Magnesium in PDB 1r2c: Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
Protein crystallography data
The structure of Photosynthetic Reaction Center Blastochloris Viridis (Atcc), PDB code: 1r2c
was solved by
R.H.Baxter,
N.Ponomarenko,
R.Pahl,
V.Srajer,
K.Moffat,
J.R.Norris,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.83 /
2.86
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
223.500,
223.500,
112.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.2 /
22.8
|
Other elements in 1r2c:
The structure of Photosynthetic Reaction Center Blastochloris Viridis (Atcc) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
(pdb code 1r2c). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Photosynthetic Reaction Center Blastochloris Viridis (Atcc), PDB code: 1r2c:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1r2c
Go back to
Magnesium Binding Sites List in 1r2c
Magnesium binding site 1 out
of 4 in the Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Photosynthetic Reaction Center Blastochloris Viridis (Atcc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1301
b:41.0
occ:1.00
|
MG
|
M:BCB1301
|
0.0
|
41.0
|
1.0
|
ND
|
M:BCB1301
|
2.0
|
41.3
|
1.0
|
NB
|
M:BCB1301
|
2.0
|
43.2
|
1.0
|
NE2
|
M:HIS180
|
2.1
|
38.0
|
1.0
|
NC
|
M:BCB1301
|
2.1
|
41.3
|
1.0
|
NA
|
M:BCB1301
|
2.2
|
42.2
|
1.0
|
CD2
|
M:HIS180
|
3.0
|
35.3
|
1.0
|
C4D
|
M:BCB1301
|
3.0
|
41.2
|
1.0
|
C4B
|
M:BCB1301
|
3.1
|
44.3
|
1.0
|
C1B
|
M:BCB1301
|
3.1
|
43.4
|
1.0
|
C1D
|
M:BCB1301
|
3.1
|
41.5
|
1.0
|
C1C
|
M:BCB1301
|
3.1
|
39.6
|
1.0
|
CE1
|
M:HIS180
|
3.1
|
36.3
|
1.0
|
C4A
|
M:BCB1301
|
3.2
|
40.9
|
1.0
|
C4C
|
M:BCB1301
|
3.2
|
40.0
|
1.0
|
C1A
|
M:BCB1301
|
3.2
|
41.8
|
1.0
|
CHC
|
M:BCB1301
|
3.4
|
42.3
|
1.0
|
CHB
|
M:BCB1301
|
3.5
|
41.4
|
1.0
|
CHD
|
M:BCB1301
|
3.5
|
40.2
|
1.0
|
CHA
|
M:BCB1301
|
3.5
|
41.2
|
1.0
|
CG
|
M:HIS180
|
4.2
|
34.0
|
1.0
|
C3D
|
M:BCB1301
|
4.2
|
41.0
|
1.0
|
ND1
|
M:HIS180
|
4.2
|
34.0
|
1.0
|
C2B
|
M:BCB1301
|
4.3
|
44.7
|
1.0
|
C3B
|
M:BCB1301
|
4.3
|
45.6
|
1.0
|
C2D
|
M:BCB1301
|
4.3
|
41.6
|
1.0
|
OBB
|
M:BPB401
|
4.4
|
49.3
|
1.0
|
C2C
|
M:BCB1301
|
4.4
|
37.5
|
1.0
|
C3C
|
M:BCB1301
|
4.4
|
38.9
|
1.0
|
C3A
|
M:BCB1301
|
4.5
|
40.6
|
1.0
|
C2A
|
M:BCB1301
|
4.5
|
41.7
|
1.0
|
CE2
|
L:PHE181
|
4.9
|
34.5
|
1.0
|
CBD
|
M:BCB1301
|
5.0
|
40.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1r2c
Go back to
Magnesium Binding Sites List in 1r2c
Magnesium binding site 2 out
of 4 in the Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Photosynthetic Reaction Center Blastochloris Viridis (Atcc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:20.4
occ:1.00
|
MG
|
L:BCB302
|
0.0
|
20.4
|
1.0
|
ND
|
L:BCB302
|
2.0
|
18.5
|
1.0
|
NB
|
L:BCB302
|
2.0
|
17.0
|
1.0
|
NC
|
L:BCB302
|
2.1
|
16.0
|
1.0
|
NE2
|
L:HIS173
|
2.1
|
24.4
|
1.0
|
NA
|
L:BCB302
|
2.2
|
18.1
|
1.0
|
C4D
|
L:BCB302
|
2.9
|
19.3
|
1.0
|
C4B
|
L:BCB302
|
3.0
|
15.0
|
1.0
|
C1B
|
L:BCB302
|
3.0
|
17.6
|
1.0
|
C1C
|
L:BCB302
|
3.0
|
17.1
|
1.0
|
C1D
|
L:BCB302
|
3.1
|
19.2
|
1.0
|
CE1
|
L:HIS173
|
3.1
|
26.4
|
1.0
|
C4C
|
L:BCB302
|
3.1
|
16.9
|
1.0
|
C4A
|
L:BCB302
|
3.1
|
19.4
|
1.0
|
C1A
|
L:BCB302
|
3.2
|
20.5
|
1.0
|
CD2
|
L:HIS173
|
3.2
|
27.3
|
1.0
|
CBB
|
M:BCB1303
|
3.3
|
19.0
|
1.0
|
CHC
|
L:BCB302
|
3.4
|
15.0
|
1.0
|
CHB
|
L:BCB302
|
3.4
|
19.0
|
1.0
|
CHD
|
L:BCB302
|
3.4
|
18.1
|
1.0
|
CHA
|
L:BCB302
|
3.5
|
20.2
|
1.0
|
CAB
|
M:BCB1303
|
3.5
|
18.8
|
1.0
|
OBB
|
M:BCB1303
|
3.6
|
21.8
|
1.0
|
C3D
|
L:BCB302
|
4.2
|
19.6
|
1.0
|
ND1
|
L:HIS173
|
4.2
|
29.6
|
1.0
|
C3B
|
M:BCB1303
|
4.2
|
18.0
|
1.0
|
C3B
|
L:BCB302
|
4.3
|
15.2
|
1.0
|
C2B
|
L:BCB302
|
4.3
|
16.6
|
1.0
|
C2D
|
L:BCB302
|
4.3
|
19.9
|
1.0
|
CG
|
L:HIS173
|
4.3
|
29.5
|
1.0
|
C2C
|
L:BCB302
|
4.3
|
14.1
|
1.0
|
C3C
|
L:BCB302
|
4.4
|
15.0
|
1.0
|
CD1
|
L:TRP167
|
4.5
|
22.4
|
1.0
|
C3A
|
L:BCB302
|
4.5
|
19.9
|
1.0
|
NE1
|
L:TRP167
|
4.5
|
22.0
|
1.0
|
C2A
|
L:BCB302
|
4.5
|
20.5
|
1.0
|
C2B
|
M:BCB1303
|
4.9
|
19.3
|
1.0
|
CBD
|
L:BCB302
|
4.9
|
23.5
|
1.0
|
C4B
|
M:BCB1303
|
5.0
|
19.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1r2c
Go back to
Magnesium Binding Sites List in 1r2c
Magnesium binding site 3 out
of 4 in the Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Photosynthetic Reaction Center Blastochloris Viridis (Atcc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg1303
b:24.3
occ:1.00
|
MG
|
M:BCB1303
|
0.0
|
24.3
|
1.0
|
ND
|
M:BCB1303
|
2.0
|
22.2
|
1.0
|
NB
|
M:BCB1303
|
2.0
|
19.4
|
1.0
|
NC
|
M:BCB1303
|
2.0
|
19.4
|
1.0
|
NE2
|
M:HIS200
|
2.1
|
27.8
|
1.0
|
NA
|
M:BCB1303
|
2.1
|
22.2
|
1.0
|
C4D
|
M:BCB1303
|
2.9
|
23.8
|
1.0
|
C1C
|
M:BCB1303
|
3.0
|
21.0
|
1.0
|
C4B
|
M:BCB1303
|
3.0
|
19.1
|
1.0
|
C1B
|
M:BCB1303
|
3.1
|
19.2
|
1.0
|
C1D
|
M:BCB1303
|
3.1
|
23.1
|
1.0
|
CE1
|
M:HIS200
|
3.1
|
29.3
|
1.0
|
C4C
|
M:BCB1303
|
3.1
|
21.4
|
1.0
|
C1A
|
M:BCB1303
|
3.1
|
25.1
|
1.0
|
C4A
|
M:BCB1303
|
3.1
|
21.5
|
1.0
|
CD2
|
M:HIS200
|
3.1
|
31.8
|
1.0
|
CHC
|
M:BCB1303
|
3.3
|
19.3
|
1.0
|
CHA
|
M:BCB1303
|
3.4
|
25.7
|
1.0
|
CHD
|
M:BCB1303
|
3.5
|
20.7
|
1.0
|
CHB
|
M:BCB1303
|
3.5
|
18.1
|
1.0
|
CBB
|
L:BCB302
|
3.5
|
10.7
|
1.0
|
CAB
|
L:BCB302
|
3.6
|
14.2
|
1.0
|
OBB
|
L:BCB302
|
3.8
|
14.4
|
1.0
|
C3D
|
M:BCB1303
|
4.2
|
25.7
|
1.0
|
ND1
|
M:HIS200
|
4.2
|
33.5
|
1.0
|
C3B
|
M:BCB1303
|
4.3
|
18.0
|
1.0
|
C2B
|
M:BCB1303
|
4.3
|
19.3
|
1.0
|
C2D
|
M:BCB1303
|
4.3
|
24.9
|
1.0
|
C2C
|
M:BCB1303
|
4.3
|
22.6
|
1.0
|
CG
|
M:HIS200
|
4.3
|
33.4
|
1.0
|
C3B
|
L:BCB302
|
4.3
|
15.2
|
1.0
|
C3C
|
M:BCB1303
|
4.3
|
21.2
|
1.0
|
C2A
|
M:BCB1303
|
4.4
|
24.5
|
1.0
|
C3A
|
M:BCB1303
|
4.4
|
22.3
|
1.0
|
CBD
|
M:BCB1303
|
4.9
|
29.8
|
1.0
|
C4B
|
L:BCB302
|
4.9
|
15.0
|
1.0
|
CD1
|
M:ILE204
|
4.9
|
21.9
|
1.0
|
C2B
|
L:BCB302
|
5.0
|
16.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1r2c
Go back to
Magnesium Binding Sites List in 1r2c
Magnesium binding site 4 out
of 4 in the Photosynthetic Reaction Center Blastochloris Viridis (Atcc)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Photosynthetic Reaction Center Blastochloris Viridis (Atcc) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg304
b:29.6
occ:1.00
|
MG
|
L:BCB304
|
0.0
|
29.6
|
1.0
|
ND
|
L:BCB304
|
2.0
|
27.1
|
1.0
|
NB
|
L:BCB304
|
2.0
|
27.7
|
1.0
|
NE2
|
L:HIS153
|
2.1
|
31.9
|
1.0
|
NC
|
L:BCB304
|
2.1
|
28.2
|
1.0
|
NA
|
L:BCB304
|
2.2
|
28.1
|
1.0
|
C4D
|
L:BCB304
|
3.0
|
27.2
|
1.0
|
CD2
|
L:HIS153
|
3.0
|
34.3
|
1.0
|
C4B
|
L:BCB304
|
3.1
|
27.2
|
1.0
|
C1B
|
L:BCB304
|
3.1
|
28.7
|
1.0
|
C1D
|
L:BCB304
|
3.1
|
27.1
|
1.0
|
C1C
|
L:BCB304
|
3.1
|
26.5
|
1.0
|
C4A
|
L:BCB304
|
3.1
|
29.9
|
1.0
|
C4C
|
L:BCB304
|
3.2
|
27.7
|
1.0
|
CE1
|
L:HIS153
|
3.2
|
33.4
|
1.0
|
C1A
|
L:BCB304
|
3.2
|
27.1
|
1.0
|
CHC
|
L:BCB304
|
3.4
|
27.4
|
1.0
|
CHB
|
L:BCB304
|
3.5
|
28.4
|
1.0
|
CHA
|
L:BCB304
|
3.5
|
27.2
|
1.0
|
CHD
|
L:BCB304
|
3.5
|
26.3
|
1.0
|
C3D
|
L:BCB304
|
4.2
|
27.7
|
1.0
|
CG
|
L:HIS153
|
4.3
|
35.1
|
1.0
|
C2B
|
L:BCB304
|
4.3
|
28.2
|
1.0
|
C2D
|
L:BCB304
|
4.3
|
27.1
|
1.0
|
ND1
|
L:HIS153
|
4.3
|
35.3
|
1.0
|
C3B
|
L:BCB304
|
4.3
|
28.1
|
1.0
|
C2C
|
L:BCB304
|
4.4
|
25.0
|
1.0
|
C3C
|
L:BCB304
|
4.4
|
26.7
|
1.0
|
C3A
|
L:BCB304
|
4.5
|
29.9
|
1.0
|
C2A
|
L:BCB304
|
4.5
|
28.2
|
1.0
|
OBB
|
L:BPB402
|
4.5
|
45.4
|
1.0
|
CE2
|
M:TYR208
|
4.5
|
25.0
|
1.0
|
CBD
|
L:BCB304
|
5.0
|
29.2
|
1.0
|
CD2
|
L:LEU154
|
5.0
|
32.9
|
1.0
|
CBA
|
L:BCB304
|
5.0
|
30.4
|
1.0
|
C20
|
L:BPB402
|
5.0
|
40.7
|
1.0
|
|
Reference:
R.H.Baxter,
N.Ponomarenko,
V.Srajer,
R.Pahl,
K.Moffat,
J.R.Norris.
Time-Resolved Crystallographic Studies of Light-Induced Structural Changes in the Photosynthetic Reaction Center. Proc.Natl.Acad.Sci.Usa V. 101 5982 2004.
ISSN: ISSN 0027-8424
PubMed: 15073325
DOI: 10.1073/PNAS.0306840101
Page generated: Tue Aug 13 12:00:52 2024
|