Magnesium in PDB 8c5x: Double Mutant A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Protein crystallography data
The structure of Double Mutant A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c5x
was solved by
A.Gabdulkhakov,
G.Selikhanov,
T.Fufina,
L.Vasilieva,
A.Atamas,
D.Uhimchuk,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.89 /
2.60
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
139.85,
139.85,
186.56,
90,
90,
120
|
R / Rfree (%)
|
18.6 /
20.7
|
Other elements in 8c5x:
The structure of Double Mutant A(L37)C/S(L99)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 A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
(pdb code 8c5x). 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 A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c5x:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8c5x
Go back to
Magnesium Binding Sites List in 8c5x
Magnesium binding site 1 out
of 4 in the Double Mutant A(L37)C/S(L99)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 A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg301
b:49.0
occ:1.00
|
MG
|
L:BCL301
|
0.0
|
49.0
|
1.0
|
NE2
|
L:HIS173
|
1.9
|
47.2
|
1.0
|
ND
|
L:BCL301
|
2.0
|
47.8
|
1.0
|
NB
|
L:BCL301
|
2.1
|
47.1
|
1.0
|
NC
|
L:BCL301
|
2.2
|
51.9
|
1.0
|
NA
|
L:BCL301
|
2.2
|
47.2
|
1.0
|
CE1
|
L:HIS173
|
2.8
|
42.8
|
1.0
|
C4D
|
L:BCL301
|
3.0
|
46.6
|
1.0
|
CD2
|
L:HIS173
|
3.1
|
40.5
|
1.0
|
C4B
|
L:BCL301
|
3.1
|
48.4
|
1.0
|
C1B
|
L:BCL301
|
3.1
|
46.4
|
1.0
|
C1C
|
L:BCL301
|
3.2
|
52.9
|
1.0
|
C4A
|
L:BCL301
|
3.2
|
45.6
|
1.0
|
C1D
|
L:BCL301
|
3.2
|
46.1
|
1.0
|
C4C
|
L:BCL301
|
3.2
|
48.8
|
1.0
|
C1A
|
L:BCL301
|
3.2
|
44.6
|
1.0
|
CHC
|
L:BCL301
|
3.4
|
50.8
|
1.0
|
CHB
|
L:BCL301
|
3.4
|
43.8
|
1.0
|
CHA
|
L:BCL301
|
3.5
|
45.1
|
1.0
|
CHD
|
L:BCL301
|
3.5
|
46.7
|
1.0
|
CBB
|
M:BCL403
|
3.6
|
43.7
|
1.0
|
ND1
|
L:HIS173
|
3.9
|
34.2
|
1.0
|
CAB
|
M:BCL403
|
4.0
|
49.9
|
1.0
|
CG
|
L:HIS173
|
4.1
|
39.6
|
1.0
|
C3D
|
L:BCL301
|
4.3
|
44.6
|
1.0
|
C2D
|
L:BCL301
|
4.3
|
47.0
|
1.0
|
C2B
|
L:BCL301
|
4.3
|
47.2
|
1.0
|
OBB
|
M:BCL403
|
4.4
|
49.8
|
1.0
|
C3B
|
L:BCL301
|
4.4
|
46.8
|
1.0
|
C3A
|
L:BCL301
|
4.4
|
44.2
|
1.0
|
C2C
|
L:BCL301
|
4.5
|
48.3
|
1.0
|
C3C
|
L:BCL301
|
4.5
|
42.5
|
1.0
|
C2A
|
L:BCL301
|
4.5
|
43.6
|
1.0
|
CD2
|
L:PHE167
|
4.6
|
44.6
|
1.0
|
C3B
|
M:BCL403
|
4.7
|
48.9
|
1.0
|
CMA
|
L:BCL301
|
4.8
|
41.8
|
1.0
|
CBD
|
L:BCL301
|
5.0
|
44.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8c5x
Go back to
Magnesium Binding Sites List in 8c5x
Magnesium binding site 2 out
of 4 in the Double Mutant A(L37)C/S(L99)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 A(L37)C/S(L99)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:43.7
occ:1.00
|
MG
|
L:BCL302
|
0.0
|
43.7
|
1.0
|
NE2
|
L:HIS153
|
1.9
|
46.3
|
1.0
|
ND
|
L:BCL302
|
2.0
|
38.2
|
1.0
|
NB
|
L:BCL302
|
2.1
|
38.8
|
1.0
|
NC
|
L:BCL302
|
2.1
|
38.4
|
1.0
|
NA
|
L:BCL302
|
2.2
|
41.9
|
1.0
|
CE1
|
L:HIS153
|
2.9
|
45.6
|
1.0
|
CD2
|
L:HIS153
|
2.9
|
44.8
|
1.0
|
C4D
|
L:BCL302
|
3.0
|
37.6
|
1.0
|
C4B
|
L:BCL302
|
3.1
|
41.2
|
1.0
|
C1B
|
L:BCL302
|
3.1
|
40.4
|
1.0
|
C1C
|
L:BCL302
|
3.1
|
41.5
|
1.0
|
C4A
|
L:BCL302
|
3.2
|
44.5
|
1.0
|
C1D
|
L:BCL302
|
3.2
|
40.4
|
1.0
|
C4C
|
L:BCL302
|
3.2
|
40.2
|
1.0
|
C1A
|
L:BCL302
|
3.2
|
43.2
|
1.0
|
CHC
|
L:BCL302
|
3.4
|
41.8
|
1.0
|
CHB
|
L:BCL302
|
3.4
|
37.6
|
1.0
|
CHA
|
L:BCL302
|
3.5
|
42.1
|
1.0
|
CHD
|
L:BCL302
|
3.5
|
43.3
|
1.0
|
ND1
|
L:HIS153
|
4.0
|
42.9
|
1.0
|
CG
|
L:HIS153
|
4.1
|
48.5
|
1.0
|
C3D
|
L:BCL302
|
4.2
|
38.9
|
1.0
|
C2D
|
L:BCL302
|
4.3
|
43.0
|
1.0
|
C2B
|
L:BCL302
|
4.3
|
41.7
|
1.0
|
C3B
|
L:BCL302
|
4.4
|
41.3
|
1.0
|
C2C
|
L:BCL302
|
4.4
|
39.8
|
1.0
|
C3A
|
L:BCL302
|
4.4
|
40.0
|
1.0
|
C3C
|
L:BCL302
|
4.5
|
37.7
|
1.0
|
C2A
|
L:BCL302
|
4.5
|
41.8
|
1.0
|
CBB
|
L:BPH303
|
4.6
|
33.1
|
1.0
|
C19
|
L:BPH303
|
4.6
|
44.2
|
1.0
|
CD1
|
L:LEU154
|
4.7
|
43.3
|
1.0
|
CE2
|
M:TYR210
|
4.8
|
44.2
|
1.0
|
CBD
|
L:BCL302
|
4.9
|
43.4
|
1.0
|
CBC
|
L:BCL302
|
4.9
|
37.3
|
1.0
|
CMC
|
L:BCL302
|
5.0
|
38.9
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8c5x
Go back to
Magnesium Binding Sites List in 8c5x
Magnesium binding site 3 out
of 4 in the Double Mutant A(L37)C/S(L99)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 A(L37)C/S(L99)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:44.7
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
44.7
|
1.0
|
NE2
|
M:HIS182
|
1.9
|
51.5
|
1.0
|
ND
|
M:BCL402
|
2.1
|
45.5
|
1.0
|
NB
|
M:BCL402
|
2.1
|
45.7
|
1.0
|
NC
|
M:BCL402
|
2.1
|
40.3
|
1.0
|
NA
|
M:BCL402
|
2.2
|
45.8
|
1.0
|
CE1
|
M:HIS182
|
2.9
|
42.9
|
1.0
|
CD2
|
M:HIS182
|
2.9
|
44.1
|
1.0
|
C4D
|
M:BCL402
|
3.0
|
42.0
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
44.1
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
46.6
|
1.0
|
C1C
|
M:BCL402
|
3.1
|
46.9
|
1.0
|
C4A
|
M:BCL402
|
3.1
|
48.8
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
42.7
|
1.0
|
C4C
|
M:BCL402
|
3.2
|
43.8
|
1.0
|
C1A
|
M:BCL402
|
3.2
|
48.3
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
43.2
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
43.3
|
1.0
|
CHA
|
M:BCL402
|
3.5
|
46.7
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
40.6
|
1.0
|
ND1
|
M:HIS182
|
4.0
|
44.2
|
1.0
|
CG
|
M:HIS182
|
4.1
|
46.3
|
1.0
|
C3D
|
M:BCL402
|
4.2
|
37.9
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
45.6
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
52.0
|
1.0
|
C3B
|
M:BCL402
|
4.4
|
50.3
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
39.2
|
1.0
|
C3A
|
M:BCL402
|
4.4
|
46.0
|
1.0
|
C3C
|
M:BCL402
|
4.5
|
38.3
|
1.0
|
C2A
|
M:BCL402
|
4.5
|
47.8
|
1.0
|
CBB
|
M:BPH404
|
4.6
|
44.6
|
1.0
|
CM5
|
M:SPN407
|
4.9
|
41.8
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
41.0
|
1.0
|
CMA
|
M:BCL402
|
5.0
|
49.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8c5x
Go back to
Magnesium Binding Sites List in 8c5x
Magnesium binding site 4 out
of 4 in the Double Mutant A(L37)C/S(L99)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 A(L37)C/S(L99)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:43.3
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
43.3
|
1.0
|
NE2
|
M:HIS202
|
1.9
|
43.4
|
1.0
|
ND
|
M:BCL403
|
2.0
|
44.5
|
1.0
|
NB
|
M:BCL403
|
2.1
|
49.3
|
1.0
|
NC
|
M:BCL403
|
2.2
|
50.7
|
1.0
|
NA
|
M:BCL403
|
2.2
|
41.6
|
1.0
|
CE1
|
M:HIS202
|
2.8
|
41.4
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
46.2
|
1.0
|
CD2
|
M:HIS202
|
3.0
|
43.1
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
46.5
|
1.0
|
C1B
|
M:BCL403
|
3.1
|
49.3
|
1.0
|
C1C
|
M:BCL403
|
3.1
|
50.1
|
1.0
|
C4A
|
M:BCL403
|
3.2
|
45.9
|
1.0
|
C1D
|
M:BCL403
|
3.2
|
46.0
|
1.0
|
C4C
|
M:BCL403
|
3.2
|
41.9
|
1.0
|
C1A
|
M:BCL403
|
3.2
|
42.8
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
48.0
|
1.0
|
CHA
|
M:BCL403
|
3.4
|
44.6
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
46.8
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
42.4
|
1.0
|
CBB
|
L:BCL301
|
3.6
|
46.4
|
1.0
|
CAB
|
L:BCL301
|
3.9
|
48.5
|
1.0
|
ND1
|
M:HIS202
|
4.0
|
35.4
|
1.0
|
CG
|
M:HIS202
|
4.1
|
37.6
|
1.0
|
OBB
|
L:BCL301
|
4.2
|
47.8
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
44.4
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
47.2
|
1.0
|
C2D
|
M:BCL403
|
4.3
|
45.1
|
1.0
|
C3B
|
M:BCL403
|
4.3
|
48.9
|
1.0
|
C2C
|
M:BCL403
|
4.4
|
47.6
|
1.0
|
C3A
|
M:BCL403
|
4.5
|
43.4
|
1.0
|
C3C
|
M:BCL403
|
4.5
|
47.8
|
1.0
|
C2A
|
M:BCL403
|
4.5
|
46.1
|
1.0
|
C3B
|
L:BCL301
|
4.6
|
46.8
|
1.0
|
CBD
|
M:BCL403
|
4.9
|
44.6
|
1.0
|
O2D
|
M:BCL403
|
5.0
|
45.8
|
1.0
|
CD1
|
M:LEU196
|
5.0
|
39.3
|
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 20:08:59 2024
|