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Magnesium in PDB 8vu3: Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles

Enzymatic activity of Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles

All present enzymatic activity of Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles:
1.97.1.12;

Other elements in 8vu3:

The structure of Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles also contains other interesting chemical elements:

Iron (Fe) 36 atoms
Calcium (Ca) 3 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 288 in 8vu3

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Magnesium binding site 1 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:31.8
occ:1.00
MG A:CL0801 0.0 31.8 1.0
ND A:CL0801 2.0 33.2 1.0
NB A:CL0801 2.0 30.2 1.0
NC A:CL0801 2.1 25.5 1.0
NA A:CL0801 2.2 30.9 1.0
NE2 A:HIS680 2.8 30.2 1.0
C4D A:CL0801 2.9 27.4 1.0
C4B A:CL0801 3.0 32.1 1.0
C1B A:CL0801 3.0 30.1 1.0
C1D A:CL0801 3.1 29.2 1.0
C1C A:CL0801 3.1 24.7 1.0
C4A A:CL0801 3.1 27.7 1.0
C4C A:CL0801 3.2 29.2 1.0
C1A A:CL0801 3.2 30.5 1.0
CHB A:CL0801 3.4 26.4 1.0
CHC A:CL0801 3.4 18.2 1.0
CE1 A:HIS680 3.5 21.2 1.0
CHA A:CL0801 3.5 28.6 1.0
CHD A:CL0801 3.5 25.5 1.0
CHC B:CLA802 3.7 32.0 1.0
C4B B:CLA802 3.7 29.6 1.0
CAB B:CLA802 3.7 30.0 1.0
C3B B:CLA802 3.7 24.4 1.0
CD2 A:HIS680 3.9 34.0 1.0
C3D A:CL0801 4.2 29.2 1.0
C3B A:CL0801 4.3 31.3 1.0
C2D A:CL0801 4.3 30.3 1.0
C2B A:CL0801 4.4 23.7 1.0
NB B:CLA802 4.4 27.8 1.0
C3A A:CL0801 4.4 23.7 1.0
C3C A:CL0801 4.4 30.3 1.0
C2C A:CL0801 4.4 27.7 1.0
C1C B:CLA802 4.5 30.5 1.0
C2B B:CLA802 4.5 24.7 1.0
C2A A:CL0801 4.5 24.5 1.0
ND1 A:HIS680 4.7 24.3 1.0
C1B B:CLA802 4.8 22.6 1.0
CBB B:CLA802 4.8 30.4 1.0
CG A:HIS680 5.0 27.9 1.0

Magnesium binding site 2 out of 288 in 8vu3

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Magnesium binding site 2 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:44.2
occ:1.00
MG A:CLA802 0.0 44.2 1.0
ND A:CLA802 2.0 30.3 1.0
NB A:CLA802 2.1 33.0 1.0
NC A:CLA802 2.1 31.5 1.0
NA A:CLA802 2.2 39.9 1.0
C4D A:CLA802 2.9 29.8 1.0
SD A:MET688 2.9 44.1 1.0
C1B A:CLA802 3.0 32.5 1.0
C4B A:CLA802 3.0 29.7 1.0
C1D A:CLA802 3.1 36.9 1.0
C1C A:CLA802 3.1 31.1 1.0
C4A A:CLA802 3.1 35.6 1.0
C4C A:CLA802 3.1 34.8 1.0
C1A A:CLA802 3.2 37.1 1.0
NE1 B:TRP589 3.3 24.4 1.0
CHB A:CLA802 3.4 36.8 1.0
CHC A:CLA802 3.4 29.5 1.0
CHA A:CLA802 3.5 30.6 1.0
CHD A:CLA802 3.5 40.8 1.0
CE A:MET688 3.8 25.5 1.0
CG A:MET688 4.0 31.1 1.0
CE2 B:TRP589 4.0 25.6 1.0
CZ2 B:TRP589 4.0 24.8 1.0
C3D A:CLA802 4.2 31.1 1.0
CB A:MET688 4.3 28.1 1.0
C3B A:CLA802 4.3 28.3 1.0
C2D A:CLA802 4.4 33.4 1.0
C2B A:CLA802 4.4 26.0 1.0
CD1 B:TRP589 4.4 20.4 1.0
C3C A:CLA802 4.4 31.1 1.0
C2C A:CLA802 4.4 35.5 1.0
C3A A:CLA802 4.5 39.6 1.0
C2A A:CLA802 4.5 39.4 1.0
CMC B:CLA801 4.9 29.1 1.0
CBD A:CLA802 5.0 29.4 1.0

Magnesium binding site 3 out of 288 in 8vu3

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Magnesium binding site 3 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:41.0
occ:1.00
MG A:CLA803 0.0 41.0 1.0
ND A:CLA803 2.0 35.6 1.0
NB A:CLA803 2.0 30.7 1.0
NC A:CLA803 2.1 25.5 1.0
NA A:CLA803 2.2 29.0 1.0
C4D A:CLA803 2.9 26.5 1.0
C4B A:CLA803 3.0 25.5 1.0
C1B A:CLA803 3.1 23.6 1.0
C1C A:CLA803 3.1 24.3 1.0
C1D A:CLA803 3.1 21.5 1.0
C4C A:CLA803 3.2 24.7 1.0
CBB B:CLA803 3.2 8.2 1.0
C4A A:CLA803 3.2 23.4 1.0
C1A A:CLA803 3.2 26.7 1.0
CHC A:CLA803 3.4 22.1 1.0
CHA A:CLA803 3.5 23.7 1.0
CHB A:CLA803 3.5 24.7 1.0
CHD A:CLA803 3.5 24.8 1.0
CAB B:CLA803 4.0 23.0 1.0
C3D A:CLA803 4.1 21.9 1.0
C3B A:CLA803 4.3 28.2 1.0
CB B:ALA665 4.3 13.4 1.0
C2D A:CLA803 4.3 28.8 1.0
C2B A:CLA803 4.4 21.4 1.0
C2C A:CLA803 4.4 23.4 1.0
C3C A:CLA803 4.4 23.0 1.0
OD1 A:ASN604 4.5 33.9 1.0
C3A A:CLA803 4.5 24.8 1.0
C2A A:CLA803 4.5 26.3 1.0
C20 A:CL0801 4.7 24.0 1.0
C3B B:CLA803 4.7 25.3 1.0
C2 A:CL0801 4.8 32.4 1.0
CBD A:CLA803 4.9 24.8 1.0

Magnesium binding site 4 out of 288 in 8vu3

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Magnesium binding site 4 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:55.7
occ:1.00
MG A:CLA804 0.0 55.7 1.0
ND A:CLA804 2.0 60.3 1.0
NB A:CLA804 2.1 61.1 1.0
NC A:CLA804 2.1 59.1 1.0
NA A:CLA804 2.2 60.9 1.0
NE2 A:HIS52 2.8 53.5 1.0
C4D A:CLA804 2.9 58.9 1.0
C4B A:CLA804 3.0 60.7 1.0
C1B A:CLA804 3.1 59.1 1.0
C1C A:CLA804 3.1 60.8 1.0
C1D A:CLA804 3.1 59.1 1.0
C4A A:CLA804 3.2 58.8 1.0
C4C A:CLA804 3.2 60.1 1.0
C1A A:CLA804 3.2 61.7 1.0
CHC A:CLA804 3.4 59.6 1.0
CHB A:CLA804 3.4 55.2 1.0
CB J:PRO14 3.4 66.4 1.0
CHA A:CLA804 3.5 60.0 1.0
CHD A:CLA804 3.6 57.8 1.0
CG J:PRO14 3.6 65.8 1.0
CE1 A:HIS52 3.7 52.9 1.0
CD2 A:HIS52 3.7 50.0 1.0
C3D A:CLA804 4.1 56.2 1.0
C3B A:CLA804 4.3 62.7 1.0
C2D A:CLA804 4.4 56.3 1.0
C2B A:CLA804 4.4 61.7 1.0
C2C A:CLA804 4.4 62.7 1.0
C3C A:CLA804 4.5 62.3 1.0
C3A A:CLA804 4.5 61.2 1.0
CD J:PRO14 4.5 63.8 1.0
C2A A:CLA804 4.5 59.5 1.0
C29 J:BCR103 4.8 67.6 1.0
ND1 A:HIS52 4.8 53.0 1.0
CA J:PRO14 4.9 69.0 1.0
CG A:HIS52 4.9 50.9 1.0
CBD A:CLA804 5.0 58.5 1.0

Magnesium binding site 5 out of 288 in 8vu3

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Magnesium binding site 5 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:64.2
occ:1.00
MG A:CLA805 0.0 64.2 1.0
ND A:CLA805 2.0 60.9 1.0
NB A:CLA805 2.1 59.4 1.0
NC A:CLA805 2.1 60.1 1.0
NA A:CLA805 2.2 61.6 1.0
NE2 A:HIS56 2.7 53.4 1.0
C4D A:CLA805 2.9 59.9 1.0
C4B A:CLA805 3.0 57.8 1.0
C1B A:CLA805 3.1 60.6 1.0
C1C A:CLA805 3.1 59.2 1.0
C1D A:CLA805 3.1 58.1 1.0
C4A A:CLA805 3.1 61.6 1.0
C4C A:CLA805 3.2 59.4 1.0
C1A A:CLA805 3.2 56.3 1.0
CHC A:CLA805 3.4 57.9 1.0
CHB A:CLA805 3.4 61.3 1.0
CHA A:CLA805 3.5 55.6 1.0
CHD A:CLA805 3.6 58.3 1.0
CE1 A:HIS56 3.6 56.8 1.0
C7 A:CLA812 3.7 60.5 1.0
CD2 A:HIS56 3.7 52.8 1.0
C6 A:CLA812 4.1 60.8 1.0
C3D A:CLA805 4.2 58.2 1.0
C3B A:CLA805 4.3 59.8 1.0
C2D A:CLA805 4.4 55.3 1.0
C2B A:CLA805 4.4 60.3 1.0
C2C A:CLA805 4.4 59.4 1.0
C3C A:CLA805 4.4 61.0 1.0
C3A A:CLA805 4.5 56.5 1.0
C2A A:CLA805 4.5 55.9 1.0
C5 A:CLA812 4.7 61.9 1.0
C8 A:CLA812 4.7 63.3 1.0
ND1 A:HIS56 4.8 55.7 1.0
C10 A:CLA812 4.8 64.0 1.0
CG A:HIS56 4.8 53.2 1.0
CBD A:CLA805 5.0 53.6 1.0

Magnesium binding site 6 out of 288 in 8vu3

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Magnesium binding site 6 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:50.3
occ:1.00
MG A:CLA806 0.0 50.3 1.0
ND A:CLA806 2.0 34.6 1.0
NB A:CLA806 2.1 31.2 1.0
NC A:CLA806 2.1 31.6 1.0
NA A:CLA806 2.2 34.1 1.0
NE2 A:HIS76 2.7 55.4 1.0
C4D A:CLA806 2.9 32.2 1.0
C4B A:CLA806 3.0 29.9 1.0
CMB A:CLA831 3.0 45.6 1.0
C1B A:CLA806 3.1 35.9 1.0
C1C A:CLA806 3.1 35.6 1.0
C1D A:CLA806 3.1 33.9 1.0
C4A A:CLA806 3.1 36.9 1.0
C4C A:CLA806 3.2 34.8 1.0
C1A A:CLA806 3.2 36.5 1.0
CHC A:CLA806 3.4 35.4 1.0
CD2 A:HIS76 3.4 50.0 1.0
CHB A:CLA806 3.4 35.3 1.0
CHA A:CLA806 3.5 32.0 1.0
CHD A:CLA806 3.6 37.5 1.0
CE1 A:HIS76 3.8 54.7 1.0
C3D A:CLA806 4.2 32.1 1.0
C3B A:CLA806 4.3 35.3 1.0
C2D A:CLA806 4.4 30.0 1.0
C2B A:CLA806 4.4 36.2 1.0
C2C A:CLA806 4.4 39.1 1.0
C3C A:CLA806 4.4 36.9 1.0
C2B A:CLA831 4.4 42.4 1.0
C3A A:CLA806 4.5 38.5 1.0
C2A A:CLA806 4.5 41.4 1.0
CBB A:CLA831 4.6 40.9 1.0
CG A:HIS76 4.6 50.9 1.0
ND1 A:HIS76 4.8 57.2 1.0
CG2 A:ILE72 4.9 48.6 1.0
CBD A:CLA806 5.0 31.9 1.0
CD2 A:LEU356 5.0 36.5 1.0

Magnesium binding site 7 out of 288 in 8vu3

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Magnesium binding site 7 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg807

b:51.7
occ:1.00
MG A:CLA807 0.0 51.7 1.0
ND A:CLA807 2.0 46.6 1.0
NB A:CLA807 2.1 46.6 1.0
NC A:CLA807 2.1 48.9 1.0
NA A:CLA807 2.2 48.5 1.0
NE2 A:HIS79 2.7 53.5 1.0
C4D A:CLA807 2.9 42.0 1.0
C4B A:CLA807 3.0 44.6 1.0
C1B A:CLA807 3.1 47.5 1.0
C1C A:CLA807 3.1 46.2 1.0
C1D A:CLA807 3.1 46.7 1.0
C4A A:CLA807 3.1 45.8 1.0
C4C A:CLA807 3.2 46.3 1.0
C1A A:CLA807 3.2 44.6 1.0
CHC A:CLA807 3.4 41.4 1.0
CHB A:CLA807 3.4 43.8 1.0
C16 A:CLA807 3.5 42.1 1.0
CHA A:CLA807 3.5 41.7 1.0
CHD A:CLA807 3.6 44.4 1.0
CE1 A:HIS79 3.6 55.6 1.0
CD2 A:HIS79 3.7 51.6 1.0
C3D A:CLA807 4.1 46.1 1.0
C3B A:CLA807 4.3 46.5 1.0
C17 A:CLA807 4.3 47.3 1.0
C2D A:CLA807 4.4 45.2 1.0
C2B A:CLA807 4.4 47.7 1.0
C2C A:CLA807 4.4 49.1 1.0
C3C A:CLA807 4.4 48.3 1.0
C18 A:CLA807 4.5 52.0 1.0
C3A A:CLA807 4.5 51.2 1.0
C2A A:CLA807 4.5 52.0 1.0
C14 A:CLA807 4.6 50.6 1.0
C19 A:CLA807 4.6 50.9 1.0
C15 A:CLA807 4.7 48.0 1.0
ND1 A:HIS79 4.8 50.2 1.0
C13 A:CLA807 4.8 52.5 1.0
CG A:HIS79 4.8 51.0 1.0
CMA A:CLA806 4.9 41.9 1.0
CBD A:CLA807 5.0 47.7 1.0

Magnesium binding site 8 out of 288 in 8vu3

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Magnesium binding site 8 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:74.1
occ:1.00
MG A:CLA808 0.0 74.1 1.0
ND A:CLA808 2.0 67.1 1.0
NB A:CLA808 2.1 65.2 1.0
NC A:CLA808 2.1 63.6 1.0
NA A:CLA808 2.2 63.5 1.0
NE2 A:HIS93 2.9 61.7 1.0
C4D A:CLA808 2.9 62.2 1.0
C4B A:CLA808 3.0 65.2 1.0
C1C A:CLA808 3.1 65.5 1.0
C1B A:CLA808 3.1 62.9 1.0
C1D A:CLA808 3.1 64.6 1.0
C4A A:CLA808 3.2 63.0 1.0
C4C A:CLA808 3.2 62.5 1.0
C1A A:CLA808 3.2 60.9 1.0
CHC A:CLA808 3.4 66.5 1.0
CHB A:CLA808 3.5 63.8 1.0
CHA A:CLA808 3.5 63.1 1.0
CHD A:CLA808 3.6 62.8 1.0
CD2 A:HIS93 3.8 61.1 1.0
CE1 A:HIS93 3.9 64.4 1.0
C3D A:CLA808 4.2 62.3 1.0
C3B A:CLA808 4.3 63.1 1.0
C2D A:CLA808 4.4 64.3 1.0
C2B A:CLA808 4.4 61.4 1.0
C2C A:CLA808 4.4 66.4 1.0
C3C A:CLA808 4.5 64.0 1.0
C3A A:CLA808 4.5 62.5 1.0
C2A A:CLA808 4.5 60.5 1.0
CBD A:CLA808 5.0 63.6 1.0
ND1 A:HIS93 5.0 63.7 1.0

Magnesium binding site 9 out of 288 in 8vu3

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Magnesium binding site 9 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg809

b:56.0
occ:1.00
MG A:CLA809 0.0 56.0 1.0
ND A:CLA809 2.0 53.1 1.0
NB A:CLA809 2.1 51.5 1.0
NC A:CLA809 2.1 55.4 1.0
NA A:CLA809 2.2 55.1 1.0
OE1 A:GLN115 2.7 58.9 1.0
C4D A:CLA809 2.9 52.8 1.0
C4B A:CLA809 3.0 52.7 1.0
C1C A:CLA809 3.1 57.3 1.0
C1B A:CLA809 3.1 50.9 1.0
C1D A:CLA809 3.1 53.6 1.0
C4A A:CLA809 3.1 52.3 1.0
C1A A:CLA809 3.2 55.4 1.0
C4C A:CLA809 3.2 50.3 1.0
CHC A:CLA809 3.3 56.9 1.0
CHB A:CLA809 3.4 51.5 1.0
CD A:GLN115 3.5 56.8 1.0
CHA A:CLA809 3.5 52.9 1.0
CHD A:CLA809 3.6 49.8 1.0
NE2 A:GLN115 3.7 55.5 1.0
C6 A:CLA829 3.7 50.0 1.0
C4 A:CLA829 3.7 47.7 1.0
C3D A:CLA809 4.2 51.4 1.0
C3B A:CLA809 4.3 52.0 1.0
C2D A:CLA809 4.4 54.2 1.0
C2B A:CLA809 4.4 51.9 1.0
C2C A:CLA809 4.4 53.9 1.0
C3C A:CLA809 4.4 54.6 1.0
C2A A:CLA809 4.5 52.3 1.0
C3A A:CLA809 4.5 53.1 1.0
C3 A:CLA829 4.6 52.7 1.0
CG A:GLN115 4.7 58.8 1.0
C7 A:CLA829 4.7 51.2 1.0
C5 A:CLA829 4.7 54.1 1.0
O1A A:CLA829 4.8 59.5 1.0
CAA A:CLA809 5.0 58.8 1.0
CBD A:CLA809 5.0 55.1 1.0

Magnesium binding site 10 out of 288 in 8vu3

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Magnesium binding site 10 out of 288 in the Cryo-Em Structure of Cyanobacterial Psi with Bound Platinum Nanoparticles


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 Cyanobacterial Psi with Bound Platinum Nanoparticles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg810

b:54.6
occ:1.00
MG A:CLA810 0.0 54.6 1.0
ND A:CLA810 2.0 54.6 1.0
NB A:CLA810 2.1 57.8 1.0
NC A:CLA810 2.1 54.2 1.0
NA A:CLA810 2.2 57.3 1.0
OE1 A:GLN123 2.6 64.3 1.0
C4D A:CLA810 2.9 55.8 1.0
C4B A:CLA810 3.0 54.6 1.0
C1B A:CLA810 3.1 58.6 1.0
C1C A:CLA810 3.1 55.0 1.0
C1D A:CLA810 3.1 55.9 1.0
C4A A:CLA810 3.2 58.9 1.0
C4C A:CLA810 3.2 56.9 1.0
C1A A:CLA810 3.2 55.4 1.0
CHC A:CLA810 3.4 56.2 1.0
CHB A:CLA810 3.4 57.3 1.0
CHA A:CLA810 3.5 56.2 1.0
C19 A:CLA829 3.6 52.3 1.0
CHD A:CLA810 3.6 57.7 1.0
CD A:GLN123 3.6 63.4 1.0
C18 A:CLA829 4.1 51.8 1.0
C3D A:CLA810 4.2 56.6 1.0
C3B A:CLA810 4.3 57.7 1.0
C2D A:CLA810 4.4 55.6 1.0
C2B A:CLA810 4.4 59.0 1.0
CG A:GLN123 4.4 63.5 1.0
C2C A:CLA810 4.4 55.3 1.0
C3C A:CLA810 4.4 56.0 1.0
NE2 A:GLN123 4.5 64.8 1.0
C3A A:CLA810 4.5 61.4 1.0
C2A A:CLA810 4.5 59.3 1.0
CBB A:CLA809 4.8 57.8 1.0
C20 A:CLA829 4.9 52.3 1.0
CBD A:CLA810 5.0 59.5 1.0

Reference:

C.J.Gisriel, T.Malavath, G.W.Brudvig, L.M.Utschig. The Cryo-Em Structure of A Biohybrid Photosystem I Photocatalyst Reveals the Locations of Bound Platinum Nanoparticles To Be Published.
Page generated: Wed Nov 13 12:05:41 2024

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