Magnesium in PDB 8c88: Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Protein crystallography data
The structure of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c88
was solved by
A.Gabdulkhakov,
G.Selikhanov,
T.Fufina,
L.Vasilieva,
A.Atamas,
D.Yukhimchuk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.42 /
2.75
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.91,
100.91,
237.02,
90,
90,
90
|
R / Rfree (%)
|
19.9 /
27.1
|
Other elements in 8c88:
The structure of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
(pdb code 8c88). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c88:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8c88
Go back to
Magnesium Binding Sites List in 8c88
Magnesium binding site 1 out
of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg502
b:62.5
occ:1.00
|
MG
|
L:BCL502
|
0.0
|
62.5
|
1.0
|
NE2
|
L:HIS173
|
1.9
|
61.1
|
1.0
|
ND
|
L:BCL502
|
2.0
|
64.9
|
1.0
|
NB
|
L:BCL502
|
2.1
|
65.6
|
1.0
|
NC
|
L:BCL502
|
2.2
|
62.4
|
1.0
|
NA
|
L:BCL502
|
2.2
|
67.1
|
1.0
|
CE1
|
L:HIS173
|
2.7
|
58.0
|
1.0
|
C4D
|
L:BCL502
|
3.0
|
61.6
|
1.0
|
C1B
|
L:BCL502
|
3.1
|
58.1
|
1.0
|
CD2
|
L:HIS173
|
3.1
|
61.9
|
1.0
|
C4B
|
L:BCL502
|
3.1
|
61.6
|
1.0
|
C4A
|
L:BCL502
|
3.1
|
61.8
|
1.0
|
C1D
|
L:BCL502
|
3.2
|
60.3
|
1.0
|
C1C
|
L:BCL502
|
3.2
|
65.1
|
1.0
|
C4C
|
L:BCL502
|
3.2
|
63.2
|
1.0
|
C1A
|
L:BCL502
|
3.2
|
61.5
|
1.0
|
CHB
|
L:BCL502
|
3.4
|
58.6
|
1.0
|
CHC
|
L:BCL502
|
3.4
|
60.7
|
1.0
|
CHA
|
L:BCL502
|
3.5
|
63.2
|
1.0
|
CHD
|
L:BCL502
|
3.5
|
64.6
|
1.0
|
CBB
|
M:BCL403
|
3.8
|
58.0
|
1.0
|
ND1
|
L:HIS173
|
3.9
|
56.2
|
1.0
|
CAB
|
M:BCL403
|
3.9
|
62.6
|
1.0
|
OBB
|
M:BCL403
|
3.9
|
66.4
|
1.0
|
CG
|
L:HIS173
|
4.1
|
55.4
|
1.0
|
C3D
|
L:BCL502
|
4.2
|
64.9
|
1.0
|
C2D
|
L:BCL502
|
4.3
|
64.6
|
1.0
|
C2B
|
L:BCL502
|
4.3
|
55.7
|
1.0
|
C3A
|
L:BCL502
|
4.4
|
53.7
|
1.0
|
C3B
|
L:BCL502
|
4.4
|
62.0
|
1.0
|
C2C
|
L:BCL502
|
4.5
|
59.7
|
1.0
|
C2A
|
L:BCL502
|
4.5
|
55.0
|
1.0
|
C3C
|
L:BCL502
|
4.5
|
60.8
|
1.0
|
CD2
|
L:PHE167
|
4.7
|
62.9
|
1.0
|
C3B
|
M:BCL403
|
4.7
|
60.1
|
1.0
|
CMA
|
L:BCL502
|
4.8
|
56.4
|
1.0
|
CBD
|
L:BCL502
|
5.0
|
64.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8c88
Go back to
Magnesium Binding Sites List in 8c88
Magnesium binding site 2 out
of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg503
b:52.4
occ:1.00
|
MG
|
L:BCL503
|
0.0
|
52.4
|
1.0
|
NE2
|
L:HIS153
|
1.9
|
66.7
|
1.0
|
ND
|
L:BCL503
|
2.0
|
47.2
|
1.0
|
NB
|
L:BCL503
|
2.1
|
55.3
|
1.0
|
NC
|
L:BCL503
|
2.1
|
50.1
|
1.0
|
NA
|
L:BCL503
|
2.2
|
53.4
|
1.0
|
CE1
|
L:HIS153
|
2.8
|
60.2
|
1.0
|
C4D
|
L:BCL503
|
3.0
|
53.1
|
1.0
|
CD2
|
L:HIS153
|
3.1
|
59.0
|
1.0
|
C4B
|
L:BCL503
|
3.1
|
55.5
|
1.0
|
C1C
|
L:BCL503
|
3.1
|
52.3
|
1.0
|
C1B
|
L:BCL503
|
3.1
|
55.8
|
1.0
|
C4A
|
L:BCL503
|
3.2
|
51.2
|
1.0
|
C1D
|
L:BCL503
|
3.2
|
52.7
|
1.0
|
C4C
|
L:BCL503
|
3.2
|
47.9
|
1.0
|
C1A
|
L:BCL503
|
3.2
|
54.2
|
1.0
|
CHC
|
L:BCL503
|
3.4
|
55.0
|
1.0
|
CHB
|
L:BCL503
|
3.4
|
55.8
|
1.0
|
CHA
|
L:BCL503
|
3.5
|
53.3
|
1.0
|
CHD
|
L:BCL503
|
3.5
|
51.4
|
1.0
|
ND1
|
L:HIS153
|
4.0
|
59.5
|
1.0
|
CG
|
L:HIS153
|
4.1
|
56.7
|
1.0
|
C3D
|
L:BCL503
|
4.2
|
53.1
|
1.0
|
C2D
|
L:BCL503
|
4.3
|
50.1
|
1.0
|
C2B
|
L:BCL503
|
4.4
|
56.2
|
1.0
|
C2C
|
L:BCL503
|
4.4
|
52.7
|
1.0
|
C3B
|
L:BCL503
|
4.4
|
55.8
|
1.0
|
CBB
|
L:BPH504
|
4.4
|
52.5
|
1.0
|
C3A
|
L:BCL503
|
4.4
|
51.6
|
1.0
|
C19
|
L:BPH504
|
4.5
|
57.3
|
1.0
|
C3C
|
L:BCL503
|
4.5
|
44.5
|
1.0
|
C2A
|
L:BCL503
|
4.5
|
56.1
|
1.0
|
CMA
|
L:BCL503
|
4.8
|
48.5
|
1.0
|
CE2
|
M:TYR210
|
4.8
|
54.3
|
1.0
|
CMC
|
L:BCL503
|
4.9
|
57.9
|
1.0
|
CD1
|
L:LEU154
|
4.9
|
57.4
|
1.0
|
CBD
|
L:BCL503
|
4.9
|
52.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8c88
Go back to
Magnesium Binding Sites List in 8c88
Magnesium binding site 3 out
of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:58.4
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
58.4
|
1.0
|
NE2
|
M:HIS182
|
1.9
|
68.4
|
1.0
|
ND
|
M:BCL402
|
2.0
|
58.1
|
1.0
|
NB
|
M:BCL402
|
2.1
|
59.5
|
1.0
|
NC
|
M:BCL402
|
2.2
|
59.9
|
1.0
|
NA
|
M:BCL402
|
2.2
|
59.6
|
1.0
|
CE1
|
M:HIS182
|
2.9
|
58.8
|
1.0
|
CD2
|
M:HIS182
|
2.9
|
59.9
|
1.0
|
C4D
|
M:BCL402
|
3.0
|
59.8
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
59.0
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
61.0
|
1.0
|
C4A
|
M:BCL402
|
3.2
|
57.9
|
1.0
|
C1C
|
M:BCL402
|
3.2
|
63.3
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
58.9
|
1.0
|
C4C
|
M:BCL402
|
3.2
|
54.8
|
1.0
|
C1A
|
M:BCL402
|
3.2
|
60.1
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
55.7
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
57.6
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
54.0
|
1.0
|
CHA
|
M:BCL402
|
3.5
|
60.7
|
1.0
|
ND1
|
M:HIS182
|
4.0
|
54.8
|
1.0
|
CG
|
M:HIS182
|
4.0
|
60.1
|
1.0
|
C3D
|
M:BCL402
|
4.3
|
56.5
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
54.6
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
58.6
|
1.0
|
C3B
|
M:BCL402
|
4.4
|
62.4
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
57.3
|
1.0
|
CBB
|
M:BPH404
|
4.4
|
58.9
|
1.0
|
C3A
|
M:BCL402
|
4.5
|
54.9
|
1.0
|
C3C
|
M:BCL402
|
4.5
|
52.7
|
1.0
|
C2A
|
M:BCL402
|
4.5
|
55.9
|
1.0
|
CBD
|
M:BCL402
|
5.0
|
56.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8c88
Go back to
Magnesium Binding Sites List in 8c88
Magnesium binding site 4 out
of 4 in the Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Double Mutant G(M19)C/T(L214)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:58.3
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
58.3
|
1.0
|
NE2
|
M:HIS202
|
1.9
|
57.4
|
1.0
|
ND
|
M:BCL403
|
2.1
|
55.6
|
1.0
|
NB
|
M:BCL403
|
2.1
|
59.8
|
1.0
|
NC
|
M:BCL403
|
2.1
|
62.4
|
1.0
|
NA
|
M:BCL403
|
2.2
|
57.2
|
1.0
|
CE1
|
M:HIS202
|
2.8
|
50.6
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
51.3
|
1.0
|
CD2
|
M:HIS202
|
3.0
|
51.2
|
1.0
|
C1B
|
M:BCL403
|
3.1
|
62.5
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
54.0
|
1.0
|
C1C
|
M:BCL403
|
3.1
|
64.5
|
1.0
|
C1D
|
M:BCL403
|
3.2
|
62.9
|
1.0
|
C4A
|
M:BCL403
|
3.2
|
55.2
|
1.0
|
C4C
|
M:BCL403
|
3.2
|
59.6
|
1.0
|
C1A
|
M:BCL403
|
3.3
|
58.9
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
55.5
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
57.4
|
1.0
|
CHA
|
M:BCL403
|
3.5
|
52.6
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
56.0
|
1.0
|
CBB
|
L:BCL502
|
3.8
|
55.3
|
1.0
|
OBB
|
L:BCL502
|
3.9
|
67.3
|
1.0
|
CAB
|
L:BCL502
|
3.9
|
61.7
|
1.0
|
ND1
|
M:HIS202
|
3.9
|
44.7
|
1.0
|
CG
|
M:HIS202
|
4.1
|
47.8
|
1.0
|
C3D
|
M:BCL403
|
4.3
|
54.8
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
62.2
|
1.0
|
C2D
|
M:BCL403
|
4.4
|
57.1
|
1.0
|
C3B
|
M:BCL403
|
4.4
|
60.1
|
1.0
|
C2C
|
M:BCL403
|
4.4
|
55.1
|
1.0
|
C3C
|
M:BCL403
|
4.5
|
56.1
|
1.0
|
C3A
|
M:BCL403
|
4.5
|
56.5
|
1.0
|
C2A
|
M:BCL403
|
4.6
|
58.3
|
1.0
|
C3B
|
L:BCL502
|
4.8
|
62.0
|
1.0
|
CMC
|
M:BCL403
|
4.9
|
45.7
|
1.0
|
CBD
|
M:BCL403
|
4.9
|
54.5
|
1.0
|
|
Reference:
G.Selikhanov,
A.Atamas,
D.Yukhimchuk,
T.Fufina,
L.Vasilieva,
A.Gabdulkhakov.
Stabilization of Cereibacter Sphaeroides Photosynthetic Reaction Center By the Introduction of Disulfide Bonds. Membranes (Basel) V. 13 2023.
ISSN: ESSN 2077-0375
PubMed: 36837657
DOI: 10.3390/MEMBRANES13020154
Page generated: Thu Oct 3 20:11:09 2024
|