Magnesium in PDB 7q7m: Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
Protein crystallography data
The structure of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary, PDB code: 7q7m
was solved by
J.Lieske,
S.Guenther,
S.Saouane,
G.K.Selikhanov,
A.G.Gabdulkhakov,
A.Meents,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.95 /
2.55
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.21,
102.21,
237.71,
90,
90,
90
|
R / Rfree (%)
|
18.3 /
22.3
|
Other elements in 7q7m:
The structure of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
(pdb code 7q7m). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary, PDB code: 7q7m:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7q7m
Go back to
Magnesium Binding Sites List in 7q7m
Magnesium binding site 1 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:29.5
occ:1.00
|
MG
|
L:BCL302
|
0.0
|
29.5
|
1.0
|
ND
|
L:BCL302
|
2.0
|
30.6
|
1.0
|
NB
|
L:BCL302
|
2.1
|
28.9
|
1.0
|
NC
|
L:BCL302
|
2.1
|
28.9
|
1.0
|
NA
|
L:BCL302
|
2.2
|
26.9
|
1.0
|
NE2
|
L:HIS153
|
2.2
|
31.5
|
1.0
|
C4D
|
L:BCL302
|
3.0
|
30.4
|
1.0
|
C4B
|
L:BCL302
|
3.1
|
27.9
|
1.0
|
C1B
|
L:BCL302
|
3.1
|
27.6
|
1.0
|
C1C
|
L:BCL302
|
3.1
|
29.8
|
1.0
|
CE1
|
L:HIS153
|
3.1
|
31.6
|
1.0
|
C4A
|
L:BCL302
|
3.1
|
27.8
|
1.0
|
C1D
|
L:BCL302
|
3.1
|
31.4
|
1.0
|
C4C
|
L:BCL302
|
3.2
|
28.6
|
1.0
|
C1A
|
L:BCL302
|
3.2
|
27.1
|
1.0
|
CD2
|
L:HIS153
|
3.2
|
34.1
|
1.0
|
HE1
|
L:HIS153
|
3.3
|
38.0
|
1.0
|
HD2
|
L:HIS153
|
3.4
|
41.0
|
1.0
|
CHC
|
L:BCL302
|
3.4
|
29.6
|
1.0
|
CHB
|
L:BCL302
|
3.4
|
27.5
|
1.0
|
CHA
|
L:BCL302
|
3.5
|
31.2
|
1.0
|
CHD
|
L:BCL302
|
3.5
|
30.4
|
1.0
|
HE2
|
M:TYR210
|
4.0
|
30.9
|
1.0
|
HBB3
|
L:BPH301
|
4.1
|
36.5
|
1.0
|
HBB2
|
L:BPH301
|
4.2
|
36.5
|
1.0
|
HBC1
|
L:BCL302
|
4.2
|
40.0
|
1.0
|
C3D
|
L:BCL302
|
4.2
|
32.6
|
1.0
|
H201
|
L:BPH301
|
4.2
|
50.6
|
1.0
|
ND1
|
L:HIS153
|
4.2
|
32.5
|
1.0
|
C2D
|
L:BCL302
|
4.3
|
29.9
|
1.0
|
C2B
|
L:BCL302
|
4.3
|
27.4
|
1.0
|
HD12
|
L:LEU154
|
4.3
|
48.6
|
1.0
|
CG
|
L:HIS153
|
4.3
|
32.2
|
1.0
|
C3B
|
L:BCL302
|
4.3
|
30.3
|
1.0
|
HD11
|
L:LEU154
|
4.4
|
48.6
|
1.0
|
C2C
|
L:BCL302
|
4.4
|
29.3
|
1.0
|
H202
|
L:BPH301
|
4.4
|
50.6
|
1.0
|
C3A
|
L:BCL302
|
4.4
|
25.9
|
1.0
|
C3C
|
L:BCL302
|
4.5
|
28.4
|
1.0
|
C2A
|
L:BCL302
|
4.5
|
26.2
|
1.0
|
HHC
|
L:BCL302
|
4.5
|
35.5
|
1.0
|
HHB
|
L:BCL302
|
4.5
|
33.0
|
1.0
|
HBA1
|
L:BCL302
|
4.5
|
33.6
|
1.0
|
HBA2
|
L:BCL302
|
4.6
|
33.6
|
1.0
|
CBB
|
L:BPH301
|
4.6
|
30.4
|
1.0
|
HHD
|
L:BCL302
|
4.6
|
36.5
|
1.0
|
HBB1
|
L:BPH301
|
4.6
|
36.5
|
1.0
|
HMC1
|
L:BCL302
|
4.7
|
38.5
|
1.0
|
HMA1
|
L:BCL302
|
4.7
|
33.3
|
1.0
|
CD1
|
L:LEU154
|
4.8
|
40.5
|
1.0
|
HBC3
|
L:BCL302
|
4.8
|
40.0
|
1.0
|
CE2
|
M:TYR210
|
4.9
|
25.7
|
1.0
|
C20
|
L:BPH301
|
4.9
|
42.1
|
1.0
|
CBD
|
L:BCL302
|
4.9
|
37.4
|
1.0
|
CBC
|
L:BCL302
|
4.9
|
33.3
|
1.0
|
HD1
|
L:HIS153
|
5.0
|
39.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7q7m
Go back to
Magnesium Binding Sites List in 7q7m
Magnesium binding site 2 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg303
b:28.1
occ:1.00
|
MG
|
L:BCL303
|
0.0
|
28.1
|
1.0
|
ND
|
L:BCL303
|
2.0
|
36.6
|
1.0
|
NB
|
L:BCL303
|
2.1
|
30.0
|
1.0
|
NC
|
L:BCL303
|
2.1
|
35.9
|
1.0
|
NE2
|
L:HIS173
|
2.1
|
43.7
|
1.0
|
NA
|
L:BCL303
|
2.2
|
31.3
|
1.0
|
HBB3
|
M:BCL402
|
2.7
|
44.7
|
1.0
|
CE1
|
L:HIS173
|
2.9
|
40.5
|
1.0
|
HE1
|
L:HIS173
|
3.0
|
48.7
|
1.0
|
C4D
|
L:BCL303
|
3.0
|
35.7
|
1.0
|
C1B
|
L:BCL303
|
3.1
|
30.9
|
1.0
|
C4B
|
L:BCL303
|
3.1
|
32.2
|
1.0
|
C1C
|
L:BCL303
|
3.1
|
42.0
|
1.0
|
C4A
|
L:BCL303
|
3.1
|
31.2
|
1.0
|
C1D
|
L:BCL303
|
3.2
|
33.8
|
1.0
|
C4C
|
L:BCL303
|
3.2
|
36.0
|
1.0
|
C1A
|
L:BCL303
|
3.2
|
30.6
|
1.0
|
CD2
|
L:HIS173
|
3.3
|
40.2
|
1.0
|
CHC
|
L:BCL303
|
3.4
|
34.9
|
1.0
|
CHB
|
L:BCL303
|
3.4
|
29.8
|
1.0
|
CHA
|
L:BCL303
|
3.5
|
34.5
|
1.0
|
CHD
|
L:BCL303
|
3.5
|
36.5
|
1.0
|
HD2
|
L:HIS173
|
3.6
|
48.3
|
1.0
|
CBB
|
M:BCL402
|
3.6
|
37.2
|
1.0
|
HBB2
|
M:BCL402
|
3.6
|
44.7
|
1.0
|
HD2
|
L:PHE167
|
4.0
|
57.0
|
1.0
|
ND1
|
L:HIS173
|
4.1
|
40.6
|
1.0
|
CAB
|
M:BCL402
|
4.2
|
38.7
|
1.0
|
C3D
|
L:BCL303
|
4.3
|
32.2
|
1.0
|
CG
|
L:HIS173
|
4.3
|
40.4
|
1.0
|
C2B
|
L:BCL303
|
4.3
|
35.2
|
1.0
|
C2D
|
L:BCL303
|
4.3
|
34.4
|
1.0
|
C3B
|
L:BCL303
|
4.3
|
36.5
|
1.0
|
HD11
|
L:ILE177
|
4.4
|
35.8
|
1.0
|
C3A
|
L:BCL303
|
4.4
|
29.2
|
1.0
|
C2C
|
L:BCL303
|
4.4
|
41.0
|
1.0
|
HBB1
|
M:BCL402
|
4.5
|
44.7
|
1.0
|
C3C
|
L:BCL303
|
4.5
|
40.5
|
1.0
|
HHB
|
L:BCL303
|
4.5
|
35.8
|
1.0
|
HHC
|
L:BCL303
|
4.5
|
41.9
|
1.0
|
C2A
|
L:BCL303
|
4.5
|
30.7
|
1.0
|
HHD
|
L:BCL303
|
4.6
|
43.9
|
1.0
|
OBB
|
M:BCL402
|
4.6
|
33.5
|
1.0
|
HMA1
|
L:BCL303
|
4.6
|
35.9
|
1.0
|
CD2
|
L:PHE167
|
4.7
|
47.5
|
1.0
|
HB3
|
L:PHE167
|
4.7
|
53.3
|
1.0
|
HMB2
|
M:BCL402
|
4.7
|
41.6
|
1.0
|
C3B
|
M:BCL402
|
4.7
|
39.5
|
1.0
|
HMC1
|
L:BCL303
|
4.8
|
44.8
|
1.0
|
HD1
|
L:HIS173
|
4.8
|
48.8
|
1.0
|
CBD
|
L:BCL303
|
5.0
|
31.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7q7m
Go back to
Magnesium Binding Sites List in 7q7m
Magnesium binding site 3 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:35.5
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
35.5
|
1.0
|
ND
|
M:BCL402
|
2.0
|
34.1
|
1.0
|
NB
|
M:BCL402
|
2.1
|
39.2
|
1.0
|
NC
|
M:BCL402
|
2.1
|
37.5
|
1.0
|
NA
|
M:BCL402
|
2.2
|
33.7
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
30.6
|
1.0
|
C4D
|
M:BCL402
|
3.0
|
30.8
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
38.8
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
36.7
|
1.0
|
C1C
|
M:BCL402
|
3.1
|
36.2
|
1.0
|
C1D
|
M:BCL402
|
3.1
|
33.1
|
1.0
|
C4A
|
M:BCL402
|
3.1
|
30.2
|
1.0
|
C4C
|
M:BCL402
|
3.2
|
33.2
|
1.0
|
C1A
|
M:BCL402
|
3.2
|
31.8
|
1.0
|
HBB1
|
L:BCL303
|
3.3
|
41.4
|
1.0
|
CD2
|
M:HIS202
|
3.3
|
31.3
|
1.0
|
CE1
|
M:HIS202
|
3.3
|
33.3
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
37.1
|
1.0
|
HBB2
|
L:BCL303
|
3.4
|
41.4
|
1.0
|
CHA
|
M:BCL402
|
3.4
|
31.4
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
33.8
|
1.0
|
HD2
|
M:HIS202
|
3.5
|
37.6
|
1.0
|
HE1
|
M:HIS202
|
3.5
|
40.0
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
29.2
|
1.0
|
CBB
|
L:BCL303
|
3.7
|
34.4
|
1.0
|
CAB
|
L:BCL303
|
3.9
|
34.2
|
1.0
|
OBB
|
L:BCL303
|
4.0
|
30.5
|
1.0
|
HD11
|
M:ILE206
|
4.2
|
47.0
|
1.0
|
C3D
|
M:BCL402
|
4.2
|
33.6
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
34.5
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
33.8
|
1.0
|
C3B
|
M:BCL402
|
4.3
|
39.5
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
33.9
|
1.0
|
C3C
|
M:BCL402
|
4.4
|
36.8
|
1.0
|
HHC
|
M:BCL402
|
4.5
|
44.5
|
1.0
|
ND1
|
M:HIS202
|
4.5
|
33.3
|
1.0
|
C3A
|
M:BCL402
|
4.5
|
32.9
|
1.0
|
CG
|
M:HIS202
|
4.5
|
33.4
|
1.0
|
C2A
|
M:BCL402
|
4.5
|
30.4
|
1.0
|
HHB
|
M:BCL402
|
4.5
|
40.6
|
1.0
|
HD12
|
M:LEU196
|
4.5
|
43.9
|
1.0
|
C3B
|
L:BCL303
|
4.6
|
36.5
|
1.0
|
HHD
|
M:BCL402
|
4.6
|
35.1
|
1.0
|
HMC1
|
M:BCL402
|
4.6
|
38.5
|
1.0
|
HBB3
|
L:BCL303
|
4.7
|
41.4
|
1.0
|
HG13
|
M:ILE206
|
4.8
|
45.5
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
34.8
|
1.0
|
HMB1
|
L:BCL303
|
4.9
|
36.2
|
1.0
|
CD1
|
M:ILE206
|
4.9
|
39.2
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7q7m
Go back to
Magnesium Binding Sites List in 7q7m
Magnesium binding site 4 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at 100 Mpa Helium Gas Pressure in A Sapphire Capillary within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:35.8
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
35.8
|
1.0
|
ND
|
M:BCL403
|
2.0
|
31.1
|
1.0
|
NB
|
M:BCL403
|
2.1
|
31.5
|
1.0
|
NC
|
M:BCL403
|
2.1
|
30.7
|
1.0
|
NA
|
M:BCL403
|
2.2
|
30.3
|
1.0
|
NE2
|
M:HIS182
|
2.2
|
33.6
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
30.2
|
1.0
|
CD2
|
M:HIS182
|
3.1
|
35.8
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
29.0
|
1.0
|
C1B
|
M:BCL403
|
3.1
|
27.7
|
1.0
|
C1C
|
M:BCL403
|
3.1
|
32.7
|
1.0
|
C4A
|
M:BCL403
|
3.1
|
29.1
|
1.0
|
C1D
|
M:BCL403
|
3.1
|
31.6
|
1.0
|
C4C
|
M:BCL403
|
3.1
|
30.6
|
1.0
|
HD2
|
M:HIS182
|
3.2
|
43.0
|
1.0
|
C1A
|
M:BCL403
|
3.2
|
30.6
|
1.0
|
CE1
|
M:HIS182
|
3.2
|
37.0
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
29.7
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
27.9
|
1.0
|
CHA
|
M:BCL403
|
3.5
|
29.9
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
30.4
|
1.0
|
HE1
|
M:HIS182
|
3.5
|
44.4
|
1.0
|
HM52
|
M:SPN410
|
3.8
|
71.2
|
0.7
|
HBB3
|
M:BPH404
|
4.1
|
43.7
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
31.0
|
1.0
|
CG
|
M:HIS182
|
4.3
|
39.0
|
1.0
|
HE2
|
L:PHE181
|
4.3
|
34.2
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
27.3
|
1.0
|
C2D
|
M:BCL403
|
4.3
|
30.4
|
1.0
|
ND1
|
M:HIS182
|
4.3
|
39.2
|
1.0
|
C3B
|
M:BCL403
|
4.3
|
31.4
|
1.0
|
C3A
|
M:BCL403
|
4.4
|
31.7
|
1.0
|
HBA2
|
M:BCL403
|
4.4
|
46.7
|
1.0
|
C2C
|
M:BCL403
|
4.4
|
31.3
|
1.0
|
C3C
|
M:BCL403
|
4.4
|
31.6
|
1.0
|
HBB2
|
M:BPH404
|
4.4
|
43.7
|
1.0
|
HHB
|
M:BCL403
|
4.5
|
33.5
|
1.0
|
C2A
|
M:BCL403
|
4.5
|
33.7
|
1.0
|
HHC
|
M:BCL403
|
4.5
|
35.6
|
1.0
|
H141
|
M:SPN410
|
4.5
|
71.4
|
0.7
|
H3A
|
M:OLC409
|
4.5
|
75.5
|
0.3
|
HMA1
|
M:BCL403
|
4.5
|
39.3
|
1.0
|
HHD
|
M:BCL403
|
4.6
|
36.5
|
1.0
|
H3
|
M:OLC409
|
4.6
|
75.5
|
0.3
|
HD23
|
M:LEU183
|
4.6
|
62.3
|
1.0
|
HBC1
|
M:BCL403
|
4.7
|
40.2
|
1.0
|
CBB
|
M:BPH404
|
4.8
|
36.4
|
1.0
|
CM5
|
M:SPN410
|
4.8
|
59.3
|
0.7
|
H2
|
M:OLC409
|
4.8
|
70.2
|
0.3
|
HM53
|
M:SPN410
|
4.9
|
71.2
|
0.7
|
H41
|
M:BCL402
|
4.9
|
48.4
|
1.0
|
HMC1
|
M:BCL403
|
4.9
|
37.2
|
1.0
|
CBD
|
M:BCL403
|
4.9
|
29.9
|
1.0
|
CMA
|
M:BCL403
|
5.0
|
32.7
|
1.0
|
H3C
|
M:BCL403
|
5.0
|
38.0
|
1.0
|
|
Reference:
J.Lieske,
S.Saouane,
S.Guenther,
J.Meyer,
T.Pakendorf,
B.Reime,
A.Burkhardt,
E.Crosas,
J.Hakanpaeae,
K.Stachnik,
J.Sieg,
M.Rarey,
M.H.Abdellatif,
A.G.Gabdulkhakov,
G.K.Selikhanov,
H.N.Chapman,
A.Meents.
Fixed-Target High-Pressure Macromolecular Crystallography To Be Published.
Page generated: Thu Oct 3 05:00:01 2024
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