Magnesium in PDB 7q7o: Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release
Protein crystallography data
The structure of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release, PDB code: 7q7o
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)
|
47.07 /
2.65
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
102.52,
102.52,
237.68,
90,
90,
90
|
R / Rfree (%)
|
17.6 /
21.5
|
Other elements in 7q7o:
The structure of Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release 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 Atmospheric Pressure After High Helium Gas Pressure Release
(pdb code 7q7o). 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 Atmospheric Pressure After High Helium Gas Pressure Release, PDB code: 7q7o:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7q7o
Go back to
Magnesium Binding Sites List in 7q7o
Magnesium binding site 1 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release
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 Atmospheric Pressure After High Helium Gas Pressure Release within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:36.1
occ:1.00
|
MG
|
L:BCL302
|
0.0
|
36.1
|
1.0
|
ND
|
L:BCL302
|
2.0
|
35.8
|
1.0
|
NB
|
L:BCL302
|
2.1
|
36.6
|
1.0
|
NC
|
L:BCL302
|
2.1
|
36.2
|
1.0
|
NA
|
L:BCL302
|
2.2
|
35.9
|
1.0
|
NE2
|
L:HIS153
|
2.2
|
44.6
|
1.0
|
C4D
|
L:BCL302
|
3.0
|
35.9
|
1.0
|
CE1
|
L:HIS153
|
3.1
|
45.7
|
1.0
|
C4B
|
L:BCL302
|
3.1
|
35.8
|
1.0
|
C1B
|
L:BCL302
|
3.1
|
35.7
|
1.0
|
C1C
|
L:BCL302
|
3.1
|
36.4
|
1.0
|
C1D
|
L:BCL302
|
3.1
|
36.0
|
1.0
|
C4A
|
L:BCL302
|
3.1
|
36.3
|
1.0
|
C4C
|
L:BCL302
|
3.2
|
35.2
|
1.0
|
C1A
|
L:BCL302
|
3.2
|
35.9
|
1.0
|
HE1
|
L:HIS153
|
3.2
|
54.8
|
1.0
|
CD2
|
L:HIS153
|
3.2
|
45.8
|
1.0
|
CHC
|
L:BCL302
|
3.4
|
35.9
|
1.0
|
CHB
|
L:BCL302
|
3.4
|
35.8
|
1.0
|
HD2
|
L:HIS153
|
3.4
|
54.9
|
1.0
|
CHA
|
L:BCL302
|
3.4
|
36.2
|
1.0
|
CHD
|
L:BCL302
|
3.5
|
35.6
|
1.0
|
HE2
|
M:TYR210
|
4.0
|
43.3
|
1.0
|
HBB2
|
L:BPH301
|
4.2
|
47.7
|
1.0
|
HBC1
|
L:BCL302
|
4.2
|
43.5
|
1.0
|
ND1
|
L:HIS153
|
4.2
|
47.6
|
1.0
|
C3D
|
L:BCL302
|
4.2
|
37.6
|
1.0
|
HD12
|
L:LEU154
|
4.2
|
58.8
|
1.0
|
HD11
|
L:LEU154
|
4.3
|
58.8
|
1.0
|
H201
|
L:BPH301
|
4.3
|
49.5
|
1.0
|
C2D
|
L:BCL302
|
4.3
|
36.6
|
1.0
|
CG
|
L:HIS153
|
4.3
|
46.5
|
1.0
|
C2B
|
L:BCL302
|
4.3
|
35.3
|
1.0
|
H202
|
L:BPH301
|
4.3
|
49.5
|
1.0
|
C3B
|
L:BCL302
|
4.3
|
35.9
|
1.0
|
HBB3
|
L:BPH301
|
4.4
|
47.7
|
1.0
|
C2C
|
L:BCL302
|
4.4
|
36.4
|
1.0
|
HBA1
|
L:BCL302
|
4.4
|
47.7
|
1.0
|
C3A
|
L:BCL302
|
4.4
|
35.9
|
1.0
|
C3C
|
L:BCL302
|
4.5
|
34.9
|
1.0
|
HHC
|
L:BCL302
|
4.5
|
43.1
|
1.0
|
C2A
|
L:BCL302
|
4.5
|
36.5
|
1.0
|
HHB
|
L:BCL302
|
4.5
|
42.9
|
1.0
|
HHD
|
L:BCL302
|
4.6
|
42.7
|
1.0
|
CBB
|
L:BPH301
|
4.6
|
39.8
|
1.0
|
HBB1
|
L:BPH301
|
4.6
|
47.7
|
1.0
|
CD1
|
L:LEU154
|
4.7
|
49.0
|
1.0
|
HBA2
|
L:BCL302
|
4.7
|
47.7
|
1.0
|
HMA1
|
L:BCL302
|
4.8
|
42.2
|
1.0
|
HMC1
|
L:BCL302
|
4.8
|
45.5
|
1.0
|
C20
|
L:BPH301
|
4.8
|
41.3
|
1.0
|
CE2
|
M:TYR210
|
4.9
|
36.1
|
1.0
|
CBD
|
L:BCL302
|
4.9
|
38.0
|
1.0
|
HD13
|
L:LEU154
|
4.9
|
58.8
|
1.0
|
HD1
|
L:HIS153
|
4.9
|
57.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7q7o
Go back to
Magnesium Binding Sites List in 7q7o
Magnesium binding site 2 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release
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 Atmospheric Pressure After High Helium Gas Pressure Release within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg303
b:38.1
occ:1.00
|
MG
|
L:BCL303
|
0.0
|
38.1
|
1.0
|
ND
|
L:BCL303
|
2.0
|
42.6
|
1.0
|
NB
|
L:BCL303
|
2.1
|
42.0
|
1.0
|
NE2
|
L:HIS173
|
2.1
|
53.2
|
1.0
|
NC
|
L:BCL303
|
2.1
|
45.1
|
1.0
|
NA
|
L:BCL303
|
2.2
|
40.8
|
1.0
|
HBB3
|
M:BCL402
|
2.7
|
54.6
|
1.0
|
CE1
|
L:HIS173
|
2.9
|
50.0
|
1.0
|
HE1
|
L:HIS173
|
2.9
|
59.9
|
1.0
|
C4D
|
L:BCL303
|
3.0
|
43.0
|
1.0
|
C4B
|
L:BCL303
|
3.1
|
43.9
|
1.0
|
C1B
|
L:BCL303
|
3.1
|
42.3
|
1.0
|
C1C
|
L:BCL303
|
3.1
|
46.7
|
1.0
|
C4A
|
L:BCL303
|
3.1
|
41.0
|
1.0
|
C1D
|
L:BCL303
|
3.2
|
43.8
|
1.0
|
C4C
|
L:BCL303
|
3.2
|
46.0
|
1.0
|
C1A
|
L:BCL303
|
3.2
|
40.8
|
1.0
|
CD2
|
L:HIS173
|
3.3
|
49.8
|
1.0
|
CHC
|
L:BCL303
|
3.4
|
45.2
|
1.0
|
CHB
|
L:BCL303
|
3.4
|
41.6
|
1.0
|
CHA
|
L:BCL303
|
3.5
|
41.7
|
1.0
|
CHD
|
L:BCL303
|
3.5
|
45.3
|
1.0
|
CBB
|
M:BCL402
|
3.6
|
45.5
|
1.0
|
HD2
|
L:HIS173
|
3.6
|
59.7
|
1.0
|
HBB2
|
M:BCL402
|
3.7
|
54.6
|
1.0
|
ND1
|
L:HIS173
|
4.1
|
49.7
|
1.0
|
CAB
|
M:BCL402
|
4.1
|
45.5
|
1.0
|
HD2
|
L:PHE167
|
4.2
|
62.9
|
1.0
|
C3D
|
L:BCL303
|
4.2
|
43.0
|
1.0
|
C2B
|
L:BCL303
|
4.3
|
42.7
|
1.0
|
CG
|
L:HIS173
|
4.3
|
48.0
|
1.0
|
C2D
|
L:BCL303
|
4.3
|
43.9
|
1.0
|
C3B
|
L:BCL303
|
4.3
|
43.7
|
1.0
|
C3A
|
L:BCL303
|
4.4
|
40.3
|
1.0
|
C2C
|
L:BCL303
|
4.4
|
47.8
|
1.0
|
HBB1
|
M:BCL402
|
4.5
|
54.6
|
1.0
|
C3C
|
L:BCL303
|
4.5
|
47.7
|
1.0
|
HD11
|
L:ILE177
|
4.5
|
45.1
|
1.0
|
HHC
|
L:BCL303
|
4.5
|
54.1
|
1.0
|
HHB
|
L:BCL303
|
4.5
|
49.9
|
1.0
|
C2A
|
L:BCL303
|
4.5
|
39.9
|
1.0
|
OBB
|
M:BCL402
|
4.5
|
44.6
|
1.0
|
HHD
|
L:BCL303
|
4.6
|
54.3
|
1.0
|
HMA1
|
L:BCL303
|
4.6
|
49.2
|
1.0
|
HMB2
|
M:BCL402
|
4.7
|
53.9
|
1.0
|
C3B
|
M:BCL402
|
4.7
|
45.9
|
1.0
|
HD1
|
L:HIS173
|
4.8
|
59.6
|
1.0
|
HB3
|
L:PHE167
|
4.8
|
62.6
|
1.0
|
CD2
|
L:PHE167
|
4.9
|
52.5
|
1.0
|
HMC1
|
L:BCL303
|
4.9
|
57.8
|
1.0
|
CBD
|
L:BCL303
|
5.0
|
40.0
|
1.0
|
HAC2
|
L:BCL303
|
5.0
|
59.7
|
1.0
|
CMA
|
L:BCL303
|
5.0
|
41.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7q7o
Go back to
Magnesium Binding Sites List in 7q7o
Magnesium binding site 3 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release
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 Atmospheric Pressure After High Helium Gas Pressure Release within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg402
b:43.0
occ:1.00
|
MG
|
M:BCL402
|
0.0
|
43.0
|
1.0
|
ND
|
M:BCL402
|
2.0
|
42.0
|
1.0
|
NB
|
M:BCL402
|
2.1
|
45.0
|
1.0
|
NC
|
M:BCL402
|
2.1
|
44.7
|
1.0
|
NA
|
M:BCL402
|
2.2
|
44.1
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
36.8
|
1.0
|
C4D
|
M:BCL402
|
3.0
|
41.2
|
1.0
|
C4B
|
M:BCL402
|
3.1
|
45.1
|
1.0
|
C1B
|
M:BCL402
|
3.1
|
44.9
|
1.0
|
C1C
|
M:BCL402
|
3.1
|
43.8
|
1.0
|
C4A
|
M:BCL402
|
3.1
|
44.1
|
1.0
|
C4C
|
M:BCL402
|
3.1
|
43.7
|
1.0
|
C1D
|
M:BCL402
|
3.2
|
41.9
|
1.0
|
C1A
|
M:BCL402
|
3.2
|
42.5
|
1.0
|
CD2
|
M:HIS202
|
3.3
|
38.0
|
1.0
|
HBB1
|
L:BCL303
|
3.3
|
54.6
|
1.0
|
CE1
|
M:HIS202
|
3.4
|
38.2
|
1.0
|
CHC
|
M:BCL402
|
3.4
|
44.0
|
1.0
|
HBB2
|
L:BCL303
|
3.4
|
54.6
|
1.0
|
CHB
|
M:BCL402
|
3.4
|
44.4
|
1.0
|
CHA
|
M:BCL402
|
3.4
|
41.4
|
1.0
|
HD2
|
M:HIS202
|
3.4
|
45.6
|
1.0
|
CHD
|
M:BCL402
|
3.5
|
41.8
|
1.0
|
HE1
|
M:HIS202
|
3.5
|
45.8
|
1.0
|
CBB
|
L:BCL303
|
3.7
|
45.5
|
1.0
|
CAB
|
L:BCL303
|
3.9
|
44.1
|
1.0
|
OBB
|
L:BCL303
|
4.0
|
42.3
|
1.0
|
HD11
|
M:ILE206
|
4.2
|
50.2
|
1.0
|
C3D
|
M:BCL402
|
4.2
|
41.4
|
1.0
|
C2B
|
M:BCL402
|
4.3
|
45.3
|
1.0
|
C3B
|
M:BCL402
|
4.3
|
45.9
|
1.0
|
C2D
|
M:BCL402
|
4.3
|
41.4
|
1.0
|
C2C
|
M:BCL402
|
4.4
|
43.6
|
1.0
|
C3C
|
M:BCL402
|
4.4
|
44.5
|
1.0
|
C3A
|
M:BCL402
|
4.4
|
43.3
|
1.0
|
C2A
|
M:BCL402
|
4.5
|
43.0
|
1.0
|
HHC
|
M:BCL402
|
4.5
|
52.7
|
1.0
|
ND1
|
M:HIS202
|
4.5
|
38.4
|
1.0
|
CG
|
M:HIS202
|
4.5
|
38.9
|
1.0
|
HHB
|
M:BCL402
|
4.5
|
53.2
|
1.0
|
HHD
|
M:BCL402
|
4.6
|
50.1
|
1.0
|
HD12
|
M:LEU196
|
4.6
|
53.7
|
1.0
|
C3B
|
L:BCL303
|
4.6
|
43.7
|
1.0
|
HMC1
|
M:BCL402
|
4.7
|
52.1
|
1.0
|
HBB3
|
L:BCL303
|
4.8
|
54.6
|
1.0
|
CBD
|
M:BCL402
|
4.9
|
41.7
|
1.0
|
HG13
|
M:ILE206
|
4.9
|
47.9
|
1.0
|
O2D
|
M:BCL402
|
4.9
|
41.3
|
1.0
|
HMA1
|
M:BCL402
|
5.0
|
50.1
|
1.0
|
H2A
|
M:BCL402
|
5.0
|
51.5
|
1.0
|
CD1
|
M:ILE206
|
5.0
|
41.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7q7o
Go back to
Magnesium Binding Sites List in 7q7o
Magnesium binding site 4 out
of 4 in the Room Temperature Structure of the Rhodobacter Sphaeroides Photosynthetic Reaction Center F(M197)H Mutant at Atmospheric Pressure After High Helium Gas Pressure Release
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 Atmospheric Pressure After High Helium Gas Pressure Release within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg403
b:34.1
occ:1.00
|
MG
|
M:BCL403
|
0.0
|
34.1
|
1.0
|
ND
|
M:BCL403
|
2.0
|
31.4
|
1.0
|
NB
|
M:BCL403
|
2.1
|
32.2
|
1.0
|
NC
|
M:BCL403
|
2.1
|
34.9
|
1.0
|
NA
|
M:BCL403
|
2.2
|
34.0
|
1.0
|
NE2
|
M:HIS182
|
2.2
|
49.1
|
1.0
|
C4D
|
M:BCL403
|
3.0
|
32.8
|
1.0
|
CE1
|
M:HIS182
|
3.0
|
49.9
|
1.0
|
C1B
|
M:BCL403
|
3.1
|
31.6
|
1.0
|
C4B
|
M:BCL403
|
3.1
|
33.3
|
1.0
|
HE1
|
M:HIS182
|
3.1
|
59.8
|
1.0
|
C1D
|
M:BCL403
|
3.1
|
32.5
|
1.0
|
C1C
|
M:BCL403
|
3.1
|
35.4
|
1.0
|
C4A
|
M:BCL403
|
3.1
|
32.2
|
1.0
|
C4C
|
M:BCL403
|
3.1
|
34.5
|
1.0
|
C1A
|
M:BCL403
|
3.2
|
34.7
|
1.0
|
CD2
|
M:HIS182
|
3.3
|
50.3
|
1.0
|
CHB
|
M:BCL403
|
3.4
|
31.2
|
1.0
|
CHC
|
M:BCL403
|
3.4
|
34.3
|
1.0
|
CHD
|
M:BCL403
|
3.5
|
32.7
|
1.0
|
CHA
|
M:BCL403
|
3.5
|
34.6
|
1.0
|
HD2
|
M:HIS182
|
3.5
|
60.3
|
1.0
|
HM52
|
M:SPN409
|
3.9
|
78.3
|
0.5
|
HBB3
|
M:BPH304
|
4.1
|
45.7
|
1.0
|
ND1
|
M:HIS182
|
4.2
|
50.7
|
1.0
|
C3D
|
M:BCL403
|
4.2
|
33.6
|
1.0
|
HBA2
|
M:BCL403
|
4.2
|
48.4
|
1.0
|
C2B
|
M:BCL403
|
4.3
|
30.5
|
1.0
|
C2D
|
M:BCL403
|
4.3
|
32.6
|
1.0
|
HE2
|
L:PHE181
|
4.3
|
42.5
|
1.0
|
C3B
|
M:BCL403
|
4.3
|
32.8
|
1.0
|
CG
|
M:HIS182
|
4.3
|
50.1
|
1.0
|
C2C
|
M:BCL403
|
4.4
|
36.7
|
1.0
|
C3A
|
M:BCL403
|
4.4
|
33.3
|
1.0
|
HM53
|
M:SPN409
|
4.4
|
78.3
|
0.5
|
HBB2
|
M:BPH304
|
4.4
|
45.7
|
1.0
|
C3C
|
M:BCL403
|
4.4
|
36.5
|
1.0
|
HHB
|
M:BCL403
|
4.5
|
37.4
|
1.0
|
H2
|
M:OLC408
|
4.5
|
77.2
|
0.5
|
HHC
|
M:BCL403
|
4.5
|
41.2
|
1.0
|
C2A
|
M:BCL403
|
4.5
|
35.2
|
1.0
|
HHD
|
M:BCL403
|
4.5
|
39.1
|
1.0
|
HD23
|
M:LEU183
|
4.6
|
59.6
|
1.0
|
HMA1
|
M:BCL403
|
4.6
|
38.8
|
1.0
|
CM5
|
M:SPN409
|
4.7
|
65.3
|
0.5
|
H3A
|
M:OLC408
|
4.7
|
78.3
|
0.5
|
H141
|
M:SPN409
|
4.7
|
76.8
|
0.5
|
CBB
|
M:BPH304
|
4.8
|
38.1
|
1.0
|
H3
|
M:OLC408
|
4.8
|
78.3
|
0.5
|
HBC1
|
M:BCL403
|
4.8
|
47.1
|
1.0
|
HD21
|
M:LEU183
|
4.9
|
59.6
|
1.0
|
HD1
|
M:HIS182
|
4.9
|
60.8
|
1.0
|
H3C
|
M:BCL403
|
4.9
|
43.8
|
1.0
|
CBD
|
M:BCL403
|
4.9
|
35.9
|
1.0
|
HMC1
|
M:BCL403
|
4.9
|
45.3
|
1.0
|
H41
|
M:BCL402
|
5.0
|
52.1
|
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 05:00:18 2024
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