Magnesium in PDB 1yf6: Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Protein crystallography data
The structure of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 1yf6
was solved by
M.L.Paddock,
C.Chang,
Q.Xu,
E.C.Abresch,
H.L.Axelrod,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.34 /
2.25
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
139.442,
139.442,
185.460,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.7 /
21.6
|
Other elements in 1yf6:
The structure of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
(pdb code 1yf6). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 1yf6:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 1yf6
Go back to
Magnesium Binding Sites List in 1yf6
Magnesium binding site 1 out
of 5 in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg852
b:21.6
occ:1.00
|
MG
|
L:BCL852
|
0.0
|
21.6
|
1.0
|
NB
|
L:BCL852
|
2.0
|
22.7
|
1.0
|
ND
|
L:BCL852
|
2.1
|
24.3
|
1.0
|
NA
|
L:BCL852
|
2.1
|
22.6
|
1.0
|
NC
|
L:BCL852
|
2.1
|
22.9
|
1.0
|
NE2
|
L:HIS173
|
2.2
|
20.7
|
1.0
|
C4D
|
L:BCL852
|
2.9
|
24.5
|
1.0
|
C4A
|
L:BCL852
|
3.0
|
22.9
|
1.0
|
CE1
|
L:HIS173
|
3.0
|
18.5
|
1.0
|
C4B
|
L:BCL852
|
3.0
|
23.3
|
1.0
|
C1A
|
L:BCL852
|
3.1
|
22.2
|
1.0
|
C1C
|
L:BCL852
|
3.1
|
22.8
|
1.0
|
C4C
|
L:BCL852
|
3.1
|
22.8
|
1.0
|
C1B
|
L:BCL852
|
3.1
|
22.2
|
1.0
|
C1D
|
L:BCL852
|
3.1
|
24.3
|
1.0
|
CD2
|
L:HIS173
|
3.3
|
21.2
|
1.0
|
CHA
|
L:BCL852
|
3.4
|
23.3
|
1.0
|
CHC
|
L:BCL852
|
3.4
|
23.2
|
1.0
|
CHB
|
L:BCL852
|
3.5
|
22.1
|
1.0
|
CHD
|
L:BCL852
|
3.5
|
22.9
|
1.0
|
CBB
|
M:BCL853
|
3.7
|
22.6
|
1.0
|
CAB
|
M:BCL853
|
3.8
|
24.5
|
1.0
|
OBB
|
M:BCL853
|
3.9
|
26.5
|
1.0
|
C3D
|
L:BCL852
|
4.2
|
23.6
|
1.0
|
ND1
|
L:HIS173
|
4.2
|
18.3
|
1.0
|
C3B
|
L:BCL852
|
4.3
|
22.8
|
1.0
|
C2B
|
L:BCL852
|
4.3
|
22.7
|
1.0
|
C2D
|
L:BCL852
|
4.3
|
24.6
|
1.0
|
C3A
|
L:BCL852
|
4.3
|
22.3
|
1.0
|
CG
|
L:HIS173
|
4.4
|
19.5
|
1.0
|
C2A
|
L:BCL852
|
4.4
|
22.4
|
1.0
|
C3C
|
L:BCL852
|
4.4
|
21.7
|
1.0
|
C2C
|
L:BCL852
|
4.5
|
22.9
|
1.0
|
CD2
|
L:PHE167
|
4.5
|
24.5
|
1.0
|
C3B
|
M:BCL853
|
4.6
|
23.1
|
1.0
|
CMA
|
L:BCL852
|
4.8
|
22.3
|
1.0
|
CBD
|
L:BCL852
|
4.8
|
22.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 1yf6
Go back to
Magnesium Binding Sites List in 1yf6
Magnesium binding site 2 out
of 5 in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg854
b:22.8
occ:1.00
|
MG
|
L:BCL854
|
0.0
|
22.8
|
1.0
|
NC
|
L:BCL854
|
2.0
|
22.0
|
1.0
|
ND
|
L:BCL854
|
2.1
|
21.3
|
1.0
|
NA
|
L:BCL854
|
2.1
|
23.2
|
1.0
|
NB
|
L:BCL854
|
2.1
|
22.5
|
1.0
|
NE2
|
L:HIS153
|
2.3
|
23.4
|
1.0
|
C4D
|
L:BCL854
|
3.0
|
23.1
|
1.0
|
C1C
|
L:BCL854
|
3.0
|
23.7
|
1.0
|
C4C
|
L:BCL854
|
3.0
|
21.0
|
1.0
|
C1D
|
L:BCL854
|
3.1
|
21.1
|
1.0
|
C4A
|
L:BCL854
|
3.1
|
22.7
|
1.0
|
C4B
|
L:BCL854
|
3.1
|
22.9
|
1.0
|
C1A
|
L:BCL854
|
3.1
|
23.3
|
1.0
|
CD2
|
L:HIS153
|
3.1
|
21.1
|
1.0
|
C1B
|
L:BCL854
|
3.2
|
23.0
|
1.0
|
CE1
|
L:HIS153
|
3.4
|
22.1
|
1.0
|
CHC
|
L:BCL854
|
3.4
|
21.9
|
1.0
|
CHA
|
L:BCL854
|
3.4
|
24.0
|
1.0
|
CHD
|
L:BCL854
|
3.5
|
19.8
|
1.0
|
CHB
|
L:BCL854
|
3.5
|
22.2
|
1.0
|
C3D
|
L:BCL854
|
4.2
|
21.8
|
1.0
|
C2D
|
L:BCL854
|
4.2
|
21.9
|
1.0
|
C2C
|
L:BCL854
|
4.3
|
22.6
|
1.0
|
C3B
|
L:BCL854
|
4.3
|
22.4
|
1.0
|
CG
|
L:HIS153
|
4.3
|
23.3
|
1.0
|
C2B
|
L:BCL854
|
4.3
|
22.6
|
1.0
|
C3C
|
L:BCL854
|
4.3
|
21.7
|
1.0
|
C3A
|
L:BCL854
|
4.4
|
24.6
|
1.0
|
ND1
|
L:HIS153
|
4.5
|
23.8
|
1.0
|
CBB
|
M:BCL856
|
4.5
|
20.3
|
1.0
|
C2A
|
L:BCL854
|
4.5
|
24.3
|
1.0
|
C19
|
M:BCL856
|
4.8
|
29.5
|
1.0
|
CBC
|
L:BCL854
|
4.8
|
22.5
|
1.0
|
CD2
|
L:LEU154
|
4.8
|
29.4
|
1.0
|
CBD
|
L:BCL854
|
4.9
|
25.2
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 1yf6
Go back to
Magnesium Binding Sites List in 1yf6
Magnesium binding site 3 out
of 5 in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg851
b:20.5
occ:1.00
|
MG
|
M:BCL851
|
0.0
|
20.5
|
1.0
|
ND
|
M:BCL851
|
2.0
|
19.9
|
1.0
|
NC
|
M:BCL851
|
2.0
|
19.6
|
1.0
|
NA
|
M:BCL851
|
2.1
|
21.1
|
1.0
|
NB
|
M:BCL851
|
2.1
|
19.3
|
1.0
|
NE2
|
M:HIS182
|
2.2
|
21.6
|
1.0
|
C4D
|
M:BCL851
|
2.9
|
18.9
|
1.0
|
C4A
|
M:BCL851
|
3.0
|
20.9
|
1.0
|
C1D
|
M:BCL851
|
3.1
|
18.7
|
1.0
|
C1C
|
M:BCL851
|
3.1
|
19.5
|
1.0
|
C4C
|
M:BCL851
|
3.1
|
20.3
|
1.0
|
CD2
|
M:HIS182
|
3.1
|
22.9
|
1.0
|
C1B
|
M:BCL851
|
3.1
|
18.8
|
1.0
|
C4B
|
M:BCL851
|
3.1
|
19.4
|
1.0
|
C1A
|
M:BCL851
|
3.1
|
21.6
|
1.0
|
CHB
|
M:BCL851
|
3.4
|
18.5
|
1.0
|
CE1
|
M:HIS182
|
3.4
|
22.6
|
1.0
|
CHA
|
M:BCL851
|
3.4
|
19.7
|
1.0
|
CHD
|
M:BCL851
|
3.5
|
18.6
|
1.0
|
CHC
|
M:BCL851
|
3.5
|
18.5
|
1.0
|
C3D
|
M:BCL851
|
4.1
|
17.8
|
1.0
|
C2D
|
M:BCL851
|
4.2
|
20.0
|
1.0
|
CG
|
M:HIS182
|
4.3
|
23.5
|
1.0
|
C2B
|
M:BCL851
|
4.3
|
21.0
|
1.0
|
C3B
|
M:BCL851
|
4.3
|
21.6
|
1.0
|
C3A
|
M:BCL851
|
4.3
|
23.0
|
1.0
|
C2C
|
M:BCL851
|
4.4
|
20.2
|
1.0
|
C3C
|
M:BCL851
|
4.4
|
20.8
|
1.0
|
ND1
|
M:HIS182
|
4.4
|
24.3
|
1.0
|
C2A
|
M:BCL851
|
4.5
|
23.7
|
1.0
|
CBB
|
L:BPH855
|
4.6
|
23.8
|
1.0
|
CE2
|
L:TYR181
|
4.6
|
23.9
|
1.0
|
CBD
|
M:BCL851
|
4.9
|
20.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 1yf6
Go back to
Magnesium Binding Sites List in 1yf6
Magnesium binding site 4 out
of 5 in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg853
b:22.2
occ:1.00
|
MG
|
M:BCL853
|
0.0
|
22.2
|
1.0
|
NB
|
M:BCL853
|
2.1
|
21.7
|
1.0
|
ND
|
M:BCL853
|
2.1
|
22.9
|
1.0
|
NC
|
M:BCL853
|
2.1
|
21.2
|
1.0
|
NA
|
M:BCL853
|
2.1
|
22.4
|
1.0
|
NE2
|
M:HIS202
|
2.2
|
20.4
|
1.0
|
C4D
|
M:BCL853
|
3.0
|
24.4
|
1.0
|
C4A
|
M:BCL853
|
3.0
|
22.5
|
1.0
|
C1C
|
M:BCL853
|
3.1
|
21.9
|
1.0
|
C4B
|
M:BCL853
|
3.1
|
24.2
|
1.0
|
C1D
|
M:BCL853
|
3.1
|
24.6
|
1.0
|
C1B
|
M:BCL853
|
3.1
|
23.2
|
1.0
|
C4C
|
M:BCL853
|
3.1
|
22.3
|
1.0
|
C1A
|
M:BCL853
|
3.2
|
23.5
|
1.0
|
CE1
|
M:HIS202
|
3.2
|
18.4
|
1.0
|
CD2
|
M:HIS202
|
3.3
|
20.7
|
1.0
|
CHC
|
M:BCL853
|
3.4
|
21.1
|
1.0
|
CHB
|
M:BCL853
|
3.4
|
21.7
|
1.0
|
CHA
|
M:BCL853
|
3.5
|
24.2
|
1.0
|
CHD
|
M:BCL853
|
3.5
|
23.0
|
1.0
|
CBB
|
L:BCL852
|
3.6
|
23.9
|
1.0
|
CAB
|
L:BCL852
|
3.9
|
23.8
|
1.0
|
OBB
|
L:BCL852
|
4.1
|
23.9
|
1.0
|
C3D
|
M:BCL853
|
4.1
|
24.3
|
1.0
|
C2D
|
M:BCL853
|
4.2
|
23.6
|
1.0
|
C2B
|
M:BCL853
|
4.2
|
22.5
|
1.0
|
C3B
|
M:BCL853
|
4.3
|
23.1
|
1.0
|
C3A
|
M:BCL853
|
4.4
|
23.6
|
1.0
|
CG
|
M:HIS202
|
4.4
|
17.9
|
1.0
|
ND1
|
M:HIS202
|
4.4
|
18.5
|
1.0
|
C2C
|
M:BCL853
|
4.4
|
21.7
|
1.0
|
C3C
|
M:BCL853
|
4.4
|
21.6
|
1.0
|
C2A
|
M:BCL853
|
4.5
|
23.5
|
1.0
|
C3B
|
L:BCL852
|
4.7
|
22.8
|
1.0
|
CBD
|
M:BCL853
|
4.9
|
23.7
|
1.0
|
CD1
|
M:ILE206
|
4.9
|
19.8
|
1.0
|
CMC
|
M:BCL853
|
5.0
|
19.9
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 1yf6
Go back to
Magnesium Binding Sites List in 1yf6
Magnesium binding site 5 out
of 5 in the Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of A Quintuple Mutant of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg856
b:19.2
occ:1.00
|
MG
|
M:BCL856
|
0.0
|
19.2
|
1.0
|
ND
|
M:BCL856
|
2.0
|
19.5
|
1.0
|
NB
|
M:BCL856
|
2.0
|
18.0
|
1.0
|
NC
|
M:BCL856
|
2.1
|
19.4
|
1.0
|
ND1
|
M:HIS214
|
2.1
|
20.0
|
1.0
|
NA
|
M:BCL856
|
2.1
|
19.7
|
1.0
|
CE1
|
M:HIS214
|
2.6
|
20.1
|
1.0
|
C4D
|
M:BCL856
|
2.9
|
19.1
|
1.0
|
C1D
|
M:BCL856
|
3.0
|
19.3
|
1.0
|
C4B
|
M:BCL856
|
3.1
|
20.0
|
1.0
|
C1C
|
M:BCL856
|
3.1
|
17.8
|
1.0
|
C4C
|
M:BCL856
|
3.1
|
19.2
|
1.0
|
C4A
|
M:BCL856
|
3.1
|
20.1
|
1.0
|
C1B
|
M:BCL856
|
3.1
|
19.1
|
1.0
|
C1A
|
M:BCL856
|
3.2
|
19.8
|
1.0
|
CG
|
M:HIS214
|
3.3
|
20.1
|
1.0
|
CHC
|
M:BCL856
|
3.4
|
17.5
|
1.0
|
CHB
|
M:BCL856
|
3.5
|
19.0
|
1.0
|
CHA
|
M:BCL856
|
3.5
|
18.8
|
1.0
|
CHD
|
M:BCL856
|
3.5
|
19.6
|
1.0
|
NE2
|
M:HIS214
|
3.8
|
19.9
|
1.0
|
CB
|
M:HIS214
|
4.1
|
18.7
|
1.0
|
C3D
|
M:BCL856
|
4.1
|
18.3
|
1.0
|
C2D
|
M:BCL856
|
4.2
|
17.8
|
1.0
|
CD2
|
M:HIS214
|
4.2
|
19.3
|
1.0
|
C3B
|
M:BCL856
|
4.3
|
20.0
|
1.0
|
C2B
|
M:BCL856
|
4.3
|
19.7
|
1.0
|
C3C
|
M:BCL856
|
4.4
|
17.9
|
1.0
|
C3A
|
M:BCL856
|
4.4
|
21.1
|
1.0
|
C2C
|
M:BCL856
|
4.4
|
18.0
|
1.0
|
C2A
|
M:BCL856
|
4.4
|
21.4
|
1.0
|
CA
|
M:HIS214
|
4.6
|
17.6
|
1.0
|
CB
|
L:ALA124
|
4.9
|
21.1
|
1.0
|
CBD
|
M:BCL856
|
4.9
|
18.9
|
1.0
|
CE1
|
L:PHE121
|
5.0
|
21.1
|
1.0
|
CD1
|
L:PHE121
|
5.0
|
20.8
|
1.0
|
|
Reference:
M.L.Paddock,
C.Chang,
Q.Xu,
E.C.Abresch,
H.L.Axelrod,
G.Feher,
M.Y.Okamura.
Quinone (Q(B)) Reduction By B-Branch Electron Transfer in Mutant Bacterial Reaction Centers From Rhodobacter Sphaeroides: Quantum Efficiency and X-Ray Structure. Biochemistry V. 44 6920 2005.
ISSN: ISSN 0006-2960
PubMed: 15865437
DOI: 10.1021/BI047559M
Page generated: Tue Aug 13 18:37:17 2024
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