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Magnesium in PDB 8h2u: X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.

Enzymatic activity of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.

All present enzymatic activity of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.:
1.97.1.12;

Protein crystallography data

The structure of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii., PDB code: 8h2u was solved by H.Tanaka, H.Kubota-Kawai, Y.Misumi, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.74 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 194.57, 98.12, 210.13, 90, 94.56, 90
R / Rfree (%) 29.1 / 35.9

Other elements in 8h2u:

The structure of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Magnesium Binding Sites:

Magnesium binding site 1 out of 211 in 8h2u

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Magnesium binding site 1 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:115.0
occ:1.00
MG A:CLA801 0.0 115.0 1.0
NA A:CLA801 1.9 114.1 1.0
NC A:CLA801 2.0 110.4 1.0
NB A:CLA801 2.0 105.8 1.0
ND A:CLA801 2.0 121.5 1.0
C4D A:CLA801 2.9 131.0 1.0
C4A A:CLA801 2.9 120.4 1.0
C1C A:CLA801 3.0 102.0 1.0
C1A A:CLA801 3.0 125.5 1.0
C1B A:CLA801 3.0 108.7 1.0
C4B A:CLA801 3.1 96.2 1.0
C4C A:CLA801 3.1 111.1 1.0
C1D A:CLA801 3.2 117.8 1.0
CHB A:CLA801 3.3 114.5 1.0
CAB B:CLA805 3.4 92.9 1.0
CHA A:CLA801 3.4 138.5 1.0
CHC A:CLA801 3.4 93.2 1.0
CHD A:CLA801 3.5 113.7 1.0
NE2 A:HIS676 3.5 151.6 1.0
C3B B:CLA805 3.6 89.5 1.0
CE1 A:HIS676 3.6 149.6 1.0
C4B B:CLA805 3.9 91.4 1.0
CHC B:CLA805 4.1 90.4 1.0
CBB B:CLA805 4.2 96.9 1.0
C3D A:CLA801 4.2 130.9 1.0
C2B B:CLA805 4.2 87.3 1.0
C2B A:CLA801 4.2 107.8 1.0
C2C A:CLA801 4.2 105.1 1.0
C3A A:CLA801 4.3 131.0 1.0
C3B A:CLA801 4.3 100.0 1.0
C3C A:CLA801 4.3 108.0 1.0
C2D A:CLA801 4.3 120.7 1.0
C2A A:CLA801 4.3 132.6 1.0
CD2 A:HIS676 4.6 149.7 1.0
ND1 A:HIS676 4.7 142.2 1.0
NB B:CLA805 4.7 93.8 1.0
CMB B:CLA805 4.7 93.1 1.0
C1B B:CLA805 4.9 89.5 1.0
CBD A:CLA801 4.9 156.0 1.0
C1C B:CLA805 5.0 94.9 1.0

Magnesium binding site 2 out of 211 in 8h2u

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Magnesium binding site 2 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:80.7
occ:1.00
MG A:CLA802 0.0 80.7 1.0
NB A:CLA802 1.9 73.7 1.0
NC A:CLA802 2.0 78.7 1.0
NA A:CLA802 2.0 95.8 1.0
ND A:CLA802 2.0 83.2 1.0
CE1 A:HIS53 2.7 133.3 1.0
C4D A:CLA802 2.9 85.9 1.0
C1C A:CLA802 3.0 77.5 1.0
C4A A:CLA802 3.0 99.3 1.0
C1B A:CLA802 3.0 78.2 1.0
C1A A:CLA802 3.1 102.8 1.0
C4B A:CLA802 3.1 68.2 1.0
NE2 A:HIS53 3.1 134.8 1.0
C1D A:CLA802 3.1 90.5 1.0
C4C A:CLA802 3.2 83.0 1.0
CHB A:CLA802 3.4 87.0 1.0
CHC A:CLA802 3.4 71.2 1.0
CHA A:CLA802 3.4 95.1 1.0
CHD A:CLA802 3.5 85.8 1.0
ND1 A:HIS53 3.8 129.2 1.0
CB J:PRO12 4.0 113.5 1.0
CG J:PRO12 4.0 115.0 1.0
C3D A:CLA802 4.2 89.1 1.0
C2B A:CLA802 4.2 75.4 1.0
C3B A:CLA802 4.2 68.7 1.0
C2D A:CLA802 4.3 97.5 1.0
CD2 A:HIS53 4.3 128.8 1.0
C2C A:CLA802 4.3 81.6 1.0
C3A A:CLA802 4.3 106.8 1.0
C3C A:CLA802 4.3 85.8 1.0
C2A A:CLA802 4.4 108.8 1.0
CG A:HIS53 4.6 123.0 1.0
C22 J:LUT104 4.8 88.9 1.0
CBD A:CLA802 5.0 98.0 1.0

Magnesium binding site 3 out of 211 in 8h2u

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Magnesium binding site 3 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:91.4
occ:1.00
MG A:CLA803 0.0 91.4 1.0
NB A:CLA803 2.0 89.2 1.0
ND A:CLA803 2.0 84.9 1.0
NA A:CLA803 2.0 95.4 1.0
NC A:CLA803 2.0 84.7 1.0
C4D A:CLA803 2.9 88.5 1.0
C1C A:CLA803 3.0 83.2 1.0
C4A A:CLA803 3.0 93.6 1.0
C1A A:CLA803 3.1 97.5 1.0
C1B A:CLA803 3.1 89.7 1.0
C4B A:CLA803 3.1 90.3 1.0
CE1 A:HIS57 3.1 125.5 1.0
C1D A:CLA803 3.2 82.2 1.0
C4C A:CLA803 3.2 82.0 1.0
CHA A:CLA803 3.4 94.3 1.0
CHB A:CLA803 3.4 89.8 1.0
CHC A:CLA803 3.4 86.0 1.0
CHD A:CLA803 3.6 81.0 1.0
NE2 A:HIS57 3.7 125.9 1.0
CBB A:CLA802 3.9 74.8 1.0
ND1 A:HIS57 4.1 125.3 1.0
C3D A:CLA803 4.2 86.3 1.0
C2B A:CLA803 4.2 88.9 1.0
C2D A:CLA803 4.3 82.5 1.0
C3B A:CLA803 4.3 91.3 1.0
C2C A:CLA803 4.3 80.9 1.0
C3A A:CLA803 4.4 100.3 1.0
C3C A:CLA803 4.4 81.5 1.0
C2A A:CLA803 4.4 101.2 1.0
CBD A:CLA803 4.9 94.3 1.0
CD2 A:HIS57 4.9 130.7 1.0

Magnesium binding site 4 out of 211 in 8h2u

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Magnesium binding site 4 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:145.9
occ:1.00
MG A:CLA804 0.0 145.9 1.0
NB A:CLA804 2.0 145.1 1.0
ND A:CLA804 2.0 142.4 1.0
NC A:CLA804 2.0 140.9 1.0
NA A:CLA804 2.0 146.6 1.0
CE1 A:HIS77 2.4 110.9 1.0
NE2 A:HIS77 2.8 111.4 1.0
C4D A:CLA804 2.9 143.8 1.0
C1C A:CLA804 3.0 139.7 1.0
C4A A:CLA804 3.0 143.3 1.0
C1A A:CLA804 3.0 148.7 1.0
C1B A:CLA804 3.1 143.1 1.0
C4B A:CLA804 3.1 142.5 1.0
C1D A:CLA804 3.2 139.4 1.0
C4C A:CLA804 3.2 133.3 1.0
ND1 A:HIS77 3.3 116.8 1.0
CHA A:CLA804 3.4 146.6 1.0
CHB A:CLA804 3.4 146.0 1.0
CHC A:CLA804 3.4 144.3 1.0
CMB A:CLA829 3.5 112.6 1.0
CHD A:CLA804 3.6 131.7 1.0
CD2 A:HIS77 3.9 118.8 1.0
CBB A:CLA829 4.1 126.5 1.0
CG A:HIS77 4.1 123.5 1.0
C3D A:CLA804 4.2 145.8 1.0
C2B A:CLA804 4.2 132.3 1.0
C2D A:CLA804 4.3 147.1 1.0
C3B A:CLA804 4.3 135.7 1.0
C2C A:CLA804 4.3 130.3 1.0
C3A A:CLA804 4.3 142.5 1.0
C3C A:CLA804 4.4 131.4 1.0
C2A A:CLA804 4.4 146.2 1.0
CG1 A:VAL73 4.6 131.2 1.0
O A:VAL73 4.6 146.7 1.0
C2B A:CLA829 4.8 114.7 1.0
CBD A:CLA804 4.9 145.1 1.0
CAB A:CLA829 4.9 125.0 1.0

Magnesium binding site 5 out of 211 in 8h2u

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Magnesium binding site 5 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg805

b:122.9
occ:1.00
MG A:CLA805 0.0 122.9 1.0
NB A:CLA805 2.0 125.0 1.0
NA A:CLA805 2.0 122.3 1.0
ND A:CLA805 2.0 127.0 1.0
NC A:CLA805 2.0 129.3 1.0
NE2 A:GLN80 2.4 127.2 1.0
C4D A:CLA805 2.9 125.5 1.0
C4A A:CLA805 3.0 128.8 1.0
C1C A:CLA805 3.0 123.4 1.0
C1A A:CLA805 3.0 118.2 1.0
C1B A:CLA805 3.1 127.3 1.0
C4B A:CLA805 3.1 120.7 1.0
C1D A:CLA805 3.1 121.9 1.0
C4C A:CLA805 3.2 124.5 1.0
CD A:GLN80 3.3 127.0 1.0
CHB A:CLA805 3.4 130.3 1.0
CHA A:CLA805 3.4 121.2 1.0
CHC A:CLA805 3.4 118.8 1.0
OE1 A:GLN80 3.6 128.7 1.0
CHD A:CLA805 3.6 123.6 1.0
C3D A:CLA805 4.2 119.1 1.0
C2B A:CLA805 4.2 123.3 1.0
C2D A:CLA805 4.3 117.2 1.0
C3B A:CLA805 4.3 120.3 1.0
C2C A:CLA805 4.3 117.2 1.0
C3A A:CLA805 4.3 126.8 1.0
C2A A:CLA805 4.3 121.4 1.0
C3C A:CLA805 4.4 114.9 1.0
CMA A:CLA804 4.5 142.9 1.0
CG A:GLN80 4.6 123.5 1.0
CBD A:CLA805 4.9 117.9 1.0

Magnesium binding site 6 out of 211 in 8h2u

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Magnesium binding site 6 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg806

b:119.7
occ:1.00
MG A:CLA806 0.0 119.7 1.0
NB A:CLA806 1.9 116.0 1.0
ND A:CLA806 2.0 119.5 1.0
NC A:CLA806 2.0 114.1 1.0
NA A:CLA806 2.0 118.7 1.0
NE2 A:HIS94 2.9 110.4 1.0
C4D A:CLA806 2.9 123.4 1.0
C1C A:CLA806 3.0 113.1 1.0
C1B A:CLA806 3.0 117.0 1.0
C4A A:CLA806 3.0 113.2 1.0
C4B A:CLA806 3.1 114.9 1.0
C1A A:CLA806 3.1 114.8 1.0
C1D A:CLA806 3.1 112.4 1.0
C4C A:CLA806 3.2 108.2 1.0
CHB A:CLA806 3.4 114.1 1.0
CHA A:CLA806 3.4 121.2 1.0
CHC A:CLA806 3.4 113.9 1.0
CHD A:CLA806 3.6 111.8 1.0
CD2 A:HIS94 3.8 118.4 1.0
CE1 A:HIS94 3.9 113.6 1.0
C3D A:CLA806 4.2 115.5 1.0
C2B A:CLA806 4.2 124.0 1.0
C3B A:CLA806 4.2 120.4 1.0
C2D A:CLA806 4.3 105.4 1.0
C2C A:CLA806 4.3 101.8 1.0
C3C A:CLA806 4.4 97.6 1.0
C3A A:CLA806 4.4 113.0 1.0
C2A A:CLA806 4.4 112.3 1.0
CBD A:CLA806 4.9 123.9 1.0
ND1 A:HIS94 5.0 115.6 1.0
CG A:HIS94 5.0 120.0 1.0

Magnesium binding site 7 out of 211 in 8h2u

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Magnesium binding site 7 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg807

b:136.5
occ:1.00
MG A:CLA807 0.0 136.5 1.0
NB A:CLA807 2.0 133.8 1.0
ND A:CLA807 2.0 132.9 1.0
NC A:CLA807 2.0 126.6 1.0
NA A:CLA807 2.0 129.2 1.0
C4D A:CLA807 2.9 134.0 1.0
C1C A:CLA807 3.0 126.7 1.0
C4A A:CLA807 3.0 125.7 1.0
C1A A:CLA807 3.0 129.7 1.0
C1B A:CLA807 3.1 135.7 1.0
C4B A:CLA807 3.1 131.5 1.0
C4C A:CLA807 3.1 118.1 1.0
C1D A:CLA807 3.2 131.0 1.0
OE1 A:GLN116 3.2 125.2 1.0
CHA A:CLA807 3.4 134.9 1.0
CHB A:CLA807 3.4 130.3 1.0
CHC A:CLA807 3.4 129.6 1.0
CHD A:CLA807 3.6 123.3 1.0
CD A:GLN116 4.1 124.7 1.0
C3D A:CLA807 4.2 133.1 1.0
NE2 A:GLN116 4.2 117.7 1.0
C2B A:CLA807 4.2 136.5 1.0
C3B A:CLA807 4.2 138.5 1.0
C2D A:CLA807 4.3 133.2 1.0
C2C A:CLA807 4.3 123.2 1.0
C3A A:CLA807 4.3 128.3 1.0
C3C A:CLA807 4.3 117.6 1.0
C2A A:CLA807 4.3 129.8 1.0
O1A A:CLA807 4.8 131.3 1.0
CBD A:CLA807 4.9 138.1 1.0
O2A A:CLA827 4.9 154.6 1.0

Magnesium binding site 8 out of 211 in 8h2u

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Magnesium binding site 8 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg808

b:113.3
occ:1.00
MG A:CLA808 0.0 113.3 1.0
NB A:CLA808 2.0 115.0 1.0
NA A:CLA808 2.0 114.6 1.0
ND A:CLA808 2.0 114.0 1.0
NC A:CLA808 2.0 108.2 1.0
C4D A:CLA808 2.9 109.6 1.0
C4A A:CLA808 3.0 113.4 1.0
C1C A:CLA808 3.0 106.7 1.0
C1A A:CLA808 3.1 114.1 1.0
C1B A:CLA808 3.1 113.1 1.0
C4B A:CLA808 3.1 113.7 1.0
C1D A:CLA808 3.1 112.2 1.0
C4C A:CLA808 3.2 108.3 1.0
CHB A:CLA808 3.4 111.3 1.0
OE1 A:GLN124 3.4 109.2 1.0
CD A:GLN124 3.4 120.4 1.0
CHC A:CLA808 3.4 108.5 1.0
CHA A:CLA808 3.4 110.8 1.0
CHD A:CLA808 3.5 112.2 1.0
NE2 A:GLN124 3.6 127.6 1.0
CG A:GLN124 4.1 124.9 1.0
C3D A:CLA808 4.2 105.1 1.0
C2B A:CLA808 4.2 114.7 1.0
C2D A:CLA808 4.3 109.9 1.0
C3B A:CLA808 4.3 112.5 1.0
C2C A:CLA808 4.3 102.3 1.0
C3A A:CLA808 4.3 114.4 1.0
C3C A:CLA808 4.3 105.0 1.0
C2A A:CLA808 4.4 114.1 1.0
CBD A:CLA808 5.0 112.2 1.0

Magnesium binding site 9 out of 211 in 8h2u

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Magnesium binding site 9 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg809

b:134.6
occ:1.00
MG A:CLA809 0.0 134.6 1.0
NB A:CLA809 2.0 124.5 1.0
ND A:CLA809 2.0 130.9 1.0
NA A:CLA809 2.0 125.0 1.0
NC A:CLA809 2.0 126.1 1.0
C4D A:CLA809 2.9 126.0 1.0
C1C A:CLA809 3.0 123.1 1.0
C4A A:CLA809 3.0 118.2 1.0
NE2 A:HIS180 3.0 143.9 1.0
C1A A:CLA809 3.0 115.7 1.0
C1B A:CLA809 3.1 121.4 1.0
C4B A:CLA809 3.1 126.9 1.0
C1D A:CLA809 3.2 130.3 1.0
C4C A:CLA809 3.2 120.5 1.0
CHB A:CLA809 3.4 115.3 1.0
CHA A:CLA809 3.4 117.2 1.0
CHC A:CLA809 3.4 124.7 1.0
CHD A:CLA809 3.6 123.5 1.0
CE1 A:HIS180 3.9 139.6 1.0
CD2 A:HIS180 4.1 141.6 1.0
C3D A:CLA809 4.2 127.4 1.0
C2B A:CLA809 4.2 128.7 1.0
C3B A:CLA809 4.2 134.8 1.0
C2D A:CLA809 4.3 131.8 1.0
C2C A:CLA809 4.3 116.9 1.0
C3A A:CLA809 4.3 116.8 1.0
C2A A:CLA809 4.3 112.4 1.0
C3C A:CLA809 4.4 117.5 1.0
CBA A:CLA809 4.7 111.3 1.0
CBD A:CLA809 4.9 120.4 1.0

Magnesium binding site 10 out of 211 in 8h2u

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Magnesium binding site 10 out of 211 in the X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of X-Ray Structure of Photosystem I-Lhci Super Complex From Chlamydomonas Reinhardtii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg810

b:121.7
occ:1.00
MG A:CLA810 0.0 121.7 1.0
NB A:CLA810 1.9 123.1 1.0
NA A:CLA810 2.0 123.7 1.0
NC A:CLA810 2.0 126.4 1.0
ND A:CLA810 2.0 123.0 1.0
O1A A:CLA803 2.7 115.6 1.0
C4D A:CLA810 2.9 122.7 1.0
C4A A:CLA810 3.0 128.8 1.0
C1C A:CLA810 3.0 123.0 1.0
NE2 A:HIS182 3.0 145.8 1.0
C1B A:CLA810 3.0 128.3 1.0
C1A A:CLA810 3.1 123.7 1.0
C4B A:CLA810 3.1 119.1 1.0
CGA A:CLA803 3.1 117.9 1.0
C4C A:CLA810 3.1 130.1 1.0
C1D A:CLA810 3.2 125.1 1.0
CHB A:CLA810 3.3 129.6 1.0
CHC A:CLA810 3.4 115.7 1.0
CHA A:CLA810 3.5 123.4 1.0
CHD A:CLA810 3.6 129.9 1.0
O2A A:CLA803 3.7 114.3 1.0
CE1 A:HIS182 3.8 149.4 1.0
CBA A:CLA803 3.9 117.2 1.0
CD2 A:HIS182 4.0 144.4 1.0
O1A A:CLA810 4.1 118.5 1.0
C3D A:CLA810 4.2 118.1 1.0
C2B A:CLA810 4.2 128.3 1.0
C3B A:CLA810 4.2 124.3 1.0
C2C A:CLA810 4.3 128.8 1.0
C2D A:CLA810 4.3 121.3 1.0
C3A A:CLA810 4.3 132.2 1.0
C3C A:CLA810 4.3 129.1 1.0
C2A A:CLA810 4.4 127.0 1.0
NE1 A:TRP29 4.9 113.0 1.0
CBD A:CLA810 5.0 117.3 1.0
ND1 A:HIS182 5.0 145.2 1.0
CAA A:CLA803 5.0 111.8 1.0

Reference:

C.Gerle, Y.Misumi, A.Kawamoto, H.Tanaka, H.Kawai-Kubota, R.Tokutsu, E.Kim, D.Chorev, K.Abe, C.V.Robinson, K.Mitsuoka, J.Minagawa, G.Kurisu. Three Structures of Psi-Lhci From Chlamydomonas Reinhardtii Suggest A Resting State Re-Activated By Ferredoxin. Biochim Biophys Acta 48986 2023BIOENERG.
ISSN: ISSN 1879-2650
PubMed: 37270022
DOI: 10.1016/J.BBABIO.2023.148986
Page generated: Fri Oct 4 04:17:52 2024

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