Magnesium in PDB 1yst: Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
Protein crystallography data
The structure of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution, PDB code: 1yst
was solved by
B.Arnoux,
J.F.Gaucher,
A.Ducruix,
F.Reiss-Husson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
7.00 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
143.700,
139.800,
78.650,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.4 /
n/a
|
Other elements in 1yst:
The structure of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
(pdb code 1yst). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution, PDB code: 1yst:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 1yst
Go back to
Magnesium Binding Sites List in 1yst
Magnesium binding site 1 out
of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg307
b:25.7
occ:1.00
|
MG
|
M:BCL307
|
0.0
|
25.7
|
1.0
|
NB
|
M:BCL307
|
1.9
|
25.4
|
1.0
|
ND
|
M:BCL307
|
2.1
|
23.2
|
1.0
|
NC
|
M:BCL307
|
2.1
|
21.2
|
1.0
|
NA
|
M:BCL307
|
2.1
|
19.5
|
1.0
|
NE2
|
M:HIS182
|
2.3
|
24.4
|
1.0
|
C4B
|
M:BCL307
|
2.9
|
26.6
|
1.0
|
C1B
|
M:BCL307
|
2.9
|
22.2
|
1.0
|
C4D
|
M:BCL307
|
2.9
|
22.9
|
1.0
|
C1C
|
M:BCL307
|
3.0
|
21.9
|
1.0
|
C4C
|
M:BCL307
|
3.1
|
19.9
|
1.0
|
C4A
|
M:BCL307
|
3.1
|
16.5
|
1.0
|
C1A
|
M:BCL307
|
3.1
|
22.4
|
1.0
|
CD2
|
M:HIS182
|
3.2
|
19.6
|
1.0
|
C1D
|
M:BCL307
|
3.2
|
18.4
|
1.0
|
CHC
|
M:BCL307
|
3.3
|
23.6
|
1.0
|
CE1
|
M:HIS182
|
3.3
|
24.0
|
1.0
|
CHB
|
M:BCL307
|
3.4
|
14.8
|
1.0
|
CHA
|
M:BCL307
|
3.4
|
20.9
|
1.0
|
CHD
|
M:BCL307
|
3.5
|
14.9
|
1.0
|
C2B
|
M:BCL307
|
4.1
|
23.1
|
1.0
|
C3B
|
M:BCL307
|
4.1
|
25.5
|
1.0
|
C3D
|
M:BCL307
|
4.2
|
23.7
|
1.0
|
C2D
|
M:BCL307
|
4.4
|
18.9
|
1.0
|
C2C
|
M:BCL307
|
4.4
|
24.1
|
1.0
|
C3A
|
M:BCL307
|
4.4
|
18.2
|
1.0
|
CG
|
M:HIS182
|
4.4
|
22.8
|
1.0
|
C3C
|
M:BCL307
|
4.4
|
22.2
|
1.0
|
ND1
|
M:HIS182
|
4.4
|
17.6
|
1.0
|
C2A
|
M:BCL307
|
4.5
|
23.1
|
1.0
|
CE2
|
L:PHE181
|
4.5
|
31.6
|
1.0
|
CBD
|
M:BCL307
|
4.9
|
23.1
|
1.0
|
CBC
|
M:BCL307
|
5.0
|
21.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 1yst
Go back to
Magnesium Binding Sites List in 1yst
Magnesium binding site 2 out
of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg274
b:22.9
occ:1.00
|
MG
|
L:BCL274
|
0.0
|
22.9
|
1.0
|
NB
|
L:BCL274
|
1.9
|
27.2
|
1.0
|
ND
|
L:BCL274
|
2.0
|
15.3
|
1.0
|
NC
|
L:BCL274
|
2.0
|
20.5
|
1.0
|
NA
|
L:BCL274
|
2.1
|
23.0
|
1.0
|
NE2
|
L:HIS173
|
2.2
|
22.7
|
1.0
|
C4D
|
L:BCL274
|
2.9
|
21.4
|
1.0
|
C4B
|
L:BCL274
|
2.9
|
29.3
|
1.0
|
C1B
|
L:BCL274
|
2.9
|
28.8
|
1.0
|
C4A
|
L:BCL274
|
3.0
|
22.9
|
1.0
|
CE1
|
L:HIS173
|
3.0
|
29.3
|
1.0
|
C1D
|
L:BCL274
|
3.1
|
19.0
|
1.0
|
C1A
|
L:BCL274
|
3.1
|
26.5
|
1.0
|
C4C
|
L:BCL274
|
3.1
|
19.1
|
1.0
|
C1C
|
L:BCL274
|
3.1
|
24.5
|
1.0
|
CD2
|
L:HIS173
|
3.2
|
24.9
|
1.0
|
CHB
|
L:BCL274
|
3.3
|
26.2
|
1.0
|
CHC
|
L:BCL274
|
3.4
|
28.3
|
1.0
|
CHA
|
L:BCL274
|
3.4
|
27.3
|
1.0
|
CHD
|
L:BCL274
|
3.5
|
18.6
|
1.0
|
OBB
|
M:BCL308
|
3.7
|
35.5
|
1.0
|
CBB
|
M:BCL308
|
3.8
|
30.4
|
1.0
|
CAB
|
M:BCL308
|
3.9
|
33.5
|
1.0
|
C3D
|
L:BCL274
|
4.1
|
22.2
|
1.0
|
C2B
|
L:BCL274
|
4.1
|
29.6
|
1.0
|
C3B
|
L:BCL274
|
4.2
|
29.9
|
1.0
|
ND1
|
L:HIS173
|
4.2
|
21.9
|
1.0
|
C2D
|
L:BCL274
|
4.2
|
22.3
|
1.0
|
CG
|
L:HIS173
|
4.3
|
21.4
|
1.0
|
C3A
|
L:BCL274
|
4.4
|
24.2
|
1.0
|
C2C
|
L:BCL274
|
4.5
|
21.4
|
1.0
|
C2A
|
L:BCL274
|
4.5
|
25.2
|
1.0
|
C3C
|
L:BCL274
|
4.6
|
17.8
|
1.0
|
CBD
|
L:BCL274
|
4.9
|
24.1
|
1.0
|
C3B
|
M:BCL308
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 1yst
Go back to
Magnesium Binding Sites List in 1yst
Magnesium binding site 3 out
of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg308
b:28.8
occ:1.00
|
MG
|
M:BCL308
|
0.0
|
28.8
|
1.0
|
NB
|
M:BCL308
|
1.9
|
28.2
|
1.0
|
NC
|
M:BCL308
|
2.0
|
27.9
|
1.0
|
ND
|
M:BCL308
|
2.0
|
27.0
|
1.0
|
NA
|
M:BCL308
|
2.3
|
21.1
|
1.0
|
NE2
|
M:HIS202
|
2.4
|
28.5
|
1.0
|
C4B
|
M:BCL308
|
2.8
|
30.5
|
1.0
|
C4D
|
M:BCL308
|
2.9
|
25.3
|
1.0
|
C1C
|
M:BCL308
|
2.9
|
30.1
|
1.0
|
C1B
|
M:BCL308
|
3.0
|
32.5
|
1.0
|
C4C
|
M:BCL308
|
3.0
|
30.4
|
1.0
|
C1D
|
M:BCL308
|
3.0
|
29.3
|
1.0
|
CD2
|
M:HIS202
|
3.2
|
32.8
|
1.0
|
CHC
|
M:BCL308
|
3.2
|
34.9
|
1.0
|
C4A
|
M:BCL308
|
3.2
|
20.0
|
1.0
|
C1A
|
M:BCL308
|
3.2
|
20.6
|
1.0
|
CE1
|
M:HIS202
|
3.3
|
26.3
|
1.0
|
CHD
|
M:BCL308
|
3.4
|
34.0
|
1.0
|
CHA
|
M:BCL308
|
3.5
|
24.8
|
1.0
|
CHB
|
M:BCL308
|
3.5
|
27.0
|
1.0
|
OBB
|
L:BCL274
|
3.6
|
30.8
|
1.0
|
CBB
|
L:BCL274
|
4.0
|
29.8
|
1.0
|
CAB
|
L:BCL274
|
4.0
|
29.5
|
1.0
|
C3D
|
M:BCL308
|
4.1
|
28.4
|
1.0
|
C2D
|
M:BCL308
|
4.1
|
27.8
|
1.0
|
C3B
|
M:BCL308
|
4.1
|
32.4
|
1.0
|
C2B
|
M:BCL308
|
4.2
|
34.4
|
1.0
|
C3C
|
M:BCL308
|
4.2
|
28.6
|
1.0
|
C2C
|
M:BCL308
|
4.2
|
29.0
|
1.0
|
CG
|
M:HIS202
|
4.3
|
25.8
|
1.0
|
ND1
|
M:HIS202
|
4.3
|
21.9
|
1.0
|
C3A
|
M:BCL308
|
4.6
|
14.8
|
1.0
|
C2A
|
M:BCL308
|
4.6
|
18.9
|
1.0
|
CBD
|
M:BCL308
|
4.9
|
30.6
|
1.0
|
C3B
|
L:BCL274
|
4.9
|
29.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 1yst
Go back to
Magnesium Binding Sites List in 1yst
Magnesium binding site 4 out
of 4 in the Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of the Photochemical Reaction Center of A Spheroidene Containing Purple Bacterium, Rhodobacter Sphaeroides Y, at 3 Angstroms Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg275
b:18.8
occ:1.00
|
MG
|
L:BCL275
|
0.0
|
18.8
|
1.0
|
NC
|
L:BCL275
|
1.9
|
21.4
|
1.0
|
ND
|
L:BCL275
|
2.0
|
20.5
|
1.0
|
NB
|
L:BCL275
|
2.1
|
21.1
|
1.0
|
NA
|
L:BCL275
|
2.2
|
21.3
|
1.0
|
NE2
|
L:HIS153
|
2.3
|
20.8
|
1.0
|
C4C
|
L:BCL275
|
2.9
|
25.0
|
1.0
|
C4D
|
L:BCL275
|
2.9
|
23.3
|
1.0
|
C1C
|
L:BCL275
|
3.0
|
23.3
|
1.0
|
C1D
|
L:BCL275
|
3.0
|
20.6
|
1.0
|
C4B
|
L:BCL275
|
3.1
|
16.9
|
1.0
|
C1B
|
L:BCL275
|
3.1
|
21.4
|
1.0
|
CD2
|
L:HIS153
|
3.2
|
24.9
|
1.0
|
C4A
|
L:BCL275
|
3.2
|
19.3
|
1.0
|
C1A
|
L:BCL275
|
3.2
|
22.1
|
1.0
|
CE1
|
L:HIS153
|
3.3
|
22.8
|
1.0
|
CHD
|
L:BCL275
|
3.3
|
25.2
|
1.0
|
CHC
|
L:BCL275
|
3.4
|
18.0
|
1.0
|
CHA
|
L:BCL275
|
3.5
|
23.6
|
1.0
|
CHB
|
L:BCL275
|
3.5
|
22.2
|
1.0
|
C3D
|
L:BCL275
|
4.2
|
25.5
|
1.0
|
C2D
|
L:BCL275
|
4.2
|
17.4
|
1.0
|
C3C
|
L:BCL275
|
4.2
|
22.8
|
1.0
|
C3B
|
L:BCL275
|
4.3
|
14.2
|
1.0
|
C2C
|
L:BCL275
|
4.3
|
22.3
|
1.0
|
C2B
|
L:BCL275
|
4.3
|
17.9
|
1.0
|
CG
|
L:HIS153
|
4.4
|
25.1
|
1.0
|
ND1
|
L:HIS153
|
4.4
|
21.5
|
1.0
|
C3A
|
L:BCL275
|
4.5
|
20.3
|
1.0
|
C2A
|
L:BCL275
|
4.6
|
21.4
|
1.0
|
CBD
|
L:BCL275
|
5.0
|
25.2
|
1.0
|
|
Reference:
B.Arnoux,
J.F.Gaucher,
A.Ducruix,
F.Reiss-Husson.
Structure of the Photochemical Reaction Centre of A Spheroidene-Containing Purple-Bacterium, Rhodobacter Sphaeroides Y, at 3 A Resolution. Acta Crystallogr.,Sect.D V. 51 368 1995.
ISSN: ISSN 0907-4449
PubMed: 15299304
DOI: 10.1107/S0907444994013120
Page generated: Tue Aug 13 19:52:43 2024
|