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Magnesium in PDB 7y7b: Cryo-Em Structure of Cryptophyte Photosystem I

Enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem I

All present enzymatic activity of Cryo-Em Structure of Cryptophyte Photosystem I:
1.97.1.12;

Other elements in 7y7b:

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

Iron (Fe) 12 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 274 in 7y7b

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Magnesium binding site 1 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg601

b:88.8
occ:1.00
MG 1:CLA601 0.0 88.8 1.0
NA 1:CLA601 1.9 87.4 1.0
ND 1:CLA601 1.9 87.7 1.0
NB 1:CLA601 1.9 88.4 1.0
NC 1:CLA601 2.0 87.5 1.0
O 1:ALA52 2.8 85.5 1.0
C4D 1:CLA601 2.9 86.8 1.0
C4A 1:CLA601 2.9 87.2 1.0
C1C 1:CLA601 3.0 87.6 1.0
C1A 1:CLA601 3.0 87.2 1.0
C1B 1:CLA601 3.0 87.4 1.0
C4B 1:CLA601 3.1 87.6 1.0
C4C 1:CLA601 3.1 86.3 1.0
C1D 1:CLA601 3.2 88.8 1.0
CHB 1:CLA601 3.3 86.0 1.0
CHA 1:CLA601 3.4 86.9 1.0
CHC 1:CLA601 3.4 87.0 1.0
CHD 1:CLA601 3.6 87.5 1.0
C 1:ALA52 3.9 87.0 1.0
O2A 1:CLA601 4.0 89.8 1.0
C3D 1:CLA601 4.2 87.3 1.0
C3B 1:CLA601 4.2 88.6 1.0
C2B 1:CLA601 4.2 88.4 1.0
C2C 1:CLA601 4.3 87.2 1.0
C3A 1:CLA601 4.3 86.7 1.0
C2D 1:CLA601 4.3 86.5 1.0
C2A 1:CLA601 4.3 87.0 1.0
C3C 1:CLA601 4.3 84.8 1.0
CA 1:ALA52 4.7 85.7 1.0
CAA 1:CLA601 4.8 86.5 1.0
N 1:ILE53 4.9 83.9 1.0
CBD 1:CLA601 4.9 87.1 1.0
CA 1:ILE53 4.9 82.9 1.0
CGA 1:CLA601 4.9 89.7 1.0
CD 1:PRO54 5.0 86.4 1.0
CG1 1:ILE53 5.0 84.6 1.0

Magnesium binding site 2 out of 274 in 7y7b

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Magnesium binding site 2 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg602

b:70.1
occ:1.00
MG 1:CLA602 0.0 70.1 1.0
NA 1:CLA602 1.9 65.5 1.0
ND 1:CLA602 1.9 67.8 1.0
NB 1:CLA602 2.0 62.7 1.0
NC 1:CLA602 2.0 63.3 1.0
OE2 1:GLU92 2.7 62.5 1.0
C4D 1:CLA602 2.9 63.5 1.0
C4A 1:CLA602 2.9 64.7 1.0
C1C 1:CLA602 3.0 62.1 1.0
C1B 1:CLA602 3.0 64.2 1.0
C1A 1:CLA602 3.0 63.6 1.0
C4B 1:CLA602 3.1 61.1 1.0
C4C 1:CLA602 3.1 63.7 1.0
C1D 1:CLA602 3.2 65.5 1.0
C15 1:II3615 3.2 71.1 1.0
CHB 1:CLA602 3.3 66.8 1.0
CHA 1:CLA602 3.4 60.1 1.0
CHC 1:CLA602 3.4 61.4 1.0
CHD 1:CLA602 3.6 64.5 1.0
CD 1:GLU92 3.6 66.5 1.0
C3D 1:CLA602 4.2 64.0 1.0
O2A 1:CLA602 4.2 63.9 1.0
C2B 1:CLA602 4.2 60.9 1.0
C3B 1:CLA602 4.2 62.8 1.0
C2D 1:CLA602 4.3 65.6 1.0
C2C 1:CLA602 4.3 64.0 1.0
C3A 1:CLA602 4.3 61.9 1.0
C3C 1:CLA602 4.3 64.1 1.0
C2A 1:CLA602 4.3 64.2 1.0
CG 1:GLU92 4.4 63.5 1.0
OE1 1:GLU92 4.4 67.3 1.0
C07 1:II3615 4.4 71.9 1.0
NH2 1:ARG197 4.6 71.6 1.0
NE 1:ARG197 4.6 67.0 1.0
C2 1:CLA602 4.7 67.3 1.0
CBA 1:CLA602 4.8 65.6 1.0
CBD 1:CLA602 4.9 60.4 1.0
CZ 1:ARG197 4.9 69.1 1.0
C1 1:CLA602 5.0 64.1 1.0

Magnesium binding site 3 out of 274 in 7y7b

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Magnesium binding site 3 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg603

b:67.1
occ:1.00
MG 1:CLA603 0.0 67.1 1.0
NA 1:CLA603 1.9 66.1 1.0
ND 1:CLA603 1.9 60.3 1.0
NB 1:CLA603 1.9 61.3 1.0
NC 1:CLA603 2.0 63.4 1.0
NE2 1:HIS95 2.5 61.5 1.0
C4D 1:CLA603 2.9 56.1 1.0
C4A 1:CLA603 2.9 61.8 1.0
C1C 1:CLA603 3.0 64.0 1.0
C1B 1:CLA603 3.0 61.2 1.0
C1A 1:CLA603 3.0 63.3 1.0
C4B 1:CLA603 3.1 61.4 1.0
C4C 1:CLA603 3.1 62.2 1.0
C1D 1:CLA603 3.2 63.3 1.0
CHB 1:CLA603 3.3 61.7 1.0
CHA 1:CLA603 3.4 59.9 1.0
CE1 1:HIS95 3.4 64.5 1.0
CHC 1:CLA603 3.4 64.7 1.0
CD2 1:HIS95 3.5 63.0 1.0
CHD 1:CLA603 3.6 63.0 1.0
C3D 1:CLA603 4.2 58.2 1.0
C2B 1:CLA603 4.2 62.9 1.0
C3B 1:CLA603 4.2 63.1 1.0
C2C 1:CLA603 4.3 62.1 1.0
C2D 1:CLA603 4.3 62.5 1.0
C3A 1:CLA603 4.3 60.4 1.0
C3C 1:CLA603 4.3 61.5 1.0
C2A 1:CLA603 4.3 62.7 1.0
ND1 1:HIS95 4.6 64.4 1.0
CG 1:HIS95 4.6 63.0 1.0
CBD 1:CLA603 4.9 61.1 1.0

Magnesium binding site 4 out of 274 in 7y7b

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Magnesium binding site 4 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg604

b:94.1
occ:1.00
MG 1:CLA604 0.0 94.1 1.0
NA 1:CLA604 1.9 92.3 1.0
NB 1:CLA604 1.9 90.9 1.0
ND 1:CLA604 1.9 90.7 1.0
NC 1:CLA604 2.0 92.2 1.0
OE1 1:GLN109 2.9 89.6 1.0
C4D 1:CLA604 2.9 89.5 1.0
C4A 1:CLA604 2.9 91.7 1.0
C1C 1:CLA604 3.0 91.2 1.0
C1B 1:CLA604 3.0 90.1 1.0
C1A 1:CLA604 3.0 91.6 1.0
C4B 1:CLA604 3.1 90.6 1.0
C4C 1:CLA604 3.1 89.3 1.0
C1D 1:CLA604 3.2 91.1 1.0
CHB 1:CLA604 3.3 91.0 1.0
CHC 1:CLA604 3.4 91.3 1.0
CHA 1:CLA604 3.4 90.0 1.0
CHD 1:CLA604 3.6 90.0 1.0
CD 1:GLN109 3.8 91.9 1.0
O2A 1:CLA604 4.2 91.3 1.0
C3D 1:CLA604 4.2 91.8 1.0
CGA 1:CLA604 4.2 94.9 1.0
CG 1:GLN109 4.2 91.8 1.0
C2B 1:CLA604 4.2 89.1 1.0
C3B 1:CLA604 4.2 89.2 1.0
C2C 1:CLA604 4.3 91.4 1.0
C2D 1:CLA604 4.3 91.6 1.0
C3A 1:CLA604 4.3 90.0 1.0
C2A 1:CLA604 4.3 89.3 1.0
C3C 1:CLA604 4.3 89.2 1.0
CBA 1:CLA604 4.4 91.6 1.0
O1A 1:CLA604 4.6 95.1 1.0
C38 1:II0617 4.6 86.3 1.0
CA 1:GLY105 4.7 89.9 1.0
O 1:GLY105 4.8 94.3 1.0
NE2 1:GLN109 4.9 92.0 1.0
CBD 1:CLA604 4.9 90.9 1.0
CAA 1:CLA604 5.0 90.7 1.0

Magnesium binding site 5 out of 274 in 7y7b

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Magnesium binding site 5 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg605

b:86.5
occ:1.00
MG 1:CLA605 0.0 86.5 1.0
ND 1:CLA605 1.9 83.9 1.0
NB 1:CLA605 1.9 84.1 1.0
NA 1:CLA605 1.9 83.0 1.0
NC 1:CLA605 2.0 84.3 1.0
C4D 1:CLA605 2.9 82.4 1.0
C4A 1:CLA605 3.0 80.9 1.0
C1C 1:CLA605 3.0 81.8 1.0
C1B 1:CLA605 3.0 82.9 1.0
C4B 1:CLA605 3.0 81.1 1.0
C1A 1:CLA605 3.1 81.2 1.0
C4C 1:CLA605 3.1 85.0 1.0
C1D 1:CLA605 3.1 82.9 1.0
OE1 1:GLN141 3.3 82.8 1.0
CHB 1:CLA605 3.3 79.5 1.0
CHA 1:CLA605 3.4 81.9 1.0
CHC 1:CLA605 3.4 81.6 1.0
CHD 1:CLA605 3.6 83.4 1.0
O2A 2:CLA611 3.8 70.5 1.0
C3D 1:CLA605 4.2 82.9 1.0
NE1 1:TRP145 4.2 80.2 1.0
C3B 1:CLA605 4.2 80.7 1.0
C2B 1:CLA605 4.2 80.2 1.0
C2D 1:CLA605 4.3 82.1 1.0
C2C 1:CLA605 4.3 80.9 1.0
C3A 1:CLA605 4.3 80.7 1.0
C3C 1:CLA605 4.3 82.2 1.0
C2A 1:CLA605 4.4 81.8 1.0
CD 1:GLN141 4.4 82.9 1.0
CGA 2:CLA611 4.4 73.8 1.0
O1A 2:CLA611 4.5 71.4 1.0
C27 1:II0617 4.7 86.3 1.0
CD1 1:TRP145 4.9 79.9 1.0
CBD 1:CLA605 4.9 83.3 1.0
CG 1:GLN141 4.9 82.7 1.0

Magnesium binding site 6 out of 274 in 7y7b

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Magnesium binding site 6 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg606

b:85.0
occ:1.00
MG 1:CLA606 0.0 85.0 1.0
NA 1:CLA606 1.9 77.4 1.0
ND 1:CLA606 1.9 78.7 1.0
NB 1:CLA606 2.0 75.6 1.0
NC 1:CLA606 2.0 78.7 1.0
C4D 1:CLA606 2.9 77.0 1.0
C4A 1:CLA606 2.9 76.3 1.0
C1C 1:CLA606 3.0 77.2 1.0
C1B 1:CLA606 3.0 75.6 1.0
C1A 1:CLA606 3.0 76.1 1.0
C4B 1:CLA606 3.1 75.3 1.0
C4C 1:CLA606 3.1 76.2 1.0
C1D 1:CLA606 3.2 76.7 1.0
NE2 1:HIS130 3.2 78.1 1.0
CHB 1:CLA606 3.3 76.4 1.0
CHA 1:CLA606 3.4 75.7 1.0
CHC 1:CLA606 3.4 75.6 1.0
CHD 1:CLA606 3.6 78.0 1.0
CE1 1:HIS130 4.0 80.8 1.0
CD2 1:HIS130 4.1 81.3 1.0
C3D 1:CLA606 4.2 77.7 1.0
C2B 1:CLA606 4.2 75.5 1.0
C3B 1:CLA606 4.2 76.1 1.0
C2C 1:CLA606 4.3 76.1 1.0
C2D 1:CLA606 4.3 76.4 1.0
C3A 1:CLA606 4.3 76.6 1.0
C3C 1:CLA606 4.3 76.0 1.0
C2A 1:CLA606 4.3 76.2 1.0
CBA 1:CLA606 4.7 78.1 1.0
CBD 1:CLA606 4.9 76.7 1.0

Magnesium binding site 7 out of 274 in 7y7b

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Magnesium binding site 7 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg607

b:65.1
occ:1.00
MG 1:CLA607 0.0 65.1 1.0
NA 1:CLA607 1.9 63.8 1.0
ND 1:CLA607 1.9 63.3 1.0
NB 1:CLA607 2.0 66.1 1.0
NC 1:CLA607 2.0 67.2 1.0
OE2 1:GLU150 2.6 65.3 1.0
C4D 1:CLA607 2.9 63.7 1.0
C4A 1:CLA607 2.9 62.2 1.0
C1C 1:CLA607 3.0 64.4 1.0
C1B 1:CLA607 3.0 65.9 1.0
C1A 1:CLA607 3.0 66.0 1.0
C4B 1:CLA607 3.1 63.4 1.0
C4C 1:CLA607 3.1 66.1 1.0
C1D 1:CLA607 3.2 63.4 1.0
CHB 1:CLA607 3.3 63.7 1.0
CHA 1:CLA607 3.4 63.3 1.0
CHC 1:CLA607 3.4 63.3 1.0
CHD 1:CLA607 3.6 64.4 1.0
CD 1:GLU150 3.7 69.9 1.0
CMD 1:CLA603 3.8 61.4 1.0
C3D 1:CLA607 4.2 64.0 1.0
CG 1:GLU150 4.2 67.6 1.0
C2B 1:CLA607 4.2 63.2 1.0
C3B 1:CLA607 4.2 61.5 1.0
C2C 1:CLA607 4.3 63.5 1.0
C2D 1:CLA607 4.3 63.7 1.0
C3A 1:CLA607 4.3 61.9 1.0
C3C 1:CLA607 4.3 63.2 1.0
C2A 1:CLA607 4.3 64.2 1.0
CB 1:GLU150 4.7 62.3 1.0
C2D 1:CLA603 4.8 62.5 1.0
OE1 1:GLU150 4.8 71.1 1.0
CBA 1:CLA607 4.8 65.3 1.0
OBD 1:CLA603 4.9 64.5 1.0
CBD 1:CLA607 4.9 61.6 1.0

Magnesium binding site 8 out of 274 in 7y7b

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Magnesium binding site 8 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg608

b:80.3
occ:1.00
MG 1:CLA608 0.0 80.3 1.0
NA 1:CLA608 1.9 78.1 1.0
ND 1:CLA608 2.0 80.0 1.0
NB 1:CLA608 2.0 76.7 1.0
NC 1:CLA608 2.0 78.7 1.0
C19 1:II0614 2.9 82.5 1.0
C4D 1:CLA608 2.9 77.6 1.0
C4A 1:CLA608 2.9 79.2 1.0
OE2 1:GLU192 3.0 77.0 1.0
C1B 1:CLA608 3.0 76.8 1.0
C1C 1:CLA608 3.0 76.2 1.0
C1A 1:CLA608 3.0 77.7 1.0
C4B 1:CLA608 3.1 76.8 1.0
C4C 1:CLA608 3.1 76.1 1.0
C1D 1:CLA608 3.2 79.4 1.0
CHB 1:CLA608 3.3 77.5 1.0
CHA 1:CLA608 3.4 76.5 1.0
CHC 1:CLA608 3.5 77.3 1.0
CHD 1:CLA608 3.5 77.4 1.0
NH1 1:ARG97 3.6 72.7 1.0
CD 1:GLU192 4.0 77.5 1.0
C3D 1:CLA608 4.2 76.9 1.0
C2B 1:CLA608 4.2 79.4 1.0
C3B 1:CLA608 4.2 76.8 1.0
C13 1:II0614 4.3 83.1 1.0
O2A 1:CLA608 4.3 82.4 1.0
C2D 1:CLA608 4.3 78.8 1.0
C3A 1:CLA608 4.3 79.6 1.0
C2C 1:CLA608 4.3 75.9 1.0
C2 1:CLA608 4.3 80.0 1.0
C3C 1:CLA608 4.3 77.0 1.0
C2A 1:CLA608 4.3 78.4 1.0
OE1 1:GLU192 4.7 78.0 1.0
CG 1:GLU192 4.8 74.0 1.0
C21 1:II0614 4.8 83.2 1.0
CZ 1:ARG97 4.9 71.9 1.0
C1 1:CLA608 4.9 81.8 1.0
CBD 1:CLA608 4.9 76.8 1.0
C09 1:II0614 5.0 83.8 1.0

Magnesium binding site 9 out of 274 in 7y7b

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Magnesium binding site 9 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg609

b:88.4
occ:1.00
MG 1:CLA609 0.0 88.4 1.0
NA 1:CLA609 1.9 84.1 1.0
ND 1:CLA609 1.9 83.6 1.0
NB 1:CLA609 2.0 85.0 1.0
NC 1:CLA609 2.0 84.8 1.0
C4D 1:CLA609 2.9 83.6 1.0
C4A 1:CLA609 2.9 83.2 1.0
C1C 1:CLA609 3.0 83.1 1.0
C1A 1:CLA609 3.0 83.2 1.0
C1B 1:CLA609 3.0 84.5 1.0
C4B 1:CLA609 3.1 84.4 1.0
C4C 1:CLA609 3.1 83.4 1.0
C1D 1:CLA609 3.2 83.3 1.0
CHB 1:CLA609 3.3 83.7 1.0
CHA 1:CLA609 3.4 83.0 1.0
CHC 1:CLA609 3.4 83.4 1.0
CHD 1:CLA609 3.6 84.2 1.0
C3D 1:CLA609 4.2 83.5 1.0
C2B 1:CLA609 4.2 84.8 1.0
C3B 1:CLA609 4.2 84.7 1.0
C2C 1:CLA609 4.3 82.0 1.0
C2D 1:CLA609 4.3 82.0 1.0
C3A 1:CLA609 4.3 83.6 1.0
C2A 1:CLA609 4.3 84.2 1.0
C3C 1:CLA609 4.3 81.4 1.0
NZ 1:LYS194 4.7 77.1 1.0
CMD 1:KC2610 4.8 85.0 1.0
CBD 1:CLA609 4.9 82.8 1.0
CAA 1:CLA609 4.9 83.2 1.0

Magnesium binding site 10 out of 274 in 7y7b

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Magnesium binding site 10 out of 274 in the Cryo-Em Structure of Cryptophyte Photosystem I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg610

b:90.0
occ:1.00
MG 1:KC2610 0.0 90.0 1.0
ND 1:KC2610 1.9 86.1 1.0
NA 1:KC2610 2.1 86.2 1.0
NC 1:KC2610 2.1 86.9 1.0
NB 1:KC2610 2.1 85.5 1.0
C4D 1:KC2610 2.7 84.3 1.0
OD1 1:ASN195 3.0 76.6 1.0
C1D 1:KC2610 3.0 85.8 1.0
C1A 1:KC2610 3.1 86.0 1.0
C4C 1:KC2610 3.1 85.6 1.0
C4A 1:KC2610 3.1 86.0 1.0
C1C 1:KC2610 3.1 85.3 1.0
C1B 1:KC2610 3.1 85.1 1.0
C4B 1:KC2610 3.2 84.7 1.0
CHA 1:KC2610 3.3 85.1 1.0
CHD 1:KC2610 3.5 84.7 1.0
CHB 1:KC2610 3.5 84.8 1.0
CHC 1:KC2610 3.6 84.9 1.0
CG 1:ASN195 4.0 77.5 1.0
C3D 1:KC2610 4.0 84.3 1.0
C2D 1:KC2610 4.1 85.7 1.0
C2A 1:KC2610 4.3 85.8 1.0
C3C 1:KC2610 4.3 85.1 1.0
C3A 1:KC2610 4.3 87.6 1.0
C2C 1:KC2610 4.3 85.1 1.0
ND2 1:ASN195 4.3 76.7 1.0
C2B 1:KC2610 4.4 85.4 1.0
C3B 1:KC2610 4.4 85.4 1.0
C38 1:II0614 4.7 82.7 1.0
CBD 1:KC2610 4.8 85.3 1.0

Reference:

L.S.Zhao, P.Wang, K.Li, Q.B.Zhang, F.Y.He, C.Y.Li, H.N.Su, X.L.Chen, L.N.Liu, Y.Z.Zhang. Structural Basis and Evolution of the Photosystem I-Light-Harvesting Supercomplex of Cryptophyte Algae Plant Cell 2023.
ISSN: ESSN 1532-298X
DOI: 10.1093/PLCELL/KOAD087
Page generated: Thu Oct 3 13:31:04 2024

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