0
C4B D:CLA404 5.0 19.9 1.0

Magnesium binding site 6 out of 224 in 8xr6

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Magnesium binding site 6 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:20.6
occ:1.00
MG A:CLA406 0.0 20.6 1.0
NA A:CLA406 1.9 20.6 1.0
NB A:CLA406 1.9 20.6 1.0
ND A:CLA406 1.9 20.6 1.0
NC A:CLA406 2.0 20.6 1.0
C4D A:CLA406 2.9 20.6 1.0
C4A A:CLA406 2.9 20.6 1.0
O A:HOH518 3.0 50.0 1.0
C1C A:CLA406 3.0 20.6 1.0
C1B A:CLA406 3.0 20.6 1.0
C1A A:CLA406 3.0 20.6 1.0
C4B A:CLA406 3.1 20.6 1.0
C4C A:CLA406 3.1 20.6 1.0
C1D A:CLA406 3.2 20.6 1.0
CHB A:CLA406 3.3 20.6 1.0
CHC A:CLA406 3.4 20.6 1.0
CHA A:CLA406 3.4 20.6 1.0
CHD A:CLA406 3.6 20.6 1.0
CBB D:PHO403 3.6 21.0 1.0
C3D A:CLA406 4.2 20.6 1.0
C2B A:CLA406 4.2 20.6 1.0
C3B A:CLA406 4.2 20.6 1.0
C2C A:CLA406 4.3 20.6 1.0
C2D A:CLA406 4.3 20.6 1.0
C3A A:CLA406 4.3 20.6 1.0
C2A A:CLA406 4.3 20.6 1.0
C3C A:CLA406 4.3 20.6 1.0
CE2 A:PHE206 4.3 19.2 1.0
O A:HOH515 4.3 50.0 1.0
CBA A:CLA406 4.5 20.6 1.0
CD2 A:PHE206 4.8 19.2 1.0
CAB D:PHO403 4.8 21.0 1.0
CAA A:CLA406 4.9 20.6 1.0
CBD A:CLA406 4.9 20.6 1.0
C1 D:CLA404 4.9 19.9 1.0

Magnesium binding site 7 out of 224 in 8xr6

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Magnesium binding site 7 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:23.7
occ:1.00
MG A:CLA408 0.0 23.7 1.0
NA A:CLA408 1.9 23.7 1.0
ND A:CLA408 1.9 23.7 1.0
NB A:CLA408 2.0 23.7 1.0
NC A:CLA408 2.0 23.7 1.0
NE2 A:HIS118 2.9 20.4 1.0
C4D A:CLA408 2.9 23.7 1.0
C4A A:CLA408 2.9 23.7 1.0
C1C A:CLA408 3.0 23.7 1.0
C1A A:CLA408 3.0 23.7 1.0
C1B A:CLA408 3.0 23.7 1.0
C4B A:CLA408 3.1 23.7 1.0
C4C A:CLA408 3.1 23.7 1.0
C1D A:CLA408 3.2 23.7 1.0
CHB A:CLA408 3.3 23.7 1.0
CHA A:CLA408 3.4 23.7 1.0
CHC A:CLA408 3.4 23.7 1.0
CHD A:CLA408 3.5 23.7 1.0
CE1 A:HIS118 3.7 20.4 1.0
CG2 I:VAL12 3.8 24.2 1.0
CD2 A:HIS118 3.9 20.4 1.0
CG1 I:VAL8 3.9 25.7 1.0
C3D A:CLA408 4.2 23.7 1.0
C3B A:CLA408 4.2 23.7 1.0
C2B A:CLA408 4.2 23.7 1.0
C2D A:CLA408 4.3 23.7 1.0
C3A A:CLA408 4.3 23.7 1.0
C2C A:CLA408 4.3 23.7 1.0
C2A A:CLA408 4.3 23.7 1.0
C3C A:CLA408 4.3 23.7 1.0
CBA A:CLA408 4.6 23.7 1.0
ND1 A:HIS118 4.9 20.4 1.0
CBD A:CLA408 4.9 23.7 1.0
CG A:HIS118 5.0 20.4 1.0

Magnesium binding site 8 out of 224 in 8xr6

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Magnesium binding site 8 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg412

b:19.6
occ:1.00
MG A:CLA412 0.0 19.6 1.0
NA A:CLA412 1.9 19.6 1.0
ND A:CLA412 1.9 19.6 1.0
NB A:CLA412 2.0 19.6 1.0
NC A:CLA412 2.0 19.6 1.0
C4A A:CLA412 2.9 19.6 1.0
C4D A:CLA412 2.9 19.6 1.0
C1C A:CLA412 3.0 19.6 1.0
C1A A:CLA412 3.0 19.6 1.0
C1B A:CLA412 3.0 19.6 1.0
C4B A:CLA412 3.1 19.6 1.0
C4C A:CLA412 3.1 19.6 1.0
C1D A:CLA412 3.2 19.6 1.0
CHB A:CLA412 3.3 19.6 1.0
CHC A:CLA412 3.4 19.6 1.0
CHA A:CLA412 3.4 19.6 1.0
CHD A:CLA412 3.5 19.6 1.0
CBB A:PHO407 4.0 19.1 1.0
C3D A:CLA412 4.2 19.6 1.0
C2C A:CLA412 4.2 19.6 1.0
C2B A:CLA412 4.2 19.6 1.0
C3B A:CLA412 4.2 19.6 1.0
C3A A:CLA412 4.3 19.6 1.0
C3C A:CLA412 4.3 19.6 1.0
C2A A:CLA412 4.3 19.6 1.0
C2D A:CLA412 4.3 19.6 1.0
O A:HOH519 4.3 50.0 1.0
CBA A:CLA412 4.4 19.6 1.0
CAA A:CLA412 4.8 19.6 1.0
CG2 A:THR179 4.9 19.4 1.0
CBD A:CLA412 4.9 19.6 1.0

Magnesium binding site 9 out of 224 in 8xr6

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Magnesium binding site 9 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg301

b:64.4
occ:1.00
MG 0:CLA301 0.0 64.4 1.0
NA 0:CLA301 1.9 64.4 1.0
NB 0:CLA301 1.9 64.4 1.0
ND 0:CLA301 1.9 64.4 1.0
NC 0:CLA301 2.0 64.4 1.0
O 0:ALA46 2.7 64.7 1.0
C4D 0:CLA301 2.9 64.4 1.0
C4A 0:CLA301 2.9 64.4 1.0
C1C 0:CLA301 3.0 64.4 1.0
C1A 0:CLA301 3.0 64.4 1.0
C1B 0:CLA301 3.0 64.4 1.0
C4B 0:CLA301 3.0 64.4 1.0
C4C 0:CLA301 3.1 64.4 1.0
C1D 0:CLA301 3.2 64.4 1.0
CHB 0:CLA301 3.3 64.4 1.0
CHC 0:CLA301 3.4 64.4 1.0
CHA 0:CLA301 3.4 64.4 1.0
CHD 0:CLA301 3.5 64.4 1.0
C9 0:LHG317 3.6 67.2 1.0
C 0:ALA46 3.9 64.7 1.0
C11 0:LHG317 4.1 67.2 1.0
C3D 0:CLA301 4.2 64.4 1.0
C3B 0:CLA301 4.2 64.4 1.0
C2A 0:CLA301 4.2 64.4 1.0
C2B 0:CLA301 4.2 64.4 1.0
C2C 0:CLA301 4.2 64.4 1.0
C3A 0:CLA301 4.2 64.4 1.0
C2D 0:CLA301 4.3 64.4 1.0
C3C 0:CLA301 4.3 64.4 1.0
CA 0:ALA46 4.5 64.7 1.0
CAA 0:CLA301 4.6 64.4 1.0
C10 0:LHG317 4.6 67.2 1.0
C8 0:LHG317 4.6 67.2 1.0
CD 0:PRO48 4.7 62.5 1.0
CBD 0:CLA301 4.9 64.4 1.0
N 0:MET47 4.9 62.5 1.0

Magnesium binding site 10 out of 224 in 8xr6

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Magnesium binding site 10 out of 224 in the Cryo-Em Structure of Cryptophyte Photosystem II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cryo-Em Structure of Cryptophyte Photosystem II within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Mg302

b:63.2
occ:1.00
MG 0:CLA302 0.0 63.2 1.0
NA 0:CLA302 1.9 63.2 1.0
NB 0:CLA302 1.9 63.2 1.0
ND 0:CLA302 1.9 63.2 1.0
NC 0:CLA302 2.0 63.2 1.0
OE2 0:GLU84 2.7 61.0 1.0
C4D 0:CLA302 2.9 63.2 1.0
C4A 0:CLA302 2.9 63.2 1.0
C1C 0:CLA302 3.0 63.2 1.0
C1A 0:CLA302 3.0 63.2 1.0
C1B 0:CLA302 3.0 63.2 1.0
C4B 0:CLA302 3.0 63.2 1.0
C20 0:II0314 3.1 65.4 1.0
C4C 0:CLA302 3.1 63.2 1.0
C1D 0:CLA302 3.2 63.2 1.0
CHB 0:CLA302 3.3 63.2 1.0
CHA 0:CLA302 3.4 63.2 1.0
CHC 0:CLA302 3.4 63.2 1.0
CHD 0:CLA302 3.5 63.2 1.0
CD 0:GLU84 3.8 61.0 1.0
C3D 0:CLA302 4.2 63.2 1.0
C2B 0:CLA302 4.2 63.2 1.0
C3B 0:CLA302 4.2 63.2 1.0
C2C 0:CLA302 4.3 63.2 1.0
C2D 0:CLA302 4.3 63.2 1.0
C3A 0:CLA302 4.3 63.2 1.0
CBA 0:CLA302 4.3 63.2 1.0
C2A 0:CLA302 4.3 63.2 1.0
C3C 0:CLA302 4.3 63.2 1.0
CG 0:GLU84 4.4 61.0 1.0
C14 0:II0314 4.4 65.4 1.0
O2A 0:CLA302 4.4 63.2 1.0
NE 0:ARG188 4.5 64.3 1.0
CGA 0:CLA302 4.8 63.2 1.0
OE1 0:GLU84 4.8 61.0 1.0
CAA 0:CLA302 4.8 63.2 1.0
NH2 0:ARG188 4.8 64.3 1.0
CBD 0:CLA302 4.9 63.2 1.0
C12 0:II0314 5.0 65.4 1.0
C4 0:CLA302 5.0 63.2 1.0

Reference:

K.Li, L.S.Zhao, Y.Z.Zhang, L.N.Liu. Cryo-Em Structure of Cryptophyte Photosystem II To Be Published.
Page generated: Sat Oct 5 07:48:17 2024

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