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Magnesium in PDB 8iwy: Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value

Magnesium Binding Sites:

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value (pdb code 8iwy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 42 binding sites of Magnesium where determined in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value, PDB code: 8iwy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 42 in 8iwy

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Magnesium binding site 1 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:28.9
occ:1.00
MG G:CHL601 0.0 28.9 1.0
N G:LEU25 1.9 30.0 1.0
NB G:CHL601 2.0 26.2 1.0
ND G:CHL601 2.1 27.2 1.0
NC G:CHL601 2.1 26.9 1.0
NA G:CHL601 2.1 25.8 1.0
CA G:LEU25 2.7 26.6 1.0
C4D G:CHL601 3.0 23.2 1.0
C G:TYR24 3.0 23.1 1.0
C1B G:CHL601 3.1 23.6 1.0
C1C G:CHL601 3.1 23.6 1.0
C4A G:CHL601 3.1 23.8 1.0
C4B G:CHL601 3.1 23.7 1.0
C4C G:CHL601 3.1 22.8 1.0
C1D G:CHL601 3.2 24.0 1.0
C1A G:CHL601 3.2 27.5 1.0
CA G:TYR24 3.4 26.5 1.0
CHB G:CHL601 3.5 22.5 1.0
CHC G:CHL601 3.5 25.1 1.0
CHD G:CHL601 3.5 20.6 1.0
CHA G:CHL601 3.6 24.7 1.0
C G:LEU25 3.8 20.3 1.0
CB G:LEU25 3.8 20.1 1.0
CB G:TYR24 4.0 23.2 1.0
N G:GLY26 4.0 28.0 1.0
O G:TYR24 4.2 27.6 1.0
CD1 G:LEU25 4.2 21.1 1.0
C39 G:XAT617 4.3 22.2 1.0
CG G:LEU25 4.3 20.9 1.0
C3D G:CHL601 4.3 22.5 1.0
C2B G:CHL601 4.4 23.1 1.0
C2C G:CHL601 4.4 26.6 1.0
C3C G:CHL601 4.4 21.6 1.0
C3B G:CHL601 4.4 21.0 1.0
C2D G:CHL601 4.4 20.8 1.0
C3A G:CHL601 4.5 26.7 1.0
C2A G:CHL601 4.5 19.8 1.0
O G:LYS23 4.7 25.3 1.0
N G:TYR24 4.8 22.7 1.0
O G:LEU25 4.8 24.2 1.0
CG G:TYR24 4.9 22.5 1.0
CD2 G:TYR24 5.0 21.9 1.0

Magnesium binding site 2 out of 42 in 8iwy

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Magnesium binding site 2 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:27.8
occ:1.00
MG G:CLA602 0.0 27.8 1.0
NB G:CLA602 2.0 27.3 1.0
ND G:CLA602 2.0 24.7 1.0
NC G:CLA602 2.1 20.7 1.0
NA G:CLA602 2.1 22.3 1.0
OE2 G:GLU65 2.2 28.7 1.0
C4D G:CLA602 2.9 25.4 1.0
C1B G:CLA602 3.0 24.3 1.0
C4B G:CLA602 3.1 25.9 1.0
C4A G:CLA602 3.1 20.8 1.0
C1C G:CLA602 3.1 24.5 1.0
C1A G:CLA602 3.2 22.8 1.0
C4C G:CLA602 3.2 23.6 1.0
C1D G:CLA602 3.2 24.3 1.0
CD G:GLU65 3.2 23.1 1.0
CHC G:CLA602 3.4 21.2 1.0
CHB G:CLA602 3.4 23.2 1.0
C38 G:LUT616 3.4 23.7 1.0
CHA G:CLA602 3.5 22.3 1.0
CHD G:CLA602 3.6 20.3 1.0
NH2 G:ARG185 3.7 27.3 1.0
NE G:ARG185 3.8 27.6 1.0
CG G:GLU65 3.9 21.4 1.0
OE1 G:GLU65 4.0 28.0 1.0
CZ G:ARG185 4.0 27.2 1.0
C3D G:CLA602 4.3 22.8 1.0
C2B G:CLA602 4.3 25.3 1.0
C3B G:CLA602 4.3 21.1 1.0
C2C G:CLA602 4.4 20.2 1.0
C2D G:CLA602 4.4 26.6 1.0
C3C G:CLA602 4.4 22.0 1.0
C3A G:CLA602 4.4 22.8 1.0
C2A G:CLA602 4.5 21.8 1.0
CD G:ARG185 4.8 24.4 1.0
C25 G:LUT616 4.9 24.4 1.0
CBD G:CLA602 4.9 24.4 1.0
NH1 G:ARG185 5.0 26.2 1.0

Magnesium binding site 3 out of 42 in 8iwy

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Magnesium binding site 3 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:27.0
occ:1.00
MG G:CLA603 0.0 27.0 1.0
NE2 G:HIS68 1.9 25.8 1.0
NB G:CLA603 2.0 24.1 1.0
ND G:CLA603 2.0 23.8 1.0
NC G:CLA603 2.1 24.9 1.0
NA G:CLA603 2.1 28.2 1.0
CE1 G:HIS68 2.6 19.8 1.0
C4D G:CLA603 2.9 21.1 1.0
C1B G:CLA603 3.0 24.8 1.0
C4B G:CLA603 3.1 24.8 1.0
C4A G:CLA603 3.1 21.7 1.0
C1C G:CLA603 3.1 27.9 1.0
CD2 G:HIS68 3.1 24.5 1.0
C1D G:CLA603 3.2 26.1 1.0
C4C G:CLA603 3.2 23.1 1.0
C1A G:CLA603 3.2 21.4 1.0
CHB G:CLA603 3.4 25.5 1.0
CHC G:CLA603 3.5 17.5 1.0
CHA G:CLA603 3.5 27.9 1.0
CHD G:CLA603 3.6 20.2 1.0
ND1 G:HIS68 3.8 26.4 1.0
C8 G:CHL609 4.0 23.5 1.0
CG G:HIS68 4.1 26.6 1.0
C11 G:CHL609 4.2 27.8 1.0
C3D G:CLA603 4.3 22.5 1.0
C9 G:CHL609 4.3 23.2 1.0
C2B G:CLA603 4.3 22.9 1.0
C3B G:CLA603 4.3 19.1 1.0
C2C G:CLA603 4.3 22.7 1.0
C2D G:CLA603 4.4 18.9 1.0
C10 G:CHL609 4.4 21.9 1.0
C3C G:CLA603 4.4 21.7 1.0
C3A G:CLA603 4.4 28.0 1.0
C2A G:CLA603 4.5 22.4 1.0
CBD G:CLA603 5.0 21.1 1.0

Magnesium binding site 4 out of 42 in 8iwy

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Magnesium binding site 4 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg604

b:27.4
occ:1.00
MG G:CLA604 0.0 27.4 1.0
NB G:CLA604 2.0 28.5 1.0
ND G:CLA604 2.0 26.5 1.0
NC G:CLA604 2.1 26.1 1.0
NA G:CLA604 2.1 31.6 1.0
C4D G:CLA604 2.9 24.1 1.0
C1B G:CLA604 3.0 21.4 1.0
C4B G:CLA604 3.1 23.9 1.0
C4A G:CLA604 3.1 23.7 1.0
C1C G:CLA604 3.1 23.3 1.0
C1A G:CLA604 3.2 21.9 1.0
C4C G:CLA604 3.2 25.8 1.0
C1D G:CLA604 3.2 25.4 1.0
CHB G:CLA604 3.4 22.8 1.0
CHC G:CLA604 3.4 24.1 1.0
CHA G:CLA604 3.5 22.6 1.0
CHD G:CLA604 3.6 19.7 1.0
C24 G:NEX618 3.7 21.3 1.0
O23 G:NEX618 4.1 27.9 1.0
O G:GLY78 4.1 27.5 1.0
C3D G:CLA604 4.2 20.9 1.0
C2B G:CLA604 4.3 21.1 1.0
C3B G:CLA604 4.3 21.7 1.0
C2C G:CLA604 4.3 25.9 1.0
C2D G:CLA604 4.4 20.4 1.0
CA G:GLY78 4.4 23.3 1.0
C3C G:CLA604 4.4 23.5 1.0
C3A G:CLA604 4.4 23.5 1.0
C2A G:CLA604 4.5 23.5 1.0
C23 G:NEX618 4.5 22.5 1.0
C G:GLY78 4.6 19.8 1.0
C25 G:NEX618 4.9 18.9 1.0
CBD G:CLA604 4.9 21.6 1.0

Magnesium binding site 5 out of 42 in 8iwy

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Magnesium binding site 5 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg605

b:26.3
occ:1.00
MG G:CHL605 0.0 26.3 1.0
NB G:CHL605 2.0 22.6 1.0
ND G:CHL605 2.0 25.1 1.0
NA G:CHL605 2.1 25.1 1.0
NC G:CHL605 2.1 22.8 1.0
C4D G:CHL605 2.9 23.9 1.0
C1B G:CHL605 3.0 22.9 1.0
C1C G:CHL605 3.0 23.5 1.0
C4B G:CHL605 3.0 20.2 1.0
C4A G:CHL605 3.1 23.6 1.0
C1A G:CHL605 3.1 24.5 1.0
C4C G:CHL605 3.1 23.4 1.0
C1D G:CHL605 3.2 24.2 1.0
CHC G:CHL605 3.3 25.0 1.0
CHB G:CHL605 3.4 23.1 1.0
CHA G:CHL605 3.5 21.9 1.0
CHD G:CHL605 3.5 25.3 1.0
C3D G:CHL605 4.3 20.2 1.0
C2B G:CHL605 4.3 20.7 1.0
C2A G:CHL605 4.3 22.7 1.0
C3B G:CHL605 4.3 24.7 1.0
C2C G:CHL605 4.3 23.2 1.0
C3C G:CHL605 4.3 23.5 1.0
C2D G:CHL605 4.4 20.9 1.0
C3A G:CHL605 4.4 28.8 1.0
O G:HIS120 4.6 28.8 1.0
N G:HIS120 4.6 28.2 1.0
CAA G:CHL605 4.6 20.9 1.0
CBD G:CHL605 4.9 22.1 1.0

Magnesium binding site 6 out of 42 in 8iwy

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Magnesium binding site 6 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg606

b:27.6
occ:1.00
MG G:CHL606 0.0 27.6 1.0
NB G:CHL606 2.0 27.3 1.0
ND G:CHL606 2.0 27.9 1.0
NC G:CHL606 2.1 27.8 1.0
NA G:CHL606 2.1 28.1 1.0
C4D G:CHL606 3.0 21.0 1.0
C1B G:CHL606 3.0 24.8 1.0
C4A G:CHL606 3.1 21.9 1.0
C4B G:CHL606 3.1 22.5 1.0
C1C G:CHL606 3.1 24.0 1.0
C4C G:CHL606 3.1 24.5 1.0
C1D G:CHL606 3.2 24.2 1.0
C1A G:CHL606 3.2 27.7 1.0
CHB G:CHL606 3.4 23.5 1.0
CHC G:CHL606 3.5 25.8 1.0
CHA G:CHL606 3.5 20.4 1.0
CHD G:CHL606 3.5 22.6 1.0
C3D G:CHL606 4.3 25.8 1.0
C38 G:NEX618 4.3 20.4 1.0
C2B G:CHL606 4.3 23.9 1.0
C3B G:CHL606 4.3 22.6 1.0
C3C G:CHL606 4.4 21.9 1.0
C2C G:CHL606 4.4 28.2 1.0
C2D G:CHL606 4.4 20.0 1.0
C3A G:CHL606 4.4 21.1 1.0
CBA G:CLA604 4.4 22.3 1.0
C2A G:CHL606 4.5 22.7 1.0
O2A G:CLA604 4.6 26.7 1.0
CHB G:CLA604 4.7 22.8 1.0
NE2 G:GLN131 4.7 24.0 1.0
C25 G:NEX618 4.9 18.9 1.0
O24 G:NEX618 4.9 27.0 1.0
CBD G:CHL606 5.0 21.6 1.0
CGA G:CLA604 5.0 20.9 1.0

Magnesium binding site 7 out of 42 in 8iwy

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Magnesium binding site 7 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg607

b:30.8
occ:1.00
MG G:CHL607 0.0 30.8 1.0
NB G:CHL607 2.0 30.3 1.0
ND G:CHL607 2.0 29.0 1.0
NC G:CHL607 2.1 22.9 1.0
NA G:CHL607 2.1 27.3 1.0
C14 N:CHL601 2.1 78.2 1.0
C4D G:CHL607 3.0 25.4 1.0
C1B G:CHL607 3.0 24.8 1.0
C4B G:CHL607 3.1 20.6 1.0
C4A G:CHL607 3.1 26.6 1.0
C1C G:CHL607 3.1 23.1 1.0
C4C G:CHL607 3.1 27.4 1.0
C1D G:CHL607 3.2 22.2 1.0
C1A G:CHL607 3.2 25.4 1.0
CHC G:CHL607 3.4 20.4 1.0
CHB G:CHL607 3.5 27.4 1.0
CHA G:CHL607 3.5 22.3 1.0
CHD G:CHL607 3.5 20.6 1.0
C13 N:CHL601 3.6 29.3 1.0
C16 N:CHL601 3.9 37.0 1.0
C15 N:CHL601 4.1 20.6 1.0
OMC G:CHL606 4.1 33.0 1.0
C3D G:CHL607 4.3 21.1 1.0
C2B G:CHL607 4.3 24.6 1.0
C12 N:CHL601 4.3 30.4 1.0
C3B G:CHL607 4.3 22.5 1.0
C2C G:CHL607 4.4 23.1 1.0
C3C G:CHL607 4.4 17.9 1.0
C2D G:CHL607 4.4 21.8 1.0
C3A G:CHL607 4.4 22.8 1.0
C2A G:CHL607 4.4 18.9 1.0
C17 N:CHL601 4.9 16.7 1.0
CAA G:CHL607 5.0 21.6 1.0
CBD G:CHL607 5.0 22.9 1.0

Magnesium binding site 8 out of 42 in 8iwy

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Magnesium binding site 8 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg608

b:28.2
occ:1.00
MG G:CHL608 0.0 28.2 1.0
NB G:CHL608 2.0 24.1 1.0
ND G:CHL608 2.0 23.4 1.0
NA G:CHL608 2.1 27.6 1.0
NC G:CHL608 2.1 26.9 1.0
C4D G:CHL608 2.9 25.9 1.0
C1B G:CHL608 3.0 21.0 1.0
C4A G:CHL608 3.0 22.0 1.0
C1C G:CHL608 3.1 21.5 1.0
C4B G:CHL608 3.1 24.3 1.0
C4C G:CHL608 3.1 19.2 1.0
C1A G:CHL608 3.2 21.7 1.0
C1D G:CHL608 3.2 25.6 1.0
CHC G:CHL608 3.4 24.6 1.0
CHB G:CHL608 3.4 21.7 1.0
CHA G:CHL608 3.5 24.8 1.0
CZ G:PHE161 3.5 24.4 1.0
CHD G:CHL608 3.5 20.6 1.0
CE2 G:PHE161 3.7 22.0 1.0
CG1 G:VAL138 3.8 22.3 1.0
C3D G:CHL608 4.3 23.6 1.0
C2B G:CHL608 4.3 23.4 1.0
C2C G:CHL608 4.3 23.1 1.0
C3B G:CHL608 4.3 19.9 1.0
C3C G:CHL608 4.4 22.0 1.0
C2D G:CHL608 4.4 22.3 1.0
C3A G:CHL608 4.4 23.9 1.0
C2A G:CHL608 4.4 22.7 1.0
O G:VAL138 4.6 26.7 1.0
CE1 G:PHE161 4.8 20.6 1.0
CBA G:CHL608 4.8 19.4 1.0
CB G:ARG142 4.8 27.7 1.0
CBD G:CHL608 5.0 22.1 1.0

Magnesium binding site 9 out of 42 in 8iwy

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Magnesium binding site 9 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg609

b:27.1
occ:1.00
MG G:CHL609 0.0 27.1 1.0
NB G:CHL609 2.0 31.1 1.0
ND G:CHL609 2.0 25.6 1.0
NA G:CHL609 2.1 21.2 1.0
NC G:CHL609 2.1 27.3 1.0
C4D G:CHL609 2.9 20.8 1.0
C1B G:CHL609 3.0 22.7 1.0
C4B G:CHL609 3.0 26.2 1.0
C1C G:CHL609 3.0 21.9 1.0
C4A G:CHL609 3.1 26.8 1.0
C1A G:CHL609 3.1 25.9 1.0
C4C G:CHL609 3.1 23.8 1.0
C1D G:CHL609 3.2 18.8 1.0
CHC G:CHL609 3.3 27.7 1.0
CHB G:CHL609 3.4 25.2 1.0
CHA G:CHL609 3.5 22.0 1.0
CHD G:CHL609 3.5 21.8 1.0
O2A N:CHL601 4.1 31.3 1.0
CMD G:CLA603 4.1 22.0 1.0
OE2 G:GLU139 4.2 26.0 1.0
C3D G:CHL609 4.2 18.9 1.0
C2B G:CHL609 4.3 25.0 1.0
OE1 G:GLU139 4.3 25.9 1.0
C3B G:CHL609 4.3 24.7 1.0
C2C G:CHL609 4.3 25.9 1.0
C3A G:CHL609 4.3 22.8 1.0
C3C G:CHL609 4.3 19.6 1.0
C2D G:CHL609 4.4 22.4 1.0
C2A G:CHL609 4.4 16.2 1.0
CD G:GLU139 4.6 23.7 1.0
CBA G:CHL609 4.6 25.4 1.0
C1 N:CHL601 4.8 23.5 1.0
CGA N:CHL601 4.8 25.6 1.0
CAA G:CHL609 4.9 20.9 1.0
CBD G:CHL609 4.9 18.6 1.0
C2 N:CHL601 5.0 20.1 1.0

Magnesium binding site 10 out of 42 in 8iwy

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Magnesium binding site 10 out of 42 in the Cryo-Em Structure of Protonated Lhcii in Detergent Solution at Low pH Value


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 Protonated Lhcii in Detergent Solution at Low pH Value within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg610

b:25.8
occ:1.00
MG G:CLA610 0.0 25.8 1.0
NB G:CLA610 2.0 22.1 1.0
ND G:CLA610 2.0 26.3 1.0
NA G:CLA610 2.1 26.3 1.0
NC G:CLA610 2.1 27.3 1.0
C4D G:CLA610 2.9 22.6 1.0
C1B G:CLA610 3.0 21.0 1.0
C4B G:CLA610 3.0 27.9 1.0
C1C G:CLA610 3.1 20.3 1.0
C4A G:CLA610 3.1 24.2 1.0
C1A G:CLA610 3.2 23.9 1.0
C1D G:CLA610 3.2 22.6 1.0
C4C G:CLA610 3.2 24.8 1.0
NH1 G:ARG70 3.3 24.5 1.0
OE1 G:GLU180 3.3 30.4 1.0
CHC G:CLA610 3.4 22.6 1.0
CHB G:CLA610 3.5 23.2 1.0
CHA G:CLA610 3.5 25.9 1.0
CHD G:CLA610 3.6 19.3 1.0
C38 G:LUT615 3.8 23.1 1.0
CD G:GLU180 4.0 23.2 1.0
OE2 G:GLU180 4.1 28.2 1.0
C3D G:CLA610 4.2 18.8 1.0
C3B G:CLA610 4.3 18.3 1.0
C2B G:CLA610 4.3 25.8 1.0
C2C G:CLA610 4.3 26.7 1.0
C2D G:CLA610 4.3 21.7 1.0
C3C G:CLA610 4.4 22.5 1.0
C3A G:CLA610 4.4 21.3 1.0
C2A G:CLA610 4.5 22.3 1.0
CZ G:ARG70 4.6 23.4 1.0
O2A G:CLA610 4.7 28.9 1.0
C25 G:LUT615 4.9 21.6 1.0
CBD G:CLA610 4.9 21.6 1.0

Reference:

M.X.Ruan, H.Li, Y.Zhang, R.Q.Zhao, J.Zhang, Y.J.Wang, J.L.Gao, Z.Wang, Y.M.Wang, D.P.Sun, W.Ding, Y.X.Weng. Cryo-Em Structures of Lhcii in Photo-Active and Photo-Protecting States Reveal Allosteric Regulation of Light-Harvesting and Excess Energy-Dissipation To Be Published.
Page generated: Fri Oct 4 11:04:06 2024

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Mg in 7BPI
Mg in 7BOG
Mg in 7BPH
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