Magnesium in PDB 6prc: Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
Protein crystallography data
The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex), PDB code: 6prc
was solved by
C.R.D.Lancaster,
H.Michel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
10.00 /
2.30
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
223.500,
223.500,
113.600,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
22.5
|
Other elements in 6prc:
The structure of Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
(pdb code 6prc). 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 From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex), PDB code: 6prc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6prc
Go back to
Magnesium Binding Sites List in 6prc
Magnesium binding site 1 out
of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
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 From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg302
b:13.7
occ:1.00
|
MG
|
L:BCB302
|
0.0
|
13.7
|
1.0
|
ND
|
L:BCB302
|
2.0
|
11.4
|
1.0
|
NE2
|
L:HIS173
|
2.0
|
17.1
|
1.0
|
NC
|
L:BCB302
|
2.0
|
9.8
|
1.0
|
NB
|
L:BCB302
|
2.0
|
10.0
|
1.0
|
NA
|
L:BCB302
|
2.1
|
10.6
|
1.0
|
C4D
|
L:BCB302
|
2.9
|
14.3
|
1.0
|
CE1
|
L:HIS173
|
3.0
|
18.0
|
1.0
|
C1D
|
L:BCB302
|
3.0
|
11.8
|
1.0
|
C1C
|
L:BCB302
|
3.1
|
15.1
|
1.0
|
C4B
|
L:BCB302
|
3.1
|
13.8
|
1.0
|
C1B
|
L:BCB302
|
3.1
|
14.8
|
1.0
|
C4C
|
L:BCB302
|
3.1
|
14.3
|
1.0
|
CD2
|
L:HIS173
|
3.1
|
18.9
|
1.0
|
C4A
|
L:BCB302
|
3.1
|
13.4
|
1.0
|
C1A
|
L:BCB302
|
3.2
|
14.3
|
1.0
|
CHD
|
L:BCB302
|
3.4
|
11.9
|
1.0
|
CHC
|
L:BCB302
|
3.4
|
14.8
|
1.0
|
CHA
|
L:BCB302
|
3.5
|
15.4
|
1.0
|
CHB
|
L:BCB302
|
3.5
|
13.2
|
1.0
|
CBB
|
M:BCB806
|
3.5
|
12.1
|
1.0
|
CAB
|
M:BCB806
|
3.7
|
15.5
|
1.0
|
OBB
|
M:BCB806
|
3.8
|
19.3
|
1.0
|
ND1
|
L:HIS173
|
4.1
|
18.7
|
1.0
|
C3D
|
L:BCB302
|
4.2
|
12.2
|
1.0
|
CG
|
L:HIS173
|
4.2
|
19.2
|
1.0
|
NE1
|
L:TRP167
|
4.3
|
19.7
|
1.0
|
C2D
|
L:BCB302
|
4.3
|
11.9
|
1.0
|
CD1
|
L:TRP167
|
4.3
|
15.6
|
1.0
|
C3B
|
L:BCB302
|
4.3
|
13.9
|
1.0
|
C2B
|
L:BCB302
|
4.3
|
12.3
|
1.0
|
C3C
|
L:BCB302
|
4.3
|
11.2
|
1.0
|
C2C
|
L:BCB302
|
4.3
|
10.6
|
1.0
|
C3B
|
M:BCB806
|
4.4
|
12.2
|
1.0
|
C3A
|
L:BCB302
|
4.4
|
10.3
|
1.0
|
C2A
|
L:BCB302
|
4.5
|
12.7
|
1.0
|
CBD
|
L:BCB302
|
4.9
|
19.4
|
1.0
|
C2B
|
M:BCB806
|
5.0
|
8.7
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6prc
Go back to
Magnesium Binding Sites List in 6prc
Magnesium binding site 2 out
of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
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 From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg304
b:15.3
occ:1.00
|
MG
|
L:BCB304
|
0.0
|
15.3
|
1.0
|
ND
|
L:BCB304
|
2.0
|
12.6
|
1.0
|
NB
|
L:BCB304
|
2.0
|
16.0
|
1.0
|
NC
|
L:BCB304
|
2.1
|
12.8
|
1.0
|
NE2
|
L:HIS153
|
2.1
|
16.2
|
1.0
|
NA
|
L:BCB304
|
2.2
|
10.9
|
1.0
|
C4D
|
L:BCB304
|
3.0
|
12.6
|
1.0
|
C4B
|
L:BCB304
|
3.1
|
16.0
|
1.0
|
C1D
|
L:BCB304
|
3.1
|
14.6
|
1.0
|
C1B
|
L:BCB304
|
3.1
|
14.8
|
1.0
|
C1C
|
L:BCB304
|
3.1
|
13.2
|
1.0
|
CE1
|
L:HIS153
|
3.1
|
18.1
|
1.0
|
C4A
|
L:BCB304
|
3.1
|
10.1
|
1.0
|
CD2
|
L:HIS153
|
3.1
|
16.2
|
1.0
|
C4C
|
L:BCB304
|
3.1
|
10.2
|
1.0
|
C1A
|
L:BCB304
|
3.2
|
12.0
|
1.0
|
CHC
|
L:BCB304
|
3.4
|
12.4
|
1.0
|
CHD
|
L:BCB304
|
3.5
|
11.9
|
1.0
|
CHB
|
L:BCB304
|
3.5
|
11.6
|
1.0
|
CHA
|
L:BCB304
|
3.5
|
14.4
|
1.0
|
C3D
|
L:BCB304
|
4.2
|
12.6
|
1.0
|
C2D
|
L:BCB304
|
4.2
|
14.8
|
1.0
|
ND1
|
L:HIS153
|
4.3
|
17.2
|
1.0
|
C2B
|
L:BCB304
|
4.3
|
16.9
|
1.0
|
C3B
|
L:BCB304
|
4.3
|
16.7
|
1.0
|
CG
|
L:HIS153
|
4.3
|
15.4
|
1.0
|
C2C
|
L:BCB304
|
4.3
|
12.7
|
1.0
|
C3C
|
L:BCB304
|
4.4
|
6.9
|
1.0
|
OBB
|
L:BPB402
|
4.4
|
21.1
|
1.0
|
C3A
|
L:BCB304
|
4.4
|
13.0
|
1.0
|
CE2
|
M:TYR208
|
4.5
|
15.1
|
1.0
|
C2A
|
L:BCB304
|
4.5
|
12.2
|
1.0
|
CBA
|
L:BCB304
|
4.9
|
10.0
|
1.0
|
CD2
|
L:LEU154
|
4.9
|
17.6
|
1.0
|
CBD
|
L:BCB304
|
5.0
|
16.0
|
1.0
|
C20
|
L:BPB402
|
5.0
|
10.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6prc
Go back to
Magnesium Binding Sites List in 6prc
Magnesium binding site 3 out
of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
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 From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg805
b:24.1
occ:1.00
|
MG
|
M:BCB805
|
0.0
|
24.1
|
1.0
|
NB
|
M:BCB805
|
2.0
|
22.2
|
1.0
|
ND
|
M:BCB805
|
2.0
|
22.5
|
1.0
|
NE2
|
M:HIS180
|
2.1
|
19.4
|
1.0
|
NC
|
M:BCB805
|
2.1
|
17.0
|
1.0
|
NA
|
M:BCB805
|
2.2
|
25.0
|
1.0
|
C4D
|
M:BCB805
|
3.0
|
27.1
|
1.0
|
C4B
|
M:BCB805
|
3.0
|
24.2
|
1.0
|
CD2
|
M:HIS180
|
3.0
|
18.9
|
1.0
|
C1B
|
M:BCB805
|
3.0
|
24.3
|
1.0
|
C1C
|
M:BCB805
|
3.0
|
19.7
|
1.0
|
CE1
|
M:HIS180
|
3.1
|
22.0
|
1.0
|
C1D
|
M:BCB805
|
3.1
|
21.4
|
1.0
|
C4C
|
M:BCB805
|
3.1
|
19.3
|
1.0
|
C4A
|
M:BCB805
|
3.2
|
25.6
|
1.0
|
C1A
|
M:BCB805
|
3.2
|
23.4
|
1.0
|
CHC
|
M:BCB805
|
3.4
|
20.3
|
1.0
|
CHD
|
M:BCB805
|
3.5
|
22.7
|
1.0
|
CHB
|
M:BCB805
|
3.5
|
24.7
|
1.0
|
CHA
|
M:BCB805
|
3.5
|
24.1
|
1.0
|
CG
|
M:HIS180
|
4.2
|
19.2
|
1.0
|
ND1
|
M:HIS180
|
4.2
|
20.6
|
1.0
|
C3D
|
M:BCB805
|
4.3
|
26.3
|
1.0
|
C2B
|
M:BCB805
|
4.3
|
25.6
|
1.0
|
C3B
|
M:BCB805
|
4.3
|
26.4
|
1.0
|
C2C
|
M:BCB805
|
4.3
|
16.4
|
1.0
|
OBB
|
M:BPB401
|
4.3
|
34.0
|
1.0
|
C2D
|
M:BCB805
|
4.3
|
21.1
|
1.0
|
C3C
|
M:BCB805
|
4.3
|
18.7
|
1.0
|
C3A
|
M:BCB805
|
4.5
|
25.2
|
1.0
|
C2A
|
M:BCB805
|
4.5
|
25.2
|
1.0
|
CBA
|
M:BCB805
|
4.8
|
31.9
|
1.0
|
CE2
|
L:PHE181
|
4.9
|
17.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6prc
Go back to
Magnesium Binding Sites List in 6prc
Magnesium binding site 4 out
of 4 in the Photosynthetic Reaction Center From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex)
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 From Rhodopseudomonas Viridis (Dg- 420314 (Triazine) Complex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg806
b:17.0
occ:1.00
|
MG
|
M:BCB806
|
0.0
|
17.0
|
1.0
|
ND
|
M:BCB806
|
2.0
|
17.1
|
1.0
|
NB
|
M:BCB806
|
2.0
|
15.0
|
1.0
|
NC
|
M:BCB806
|
2.0
|
17.2
|
1.0
|
NE2
|
M:HIS200
|
2.0
|
17.2
|
1.0
|
NA
|
M:BCB806
|
2.2
|
15.5
|
1.0
|
C4D
|
M:BCB806
|
3.0
|
17.0
|
1.0
|
C1C
|
M:BCB806
|
3.0
|
13.3
|
1.0
|
C4B
|
M:BCB806
|
3.0
|
13.1
|
1.0
|
CD2
|
M:HIS200
|
3.0
|
15.1
|
1.0
|
CE1
|
M:HIS200
|
3.1
|
16.0
|
1.0
|
C1B
|
M:BCB806
|
3.1
|
9.9
|
1.0
|
C1D
|
M:BCB806
|
3.1
|
16.3
|
1.0
|
C4C
|
M:BCB806
|
3.1
|
14.6
|
1.0
|
C4A
|
M:BCB806
|
3.2
|
11.8
|
1.0
|
C1A
|
M:BCB806
|
3.2
|
17.4
|
1.0
|
CHC
|
M:BCB806
|
3.4
|
12.7
|
1.0
|
CHD
|
M:BCB806
|
3.4
|
16.2
|
1.0
|
CHA
|
M:BCB806
|
3.5
|
18.6
|
1.0
|
CHB
|
M:BCB806
|
3.5
|
8.5
|
1.0
|
CAB
|
L:BCB302
|
3.9
|
14.5
|
1.0
|
CBB
|
L:BCB302
|
3.9
|
13.1
|
1.0
|
OBB
|
L:BCB302
|
4.0
|
16.0
|
1.0
|
ND1
|
M:HIS200
|
4.2
|
13.4
|
1.0
|
CG
|
M:HIS200
|
4.2
|
11.1
|
1.0
|
C3D
|
M:BCB806
|
4.2
|
15.6
|
1.0
|
C2B
|
M:BCB806
|
4.3
|
8.7
|
1.0
|
C3B
|
M:BCB806
|
4.3
|
12.2
|
1.0
|
C2C
|
M:BCB806
|
4.3
|
12.4
|
1.0
|
C3C
|
M:BCB806
|
4.3
|
13.1
|
1.0
|
C2D
|
M:BCB806
|
4.3
|
13.2
|
1.0
|
C3A
|
M:BCB806
|
4.5
|
11.4
|
1.0
|
C2A
|
M:BCB806
|
4.5
|
14.2
|
1.0
|
C3B
|
L:BCB302
|
4.6
|
13.9
|
1.0
|
CMC
|
M:BCB806
|
4.8
|
9.8
|
1.0
|
CD1
|
M:ILE204
|
4.9
|
11.3
|
1.0
|
CBD
|
M:BCB806
|
4.9
|
20.6
|
1.0
|
|
Reference:
C.R.Lancaster,
H.Michel.
Refined Crystal Structures of Reaction Centres From Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to A New Model of the Bound Carotenoid. J.Mol.Biol. V. 286 883 1999.
ISSN: ISSN 0022-2836
PubMed: 10024457
DOI: 10.1006/JMBI.1998.2532
Page generated: Tue Oct 1 14:16:19 2024
|