Magnesium in PDB 2x5v: 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
Protein crystallography data
The structure of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation., PDB code: 2x5v
was solved by
A.B.Wohri,
G.Katona,
L.C.Johansson,
E.Fritz,
E.Malmerberg,
M.Andersson,
J.Vincent,
M.Eklund,
M.Cammarata,
M.Wulff,
J.Davidsson,
G.Groenhof,
R.Neutze,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.18 /
3.00
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.693,
143.470,
177.998,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
27.7 /
31.9
|
Other elements in 2x5v:
The structure of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation. also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
(pdb code 2x5v). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation., PDB code: 2x5v:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 2x5v
Go back to
Magnesium Binding Sites List in 2x5v
Magnesium binding site 1 out
of 4 in the 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg1274
b:13.1
occ:1.00
|
MG
|
L:BCB1274
|
0.0
|
13.1
|
1.0
|
NA
|
L:BCB1274
|
2.0
|
13.0
|
1.0
|
NC
|
L:BCB1274
|
2.0
|
12.6
|
1.0
|
NB
|
L:BCB1274
|
2.0
|
12.4
|
1.0
|
ND
|
L:BCB1274
|
2.1
|
12.9
|
1.0
|
NE2
|
L:HIS173
|
2.4
|
16.5
|
1.0
|
C1A
|
L:BCB1274
|
3.0
|
13.2
|
1.0
|
C4A
|
L:BCB1274
|
3.0
|
12.7
|
1.0
|
C4D
|
L:BCB1274
|
3.1
|
12.4
|
1.0
|
C1B
|
L:BCB1274
|
3.1
|
12.4
|
1.0
|
C4B
|
L:BCB1274
|
3.1
|
12.0
|
1.0
|
C4C
|
L:BCB1274
|
3.1
|
12.6
|
1.0
|
C1C
|
L:BCB1274
|
3.1
|
12.8
|
1.0
|
C1D
|
L:BCB1274
|
3.1
|
12.4
|
1.0
|
OBB
|
M:BCB1325
|
3.1
|
18.3
|
1.0
|
CE1
|
L:HIS173
|
3.2
|
17.7
|
1.0
|
CAB
|
M:BCB1325
|
3.3
|
17.4
|
1.0
|
CHB
|
L:BCB1274
|
3.4
|
12.5
|
1.0
|
CHA
|
L:BCB1274
|
3.4
|
11.9
|
1.0
|
CHC
|
L:BCB1274
|
3.5
|
12.1
|
1.0
|
CHD
|
L:BCB1274
|
3.5
|
12.8
|
1.0
|
CD2
|
L:HIS173
|
3.5
|
17.1
|
1.0
|
CBB
|
M:BCB1325
|
3.6
|
16.3
|
1.0
|
C3B
|
M:BCB1325
|
4.2
|
17.6
|
1.0
|
C2A
|
L:BCB1274
|
4.3
|
14.2
|
1.0
|
C3A
|
L:BCB1274
|
4.3
|
13.4
|
1.0
|
C3D
|
L:BCB1274
|
4.3
|
11.9
|
1.0
|
C2D
|
L:BCB1274
|
4.3
|
11.7
|
1.0
|
ND1
|
L:HIS173
|
4.3
|
17.9
|
1.0
|
C3C
|
L:BCB1274
|
4.4
|
12.6
|
1.0
|
C3B
|
L:BCB1274
|
4.4
|
11.7
|
1.0
|
C2B
|
L:BCB1274
|
4.4
|
11.9
|
1.0
|
CD1
|
L:TRP167
|
4.4
|
18.6
|
1.0
|
C2C
|
L:BCB1274
|
4.5
|
12.4
|
1.0
|
NE1
|
L:TRP167
|
4.5
|
19.0
|
1.0
|
CG
|
L:HIS173
|
4.6
|
18.2
|
1.0
|
CBD
|
L:BCB1274
|
4.9
|
11.6
|
1.0
|
C2B
|
M:BCB1325
|
4.9
|
17.6
|
1.0
|
C4B
|
M:BCB1325
|
5.0
|
18.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 2x5v
Go back to
Magnesium Binding Sites List in 2x5v
Magnesium binding site 2 out
of 4 in the 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg1275
b:22.2
occ:1.00
|
MG
|
L:BCB1275
|
0.0
|
22.2
|
1.0
|
NA
|
L:BCB1275
|
2.0
|
20.9
|
1.0
|
NB
|
L:BCB1275
|
2.0
|
20.8
|
1.0
|
NC
|
L:BCB1275
|
2.1
|
21.1
|
1.0
|
ND
|
L:BCB1275
|
2.1
|
21.2
|
1.0
|
NE2
|
L:HIS153
|
2.5
|
21.2
|
1.0
|
C1A
|
L:BCB1275
|
3.0
|
21.7
|
1.0
|
C4A
|
L:BCB1275
|
3.0
|
20.5
|
1.0
|
C4D
|
L:BCB1275
|
3.0
|
21.8
|
1.0
|
C4B
|
L:BCB1275
|
3.1
|
21.3
|
1.0
|
C1B
|
L:BCB1275
|
3.1
|
20.7
|
1.0
|
C1C
|
L:BCB1275
|
3.1
|
21.0
|
1.0
|
C4C
|
L:BCB1275
|
3.1
|
20.5
|
1.0
|
C1D
|
L:BCB1275
|
3.1
|
21.0
|
1.0
|
CD2
|
L:HIS153
|
3.4
|
21.1
|
1.0
|
CHB
|
L:BCB1275
|
3.4
|
20.9
|
1.0
|
CE1
|
L:HIS153
|
3.4
|
21.3
|
1.0
|
CHA
|
L:BCB1275
|
3.4
|
22.1
|
1.0
|
CHC
|
L:BCB1275
|
3.4
|
21.3
|
1.0
|
CHD
|
L:BCB1275
|
3.5
|
20.3
|
1.0
|
CE2
|
M:TYR208
|
4.2
|
17.0
|
1.0
|
C2A
|
L:BCB1275
|
4.3
|
21.5
|
1.0
|
OBB
|
L:BPB1276
|
4.3
|
28.5
|
1.0
|
C3A
|
L:BCB1275
|
4.3
|
20.6
|
1.0
|
C3D
|
L:BCB1275
|
4.3
|
22.0
|
1.0
|
C2D
|
L:BCB1275
|
4.4
|
21.4
|
1.0
|
C3C
|
L:BCB1275
|
4.4
|
20.2
|
1.0
|
C3B
|
L:BCB1275
|
4.4
|
20.6
|
1.0
|
C2B
|
L:BCB1275
|
4.4
|
20.2
|
1.0
|
C2C
|
L:BCB1275
|
4.5
|
20.9
|
1.0
|
ND1
|
L:HIS153
|
4.5
|
21.1
|
1.0
|
CG
|
L:HIS153
|
4.5
|
20.9
|
1.0
|
CD2
|
M:TYR208
|
4.9
|
16.6
|
1.0
|
CBA
|
L:BCB1275
|
4.9
|
22.1
|
1.0
|
CBD
|
L:BCB1275
|
4.9
|
22.8
|
1.0
|
C20
|
L:BPB1276
|
5.0
|
29.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 2x5v
Go back to
Magnesium Binding Sites List in 2x5v
Magnesium binding site 3 out
of 4 in the 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1324
b:21.0
occ:1.00
|
MG
|
M:BCB1324
|
0.0
|
21.0
|
1.0
|
NA
|
M:BCB1324
|
2.0
|
20.6
|
1.0
|
ND
|
M:BCB1324
|
2.1
|
19.0
|
1.0
|
NC
|
M:BCB1324
|
2.1
|
20.1
|
1.0
|
NB
|
M:BCB1324
|
2.1
|
20.3
|
1.0
|
NE2
|
M:HIS180
|
2.6
|
20.1
|
1.0
|
C1A
|
M:BCB1324
|
2.9
|
21.3
|
1.0
|
C4A
|
M:BCB1324
|
3.0
|
20.4
|
1.0
|
C4D
|
M:BCB1324
|
3.0
|
19.5
|
1.0
|
C4B
|
M:BCB1324
|
3.1
|
20.1
|
1.0
|
C1B
|
M:BCB1324
|
3.1
|
20.1
|
1.0
|
C1C
|
M:BCB1324
|
3.1
|
19.9
|
1.0
|
C4C
|
M:BCB1324
|
3.1
|
19.6
|
1.0
|
C1D
|
M:BCB1324
|
3.1
|
18.5
|
1.0
|
CHA
|
M:BCB1324
|
3.4
|
20.3
|
1.0
|
CHB
|
M:BCB1324
|
3.4
|
19.9
|
1.0
|
CHC
|
M:BCB1324
|
3.4
|
19.7
|
1.0
|
CD2
|
M:HIS180
|
3.5
|
20.2
|
1.0
|
CHD
|
M:BCB1324
|
3.5
|
19.1
|
1.0
|
CE1
|
M:HIS180
|
3.6
|
19.7
|
1.0
|
OBB
|
M:BPB1326
|
4.2
|
26.9
|
1.0
|
C2A
|
M:BCB1324
|
4.3
|
22.4
|
1.0
|
C3A
|
M:BCB1324
|
4.3
|
21.1
|
1.0
|
C3D
|
M:BCB1324
|
4.3
|
19.1
|
1.0
|
C2D
|
M:BCB1324
|
4.4
|
18.5
|
1.0
|
C3B
|
M:BCB1324
|
4.4
|
20.6
|
1.0
|
C3C
|
M:BCB1324
|
4.4
|
19.1
|
1.0
|
C2B
|
M:BCB1324
|
4.4
|
20.1
|
1.0
|
C2C
|
M:BCB1324
|
4.5
|
19.6
|
1.0
|
CBA
|
M:BCB1324
|
4.6
|
26.7
|
1.0
|
CG
|
M:HIS180
|
4.7
|
20.2
|
1.0
|
ND1
|
M:HIS180
|
4.7
|
19.4
|
1.0
|
CE2
|
L:PHE181
|
4.7
|
18.6
|
1.0
|
CBD
|
M:BCB1324
|
4.9
|
19.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 2x5v
Go back to
Magnesium Binding Sites List in 2x5v
Magnesium binding site 4 out
of 4 in the 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of 80 Microsecond Laue Diffraction Snapshot From Crystals of A Photosynthetic Reaction Centre 3 Millisecond Following Photoactivation. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1325
b:18.8
occ:1.00
|
MG
|
M:BCB1325
|
0.0
|
18.8
|
1.0
|
NA
|
M:BCB1325
|
2.0
|
17.6
|
1.0
|
NB
|
M:BCB1325
|
2.0
|
17.9
|
1.0
|
NC
|
M:BCB1325
|
2.0
|
18.0
|
1.0
|
ND
|
M:BCB1325
|
2.1
|
17.0
|
1.0
|
NE2
|
M:HIS200
|
2.5
|
22.3
|
1.0
|
C1A
|
M:BCB1325
|
3.0
|
18.1
|
1.0
|
C4A
|
M:BCB1325
|
3.0
|
18.3
|
1.0
|
C4D
|
M:BCB1325
|
3.0
|
17.5
|
1.0
|
C1B
|
M:BCB1325
|
3.0
|
18.0
|
1.0
|
C4B
|
M:BCB1325
|
3.1
|
18.1
|
1.0
|
C1C
|
M:BCB1325
|
3.1
|
17.6
|
1.0
|
C4C
|
M:BCB1325
|
3.1
|
17.6
|
1.0
|
C1D
|
M:BCB1325
|
3.1
|
17.1
|
1.0
|
CHB
|
M:BCB1325
|
3.3
|
18.4
|
1.0
|
CHA
|
M:BCB1325
|
3.4
|
17.2
|
1.0
|
CD2
|
M:HIS200
|
3.4
|
22.9
|
1.0
|
CHC
|
M:BCB1325
|
3.4
|
17.5
|
1.0
|
CE1
|
M:HIS200
|
3.5
|
23.3
|
1.0
|
CHD
|
M:BCB1325
|
3.5
|
17.5
|
1.0
|
CAB
|
L:BCB1274
|
3.6
|
10.3
|
1.0
|
CBB
|
L:BCB1274
|
3.6
|
10.6
|
1.0
|
OBB
|
L:BCB1274
|
3.6
|
10.0
|
1.0
|
C2A
|
M:BCB1325
|
4.3
|
19.2
|
1.0
|
C3A
|
M:BCB1325
|
4.3
|
19.0
|
1.0
|
C3B
|
L:BCB1274
|
4.3
|
11.7
|
1.0
|
C3D
|
M:BCB1325
|
4.3
|
17.8
|
1.0
|
C3C
|
M:BCB1325
|
4.4
|
17.4
|
1.0
|
C2D
|
M:BCB1325
|
4.4
|
17.6
|
1.0
|
C3B
|
M:BCB1325
|
4.4
|
17.6
|
1.0
|
C2B
|
M:BCB1325
|
4.4
|
17.6
|
1.0
|
C2C
|
M:BCB1325
|
4.4
|
17.9
|
1.0
|
CG
|
M:HIS200
|
4.6
|
23.3
|
1.0
|
ND1
|
M:HIS200
|
4.6
|
23.2
|
1.0
|
CBD
|
M:BCB1325
|
4.8
|
17.2
|
1.0
|
|
Reference:
A.B.Wohri,
G.Katona,
L.C.Johansson,
E.Fritz,
E.Malmerberg,
M.Andersson,
J.Vincent,
M.Eklund,
M.Cammarata,
M.Wulff,
J.Davidsson,
G.Groenhof,
R.Neutze.
Light-Induced Structural Changes in A Photosynthetic Reaction Center Caught By Laue Diffraction. Science V. 328 630 2010.
ISSN: ISSN 0036-8075
PubMed: 20431017
DOI: 10.1126/SCIENCE.1186159
Page generated: Wed Aug 14 06:59:43 2024
|