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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:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

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

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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

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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

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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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