Magnesium in PDB 8c7c: Double Mutant V(M84)C/A(L278)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
Protein crystallography data
The structure of Double Mutant V(M84)C/A(L278)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c7c
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)
|
41.99 /
2.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
253.13,
75.98,
65.85,
90,
95.58,
90
|
R / Rfree (%)
|
19.3 /
24.9
|
Other elements in 8c7c:
The structure of Double Mutant V(M84)C/A(L278)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 V(M84)C/A(L278)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv
(pdb code 8c7c). 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 V(M84)C/A(L278)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c7c:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8c7c
Go back to
Magnesium Binding Sites List in 8c7c
Magnesium binding site 1 out
of 4 in the Double Mutant V(M84)C/A(L278)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 V(M84)C/A(L278)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:70.9
occ:1.00
|
MG
|
L:BCL301
|
0.0
|
70.9
|
1.0
|
NE2
|
L:HIS173
|
1.9
|
66.7
|
1.0
|
ND
|
L:BCL301
|
2.1
|
76.5
|
1.0
|
NB
|
L:BCL301
|
2.1
|
74.3
|
1.0
|
NC
|
L:BCL301
|
2.2
|
77.6
|
1.0
|
NA
|
L:BCL301
|
2.2
|
78.6
|
1.0
|
CE1
|
L:HIS173
|
2.6
|
68.0
|
1.0
|
C4D
|
L:BCL301
|
3.0
|
73.7
|
1.0
|
CD2
|
L:HIS173
|
3.1
|
70.8
|
1.0
|
C1B
|
L:BCL301
|
3.1
|
74.7
|
1.0
|
C4B
|
L:BCL301
|
3.1
|
76.7
|
1.0
|
C4A
|
L:BCL301
|
3.2
|
69.9
|
1.0
|
C1C
|
L:BCL301
|
3.2
|
81.0
|
1.0
|
C1D
|
L:BCL301
|
3.2
|
74.8
|
1.0
|
C4C
|
L:BCL301
|
3.2
|
71.8
|
1.0
|
C1A
|
L:BCL301
|
3.2
|
72.0
|
1.0
|
CHB
|
L:BCL301
|
3.4
|
74.2
|
1.0
|
CHC
|
L:BCL301
|
3.4
|
75.6
|
1.0
|
CHA
|
L:BCL301
|
3.5
|
70.8
|
1.0
|
CHD
|
L:BCL301
|
3.5
|
69.4
|
1.0
|
OBB
|
M:BCL403
|
3.8
|
74.4
|
1.0
|
ND1
|
L:HIS173
|
3.8
|
67.4
|
1.0
|
CBB
|
M:BCL403
|
3.9
|
67.6
|
1.0
|
CAB
|
M:BCL403
|
3.9
|
73.0
|
1.0
|
CG
|
L:HIS173
|
4.1
|
71.2
|
1.0
|
C3D
|
L:BCL301
|
4.3
|
78.1
|
1.0
|
C2B
|
L:BCL301
|
4.3
|
71.1
|
1.0
|
C2D
|
L:BCL301
|
4.4
|
74.0
|
1.0
|
C3B
|
L:BCL301
|
4.4
|
68.8
|
1.0
|
C3A
|
L:BCL301
|
4.4
|
66.2
|
1.0
|
C2C
|
L:BCL301
|
4.5
|
79.7
|
1.0
|
C3C
|
L:BCL301
|
4.5
|
75.2
|
1.0
|
C2A
|
L:BCL301
|
4.5
|
66.2
|
1.0
|
C3B
|
M:BCL403
|
4.7
|
77.3
|
1.0
|
CD2
|
L:PHE167
|
4.8
|
74.4
|
1.0
|
CMA
|
L:BCL301
|
4.9
|
58.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8c7c
Go back to
Magnesium Binding Sites List in 8c7c
Magnesium binding site 2 out
of 4 in the Double Mutant V(M84)C/A(L278)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 V(M84)C/A(L278)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:72.5
occ:1.00
|
MG
|
L:BCL302
|
0.0
|
72.5
|
1.0
|
NE2
|
L:HIS153
|
1.9
|
72.4
|
1.0
|
ND
|
L:BCL302
|
2.1
|
69.0
|
1.0
|
NB
|
L:BCL302
|
2.1
|
61.9
|
1.0
|
NC
|
L:BCL302
|
2.1
|
70.4
|
1.0
|
NA
|
L:BCL302
|
2.2
|
67.0
|
1.0
|
CE1
|
L:HIS153
|
2.9
|
69.0
|
1.0
|
CD2
|
L:HIS153
|
3.0
|
70.9
|
1.0
|
C4D
|
L:BCL302
|
3.0
|
60.4
|
1.0
|
C4B
|
L:BCL302
|
3.1
|
61.5
|
1.0
|
C1B
|
L:BCL302
|
3.1
|
70.7
|
1.0
|
C1C
|
L:BCL302
|
3.1
|
76.9
|
1.0
|
C4A
|
L:BCL302
|
3.2
|
69.7
|
1.0
|
C1D
|
L:BCL302
|
3.2
|
70.5
|
1.0
|
C4C
|
L:BCL302
|
3.2
|
70.7
|
1.0
|
C1A
|
L:BCL302
|
3.2
|
66.9
|
1.0
|
CHC
|
L:BCL302
|
3.4
|
70.5
|
1.0
|
CHB
|
L:BCL302
|
3.4
|
67.1
|
1.0
|
CHA
|
L:BCL302
|
3.5
|
66.2
|
1.0
|
CHD
|
L:BCL302
|
3.5
|
73.2
|
1.0
|
ND1
|
L:HIS153
|
4.0
|
71.3
|
1.0
|
CG
|
L:HIS153
|
4.1
|
69.8
|
1.0
|
C3D
|
L:BCL302
|
4.2
|
67.8
|
1.0
|
C2D
|
L:BCL302
|
4.3
|
63.4
|
1.0
|
C2B
|
L:BCL302
|
4.3
|
68.9
|
1.0
|
C3B
|
L:BCL302
|
4.4
|
64.0
|
1.0
|
C3A
|
L:BCL302
|
4.4
|
69.9
|
1.0
|
C2C
|
L:BCL302
|
4.4
|
74.1
|
1.0
|
C3C
|
L:BCL302
|
4.5
|
68.0
|
1.0
|
CBB
|
L:BPH303
|
4.5
|
60.4
|
1.0
|
C2A
|
L:BCL302
|
4.5
|
69.4
|
1.0
|
CE2
|
M:TYR210
|
4.7
|
69.0
|
1.0
|
C19
|
L:BPH303
|
4.8
|
73.5
|
1.0
|
CBC
|
L:BCL302
|
4.9
|
64.8
|
1.0
|
CD1
|
L:LEU154
|
4.9
|
76.2
|
1.0
|
CBD
|
L:BCL302
|
4.9
|
67.8
|
1.0
|
CMA
|
L:BCL302
|
5.0
|
64.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8c7c
Go back to
Magnesium Binding Sites List in 8c7c
Magnesium binding site 3 out
of 4 in the Double Mutant V(M84)C/A(L278)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 V(M84)C/A(L278)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:69.0
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
69.0
|
1.0
|
NE2
|
M:HIS182
|
1.9
|
70.6
|
1.0
|
ND
|
M:BCL402
|
2.0
|
67.1
|
1.0
|
NB
|
M:BCL402
|
2.1
|
70.8
|
1.0
|
NC
|
M:BCL402
|
2.1
|
65.9
|
1.0
|
NA
|
M:BCL402
|
2.2
|
66.5
|
1.0
|
CE1
|
M:HIS182
|
2.8
|
67.3
|
1.0
|
CD2
|
M:HIS182
|
3.0
|
72.8
|
1.0
|
C4D
|
M:BCL402
|
3.0
|
71.9
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
74.9
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
66.7
|
1.0
|
C1C
|
M:BCL402
|
3.1
|
74.8
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
70.7
|
1.0
|
C4A
|
M:BCL402
|
3.2
|
75.9
|
1.0
|
C4C
|
M:BCL402
|
3.2
|
67.0
|
1.0
|
C1A
|
M:BCL402
|
3.2
|
74.4
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
76.0
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
66.8
|
1.0
|
CHA
|
M:BCL402
|
3.5
|
74.2
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
70.9
|
1.0
|
ND1
|
M:HIS182
|
4.0
|
68.7
|
1.0
|
CG
|
M:HIS182
|
4.1
|
78.0
|
1.0
|
C3D
|
M:BCL402
|
4.3
|
72.6
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
74.9
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
76.2
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
77.1
|
1.0
|
C3B
|
M:BCL402
|
4.4
|
75.2
|
1.0
|
C3C
|
M:BCL402
|
4.4
|
71.2
|
1.0
|
C3A
|
M:BCL402
|
4.5
|
77.8
|
1.0
|
CBB
|
M:BPH404
|
4.5
|
73.8
|
1.0
|
C2A
|
M:BCL402
|
4.5
|
74.3
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
71.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8c7c
Go back to
Magnesium Binding Sites List in 8c7c
Magnesium binding site 4 out
of 4 in the Double Mutant V(M84)C/A(L278)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 V(M84)C/A(L278)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:71.0
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
71.0
|
1.0
|
NE2
|
M:HIS202
|
1.9
|
70.7
|
1.0
|
ND
|
M:BCL403
|
2.0
|
75.0
|
1.0
|
NB
|
M:BCL403
|
2.1
|
73.8
|
1.0
|
NC
|
M:BCL403
|
2.2
|
79.7
|
1.0
|
NA
|
M:BCL403
|
2.2
|
70.8
|
1.0
|
CE1
|
M:HIS202
|
2.7
|
64.9
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
75.9
|
1.0
|
CD2
|
M:HIS202
|
3.1
|
67.4
|
1.0
|
C1B
|
M:BCL403
|
3.1
|
74.2
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
68.6
|
1.0
|
C4A
|
M:BCL403
|
3.2
|
67.7
|
1.0
|
C1D
|
M:BCL403
|
3.2
|
75.2
|
1.0
|
C1C
|
M:BCL403
|
3.2
|
76.1
|
1.0
|
C4C
|
M:BCL403
|
3.2
|
76.1
|
1.0
|
C1A
|
M:BCL403
|
3.2
|
75.0
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
71.3
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
71.8
|
1.0
|
CHA
|
M:BCL403
|
3.5
|
72.4
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
71.4
|
1.0
|
CBB
|
L:BCL301
|
3.7
|
71.2
|
1.0
|
CAB
|
L:BCL301
|
3.9
|
74.9
|
1.0
|
ND1
|
M:HIS202
|
3.9
|
62.4
|
1.0
|
OBB
|
L:BCL301
|
4.0
|
71.8
|
1.0
|
CG
|
M:HIS202
|
4.1
|
64.0
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
70.5
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
72.5
|
1.0
|
C2D
|
M:BCL403
|
4.3
|
71.0
|
1.0
|
C3B
|
M:BCL403
|
4.4
|
77.3
|
1.0
|
C2C
|
M:BCL403
|
4.4
|
71.4
|
1.0
|
C3A
|
M:BCL403
|
4.5
|
71.0
|
1.0
|
C3C
|
M:BCL403
|
4.5
|
75.2
|
1.0
|
C2A
|
M:BCL403
|
4.5
|
69.0
|
1.0
|
C3B
|
L:BCL301
|
4.6
|
68.8
|
1.0
|
CBD
|
M:BCL403
|
4.9
|
68.2
|
1.0
|
CD1
|
M:ILE206
|
4.9
|
57.4
|
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 20:09:45 2024
|