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
Go back to
Magnesium Binding Sites List in 6q53
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 Sites List in 6q53
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
Go back to
Magnesium Binding Sites List in 6q53
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
Go back to
Magnesium Binding Sites List in 6q53
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
Go back to
Magnesium Binding Sites List in 6q53
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
Go back to
Magnesium Binding Sites List in 6q53
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: Tue Oct 1 15:23:23 2024
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