Magnesium in PDB 6q53: Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila

Protein crystallography data

The structure of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila, PDB code: 6q53 was solved by A.G.Gabdulkhakov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.96 / 3.70
Space group P 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 177.240, 177.240, 177.240, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila (pdb code 6q53). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila, PDB code: 6q53:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6q53

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg101

b:81.2
occ:1.00
MG A:BCL101 0.0 81.2 1.0
ND A:BCL101 2.0 84.3 1.0
NB A:BCL101 2.1 78.7 1.0
NC A:BCL101 2.1 81.3 1.0
NA A:BCL101 2.2 83.3 1.0
NE2 A:HIS43 2.7 76.4 1.0
C4D A:BCL101 3.0 90.0 1.0
C1B A:BCL101 3.1 87.6 1.0
C4B A:BCL101 3.1 79.2 1.0
C1C A:BCL101 3.1 78.3 1.0
C4A A:BCL101 3.1 85.3 1.0
C4C A:BCL101 3.1 75.5 1.0
C1D A:BCL101 3.1 80.0 1.0
C1A A:BCL101 3.2 80.8 1.0
CHB A:BCL101 3.4 88.3 1.0
CHC A:BCL101 3.4 80.4 1.0
CHD A:BCL101 3.5 78.7 1.0
CHA A:BCL101 3.5 85.7 1.0
CE1 A:HIS43 3.6 83.0 1.0
CD2 A:HIS43 3.7 81.7 1.0
C3D A:BCL101 4.2 86.0 1.0
C2B A:BCL101 4.3 85.1 1.0
C2D A:BCL101 4.3 82.9 1.0
C3B A:BCL101 4.3 79.4 1.0
C2C A:BCL101 4.4 70.5 1.0
C3C A:BCL101 4.4 68.6 1.0
C3A A:BCL101 4.5 79.0 1.0
C2A A:BCL101 4.5 75.9 1.0
ND1 A:HIS43 4.8 81.7 1.0
CG A:HIS43 4.8 78.0 1.0

Magnesium binding site 2 out of 6 in 6q53

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:60.1
occ:1.00
MG A:BCL102 0.0 60.1 1.0
ND A:BCL102 2.0 64.8 1.0
NB A:BCL102 2.1 68.6 1.0
NC A:BCL102 2.1 68.4 1.0
NA A:BCL102 2.2 68.6 1.0
OD2 A:ASP15 2.6 74.3 1.0
OD1 A:ASP15 2.9 66.8 1.0
CG A:ASP15 2.9 70.5 1.0
C4D A:BCL102 3.0 68.2 1.0
C1B A:BCL102 3.1 67.6 1.0
C4B A:BCL102 3.1 67.2 1.0
C1C A:BCL102 3.1 67.5 1.0
C1D A:BCL102 3.1 66.0 1.0
C4A A:BCL102 3.1 71.3 1.0
C4C A:BCL102 3.1 64.7 1.0
C1A A:BCL102 3.2 67.3 1.0
CHB A:BCL102 3.4 71.2 1.0
CHC A:BCL102 3.4 66.7 1.0
CHA A:BCL102 3.4 66.2 1.0
CHD A:BCL102 3.5 62.3 1.0
C9 B:BCL101 4.0 73.0 1.0
CB A:ASP15 4.2 70.2 1.0
C3D A:BCL102 4.2 73.1 1.0
C2B A:BCL102 4.3 59.8 1.0
C2D A:BCL102 4.3 69.7 1.0
C3B A:BCL102 4.3 65.0 1.0
C2C A:BCL102 4.4 61.5 1.0
C3C A:BCL102 4.4 61.7 1.0
C3A A:BCL102 4.4 69.1 1.0
C2A A:BCL102 4.5 71.6 1.0
CB A:PRO12 4.6 61.4 1.0
CA A:PRO12 4.7 73.2 1.0
CBD A:BCL102 4.9 71.0 1.0
CMC A:BCL102 5.0 65.0 1.0

Magnesium binding site 3 out of 6 in 6q53

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:75.2
occ:1.00
MG B:BCL101 0.0 75.2 1.0
ND B:BCL101 2.0 84.2 1.0
NB B:BCL101 2.1 78.9 1.0
NC B:BCL101 2.1 84.0 1.0
NA B:BCL101 2.2 76.5 1.0
NE2 B:HIS35 2.5 76.5 1.0
C4D B:BCL101 3.0 85.5 1.0
C4B B:BCL101 3.1 74.5 1.0
C1B B:BCL101 3.1 80.4 1.0
C1C B:BCL101 3.1 83.7 1.0
C4A B:BCL101 3.1 73.7 1.0
C1D B:BCL101 3.1 81.9 1.0
C4C B:BCL101 3.2 83.0 1.0
C1A B:BCL101 3.2 76.3 1.0
CD2 B:HIS35 3.2 78.7 1.0
CHC B:BCL101 3.4 78.5 1.0
CHB B:BCL101 3.4 78.0 1.0
CHA B:BCL101 3.5 82.0 1.0
CHD B:BCL101 3.5 82.1 1.0
CE1 B:HIS35 3.6 85.0 1.0
CMB D:BCL101 4.0 77.0 1.0
CBB D:BCL101 4.1 81.4 1.0
C3D B:BCL101 4.2 83.2 1.0
C2B B:BCL101 4.3 79.0 1.0
C3B B:BCL101 4.3 77.0 1.0
C2D B:BCL101 4.3 79.5 1.0
C2C B:BCL101 4.4 83.1 1.0
C3C B:BCL101 4.4 79.0 1.0
C2A B:BCL101 4.5 74.7 1.0
CG B:HIS35 4.5 87.8 1.0
C3A B:BCL101 4.5 74.5 1.0
ND1 B:HIS35 4.6 86.9 1.0
C7 B:DET102 4.7 80.2 1.0
CAB D:BCL101 4.9 79.5 1.0
CBD B:BCL101 4.9 82.7 1.0
C2B D:BCL101 5.0 76.7 1.0

Magnesium binding site 4 out of 6 in 6q53

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg101

b:77.9
occ:1.00
MG D:BCL101 0.0 77.9 1.0
ND D:BCL101 2.0 76.2 1.0
NB D:BCL101 2.1 75.0 1.0
NC D:BCL101 2.1 80.6 1.0
NA D:BCL101 2.2 80.8 1.0
NE2 D:HIS43 2.8 70.1 1.0
C4D D:BCL101 3.0 80.6 1.0
C1B D:BCL101 3.1 77.5 1.0
C1C D:BCL101 3.1 75.2 1.0
C4B D:BCL101 3.1 76.8 1.0
C1D D:BCL101 3.1 78.7 1.0
C4A D:BCL101 3.1 81.3 1.0
C4C D:BCL101 3.1 79.0 1.0
C1A D:BCL101 3.2 77.8 1.0
CHB D:BCL101 3.4 81.0 1.0
CHC D:BCL101 3.4 73.8 1.0
CHA D:BCL101 3.4 77.0 1.0
CHD D:BCL101 3.5 81.6 1.0
CE1 D:HIS43 3.5 76.4 1.0
C11 E:DET103 3.6 63.2 1.0
CD2 D:HIS43 3.9 71.9 1.0
C10 E:DET103 4.1 75.0 1.0
C3D D:BCL101 4.2 81.3 1.0
C2D D:BCL101 4.3 79.4 1.0
C2B D:BCL101 4.3 76.7 1.0
C3B D:BCL101 4.4 77.6 1.0
C2C D:BCL101 4.4 71.0 1.0
CBB B:BCL101 4.4 77.2 1.0
C3C D:BCL101 4.4 75.3 1.0
C3A D:BCL101 4.4 75.1 1.0
C2A D:BCL101 4.5 77.9 1.0
ND1 D:HIS43 4.7 75.6 1.0
C9 E:DET103 4.9 79.9 1.0
CBD D:BCL101 4.9 77.9 1.0
CG D:HIS43 4.9 71.3 1.0
CAC D:BCL101 5.0 76.5 1.0
CMC D:BCL101 5.0 75.0 1.0

Magnesium binding site 5 out of 6 in 6q53

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg102

b:57.5
occ:1.00
MG D:BCL102 0.0 57.5 1.0
ND D:BCL102 2.0 64.9 1.0
NB D:BCL102 2.0 67.7 1.0
NC D:BCL102 2.1 69.4 1.0
NA D:BCL102 2.2 69.9 1.0
OD2 D:ASP15 2.5 67.5 1.0
C4D D:BCL102 3.0 65.7 1.0
OD1 D:ASP15 3.0 67.7 1.0
CG D:ASP15 3.0 71.6 1.0
C1B D:BCL102 3.0 71.6 1.0
C4B D:BCL102 3.0 68.7 1.0
C1C D:BCL102 3.1 68.6 1.0
C1D D:BCL102 3.1 66.4 1.0
C4A D:BCL102 3.1 70.3 1.0
C4C D:BCL102 3.1 65.1 1.0
C1A D:BCL102 3.2 71.2 1.0
CHB D:BCL102 3.4 69.7 1.0
CHC D:BCL102 3.4 67.2 1.0
CHA D:BCL102 3.4 67.0 1.0
CHD D:BCL102 3.5 63.9 1.0
C9 E:BCL102 3.5 72.7 1.0
C3D D:BCL102 4.2 68.4 1.0
C2B D:BCL102 4.2 67.8 1.0
C2D D:BCL102 4.3 67.9 1.0
C3B D:BCL102 4.3 69.5 1.0
CB D:ASP15 4.3 79.8 1.0
C3C D:BCL102 4.4 59.5 1.0
C2C D:BCL102 4.4 63.0 1.0
C3A D:BCL102 4.4 66.7 1.0
C2A D:BCL102 4.5 70.0 1.0
CB D:PRO12 4.6 67.8 1.0
C8 E:BCL102 4.9 66.4 1.0
CBD D:BCL102 4.9 68.5 1.0
CBC D:BCL102 4.9 66.0 1.0
CMA D:BCL102 4.9 62.8 1.0

Magnesium binding site 6 out of 6 in 6q53

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Light-Harvesting Complex II (B800-850) From Ectothiorhodospira Haloalkaliphila within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg102

b:78.8
occ:1.00
MG E:BCL102 0.0 78.8 1.0
ND E:BCL102 2.0 84.5 1.0
NB E:BCL102 2.1 83.7 1.0
NC E:BCL102 2.1 81.6 1.0
NA E:BCL102 2.2 86.3 1.0
NE2 E:HIS35 2.6 80.8 1.0
C4D E:BCL102 3.0 82.8 1.0
C4B E:BCL102 3.1 86.3 1.0
C1B E:BCL102 3.1 80.6 1.0
C1C E:BCL102 3.1 83.7 1.0
C1D E:BCL102 3.1 80.6 1.0
C4A E:BCL102 3.2 85.6 1.0
C4C E:BCL102 3.2 82.5 1.0
CD2 E:HIS35 3.2 81.8 1.0
C1A E:BCL102 3.2 78.6 1.0
CHC E:BCL102 3.4 87.2 1.0
CHB E:BCL102 3.4 83.5 1.0
CHA E:BCL102 3.5 78.6 1.0
CHD E:BCL102 3.5 82.4 1.0
CE1 E:HIS35 3.7 88.2 1.0
C3D E:BCL102 4.2 81.5 1.0
C2B E:BCL102 4.3 81.8 1.0
C2D E:BCL102 4.3 76.6 1.0
C3B E:BCL102 4.3 89.2 1.0
C2C E:BCL102 4.4 82.4 1.0
C3C E:BCL102 4.4 82.5 1.0
CG E:HIS35 4.5 88.6 1.0
C3A E:BCL102 4.5 76.8 1.0
C2A E:BCL102 4.6 74.4 1.0
ND1 E:HIS35 4.7 92.6 1.0
C7 E:DET104 4.9 92.7 1.0
CMD D:BCL101 4.9 83.6 1.0
CBD E:BCL102 5.0 80.6 1.0
CG1 D:VAL42 5.0 78.7 1.0

Reference:

K.Leiger, J.M.Linnanto, M.Ratsep, K.Timpmann, A.A.Ashikhmin, A.A.Moskalenko, T.Y.Fufina, A.G.Gabdulkhakov, A.Freiberg. Controlling Photosynthetic Excitons By Selective Pigment Photooxidation. J.Phys.Chem.B V. 123 29 2019.
ISSN: ISSN 1089-5647
PubMed: 30543422
DOI: 10.1021/ACS.JPCB.8B08083
Page generated: Mon Dec 14 23:51:36 2020

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