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Magnesium in PDB 1s00: Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State

Protein crystallography data

The structure of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State, PDB code: 1s00 was solved by Q.Xu, H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.84 / 2.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 137.731, 137.731, 277.153, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.8

Other elements in 1s00:

The structure of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State (pdb code 1s00). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State, PDB code: 1s00:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1s00

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Magnesium binding site 1 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


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 Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1001

b:33.1
occ:1.00
 MG L:BCL1001 0.0 33.1 1.0
NB L:BCL1001 1.9 27.2 1.0
NC L:BCL1001 2.0 30.3 1.0
NA L:BCL1001 2.1 30.8 1.0
ND L:BCL1001 2.1 30.2 1.0
NE2 M:HIS182 2.2 28.9 1.0
C4B L:BCL1001 2.9 29.6 1.0
C1C L:BCL1001 2.9 31.0 1.0
C1B L:BCL1001 2.9 27.4 1.0
C4D L:BCL1001 3.0 32.3 1.0
C4C L:BCL1001 3.1 33.1 1.0
C4A L:BCL1001 3.1 31.2 1.0
CD2 M:HIS182 3.2 30.2 1.0
C1D L:BCL1001 3.2 30.5 1.0
C1A L:BCL1001 3.2 35.0 1.0
CHC L:BCL1001 3.3 30.9 1.0
CE1 M:HIS182 3.3 27.4 1.0
CHB L:BCL1001 3.3 29.3 1.0
CHA L:BCL1001 3.5 34.4 1.0
CHD L:BCL1001 3.5 31.3 1.0
C3B L:BCL1001 4.2 28.8 1.0
C3D L:BCL1001 4.2 32.9 1.0
C2B L:BCL1001 4.2 27.0 1.0
C3C L:BCL1001 4.3 32.6 1.0
C2C L:BCL1001 4.3 30.7 1.0
CG M:HIS182 4.3 31.4 1.0
CBB M:BPH1005 4.3 28.1 1.0
C2D L:BCL1001 4.4 31.1 1.0
ND1 M:HIS182 4.4 30.7 1.0
C3A L:BCL1001 4.5 34.5 1.0
C2A L:BCL1001 4.5 36.0 1.0
CBA L:BCL1001 4.8 38.7 1.0
CE2 L:PHE181 5.0 30.9 1.0
CBD L:BCL1001 5.0 35.0 1.0

Magnesium binding site 2 out of 8 in 1s00

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Magnesium binding site 2 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


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 Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1002

b:36.3
occ:1.00
 MG L:BCL1002 0.0 36.3 1.0
NB L:BCL1002 1.9 35.8 1.0
NC L:BCL1002 2.0 37.7 1.0
NA L:BCL1002 2.1 36.9 1.0
ND L:BCL1002 2.2 37.5 1.0
NE2 L:HIS173 2.2 34.1 1.0
C4B L:BCL1002 2.9 36.8 1.0
CE1 L:HIS173 3.0 33.1 1.0
C1B L:BCL1002 3.0 35.6 1.0
C1C L:BCL1002 3.0 35.2 1.0
C4D L:BCL1002 3.1 38.9 1.0
C4A L:BCL1002 3.1 35.1 1.0
C4C L:BCL1002 3.1 36.2 1.0
C1D L:BCL1002 3.2 38.6 1.0
C1A L:BCL1002 3.3 36.9 1.0
CHC L:BCL1002 3.3 36.5 1.0
CHB L:BCL1002 3.3 35.1 1.0
CD2 L:HIS173 3.4 33.0 1.0
CHA L:BCL1002 3.5 38.6 1.0
CHD L:BCL1002 3.5 38.2 1.0
CBB M:BCL1003 3.6 41.8 1.0
CAB M:BCL1003 3.6 43.5 1.0
OBB M:BCL1003 3.7 47.9 1.0
ND1 L:HIS173 4.2 33.0 1.0
C3B L:BCL1002 4.2 36.9 1.0
C2B L:BCL1002 4.2 35.6 1.0
C3D L:BCL1002 4.3 40.5 1.0
C3B M:BCL1003 4.4 41.8 1.0
C2C L:BCL1002 4.4 34.9 1.0
CG L:HIS173 4.4 32.6 1.0
C3C L:BCL1002 4.4 36.1 1.0
C2D L:BCL1002 4.4 40.1 1.0
C3A L:BCL1002 4.5 35.8 1.0
C2A L:BCL1002 4.5 35.5 1.0
CD2 L:PHE167 4.8 38.4 1.0

Magnesium binding site 3 out of 8 in 1s00

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Magnesium binding site 3 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


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 Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1004

b:32.8
occ:1.00
 MG L:BCL1004 0.0 32.8 1.0
NB L:BCL1004 1.9 30.1 1.0
NC L:BCL1004 2.0 29.2 1.0
NA L:BCL1004 2.1 31.6 1.0
ND L:BCL1004 2.1 29.8 1.0
NE2 L:HIS153 2.4 33.5 1.0
C4B L:BCL1004 2.9 30.7 1.0
C1B L:BCL1004 3.0 29.6 1.0
C1C L:BCL1004 3.0 30.9 1.0
C4D L:BCL1004 3.0 30.6 1.0
C4C L:BCL1004 3.1 30.2 1.0
C4A L:BCL1004 3.1 32.1 1.0
C1D L:BCL1004 3.2 29.9 1.0
C1A L:BCL1004 3.2 35.0 1.0
CHC L:BCL1004 3.3 31.2 1.0
CHB L:BCL1004 3.3 28.1 1.0
CD2 L:HIS153 3.3 36.3 1.0
CE1 L:HIS153 3.4 36.5 1.0
CHA L:BCL1004 3.5 33.3 1.0
CHD L:BCL1004 3.5 29.1 1.0
CBB L:BPH1006 4.2 30.9 1.0
C3D L:BCL1004 4.2 30.9 1.0
C3B L:BCL1004 4.2 30.9 1.0
C2B L:BCL1004 4.3 30.7 1.0
C2C L:BCL1004 4.3 31.7 1.0
C3C L:BCL1004 4.3 30.9 1.0
C2D L:BCL1004 4.4 30.7 1.0
CG L:HIS153 4.5 38.5 1.0
C3A L:BCL1004 4.5 36.6 1.0
C2A L:BCL1004 4.5 38.5 1.0
ND1 L:HIS153 4.5 40.9 1.0
C19 L:BPH1006 4.5 36.7 1.0
CE2 M:TYR210 4.7 26.7 1.0
CD2 L:LEU154 5.0 39.2 1.0
CBD L:BCL1004 5.0 33.9 1.0

Magnesium binding site 4 out of 8 in 1s00

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Magnesium binding site 4 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


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 Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1003

b:37.9
occ:1.00
 MG M:BCL1003 0.0 37.9 1.0
NB M:BCL1003 2.0 39.7 1.0
NC M:BCL1003 2.0 39.1 1.0
NA M:BCL1003 2.1 38.0 1.0
ND M:BCL1003 2.2 38.1 1.0
NE2 M:HIS202 2.2 34.6 1.0
C4B M:BCL1003 2.9 40.7 1.0
C1C M:BCL1003 3.0 40.1 1.0
C1B M:BCL1003 3.0 39.3 1.0
C4D M:BCL1003 3.0 37.8 1.0
CE1 M:HIS202 3.0 33.0 1.0
C4C M:BCL1003 3.1 37.6 1.0
C4A M:BCL1003 3.1 37.5 1.0
C1D M:BCL1003 3.2 38.2 1.0
C1A M:BCL1003 3.2 37.9 1.0
CHC M:BCL1003 3.3 41.4 1.0
CBB L:BCL1002 3.3 36.5 1.0
CD2 M:HIS202 3.3 33.5 1.0
CHB M:BCL1003 3.4 37.5 1.0
CHA M:BCL1003 3.5 37.1 1.0
CHD M:BCL1003 3.5 37.1 1.0
CAB L:BCL1002 3.7 37.9 1.0
OBB L:BCL1002 4.1 39.1 1.0
C3D M:BCL1003 4.2 36.2 1.0
C3B M:BCL1003 4.2 41.8 1.0
ND1 M:HIS202 4.2 30.8 1.0
C2B M:BCL1003 4.3 40.5 1.0
C2C M:BCL1003 4.3 39.3 1.0
CG M:HIS202 4.4 30.7 1.0
C3C M:BCL1003 4.4 38.0 1.0
C2D M:BCL1003 4.4 37.1 1.0
C3B L:BCL1002 4.4 36.9 1.0
C3A M:BCL1003 4.5 36.9 1.0
C2A M:BCL1003 4.6 38.0 1.0
CBD M:BCL1003 5.0 33.3 1.0

Magnesium binding site 5 out of 8 in 1s00

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Magnesium binding site 5 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2002

b:55.0
occ:1.00
 MG R:BCL2002 0.0 55.0 1.0
NB R:BCL2002 2.0 54.9 1.0
NC R:BCL2002 2.0 55.8 1.0
NA R:BCL2002 2.1 55.9 1.0
ND R:BCL2002 2.2 56.2 1.0
NE2 R:HIS173 2.2 51.9 1.0
CE1 R:HIS173 2.9 50.1 1.0
C4B R:BCL2002 2.9 54.5 1.0
C1B R:BCL2002 3.0 53.7 1.0
C1C R:BCL2002 3.0 55.3 1.0
C4D R:BCL2002 3.1 56.9 1.0
C4C R:BCL2002 3.1 56.5 1.0
C4A R:BCL2002 3.1 55.0 1.0
C1D R:BCL2002 3.2 56.2 1.0
C1A R:BCL2002 3.3 55.1 1.0
CHC R:BCL2002 3.3 55.4 1.0
CHB R:BCL2002 3.3 54.4 1.0
CD2 R:HIS173 3.4 51.4 1.0
CBB S:BCL2003 3.5 48.9 1.0
CHD R:BCL2002 3.5 56.0 1.0
CHA R:BCL2002 3.6 56.1 1.0
CAB S:BCL2003 3.6 51.0 1.0
OBB S:BCL2003 3.7 54.1 1.0
ND1 R:HIS173 4.2 48.8 1.0
C3B R:BCL2002 4.3 53.7 1.0
C2B R:BCL2002 4.3 54.1 1.0
C3D R:BCL2002 4.3 56.4 1.0
C3B S:BCL2003 4.3 50.7 1.0
C2C R:BCL2002 4.4 55.8 1.0
CG R:HIS173 4.4 48.5 1.0
C3C R:BCL2002 4.4 56.8 1.0
C2D R:BCL2002 4.4 56.0 1.0
C3A R:BCL2002 4.5 53.8 1.0
C2A R:BCL2002 4.6 53.2 1.0
CD2 R:PHE167 4.6 51.1 1.0
C4B S:BCL2003 5.0 50.5 1.0

Magnesium binding site 6 out of 8 in 1s00

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Magnesium binding site 6 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2001

b:43.4
occ:1.00
 MG S:BCL2001 0.0 43.4 1.0
NB S:BCL2001 1.9 44.2 1.0
NC S:BCL2001 2.0 44.8 1.0
NA S:BCL2001 2.1 44.5 1.0
ND S:BCL2001 2.2 43.3 1.0
NE2 S:HIS182 2.4 42.2 1.0
C4B S:BCL2001 2.9 44.6 1.0
C1B S:BCL2001 2.9 44.7 1.0
C1C S:BCL2001 3.0 45.5 1.0
C4D S:BCL2001 3.1 43.7 1.0
C4C S:BCL2001 3.1 45.8 1.0
C4A S:BCL2001 3.1 44.1 1.0
C1D S:BCL2001 3.2 42.0 1.0
C1A S:BCL2001 3.2 46.8 1.0
CHC S:BCL2001 3.3 45.4 1.0
CD2 S:HIS182 3.3 42.0 1.0
CHB S:BCL2001 3.3 44.8 1.0
CE1 S:HIS182 3.4 42.1 1.0
CHD S:BCL2001 3.5 43.2 1.0
CHA S:BCL2001 3.5 45.0 1.0
C3B S:BCL2001 4.2 46.4 1.0
C2B S:BCL2001 4.2 46.3 1.0
C3D S:BCL2001 4.3 42.4 1.0
CBB S:BPH2005 4.3 35.2 1.0
C3C S:BCL2001 4.3 45.3 1.0
C2C S:BCL2001 4.3 45.6 1.0
C2D S:BCL2001 4.4 41.5 1.0
CG S:HIS182 4.5 41.8 1.0
C3A S:BCL2001 4.5 47.1 1.0
ND1 S:HIS182 4.5 41.6 1.0
C2A S:BCL2001 4.5 47.7 1.0
O1A S:BCL2001 4.6 61.7 1.0
C18 S:SPO2010 4.9 43.9 1.0
CE2 R:PHE181 4.9 35.5 1.0

Magnesium binding site 7 out of 8 in 1s00

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Magnesium binding site 7 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2003

b:49.0
occ:1.00
 MG S:BCL2003 0.0 49.0 1.0
NB S:BCL2003 1.9 49.5 1.0
NC S:BCL2003 2.0 48.5 1.0
NA S:BCL2003 2.1 48.4 1.0
ND S:BCL2003 2.2 47.5 1.0
NE2 S:HIS202 2.3 46.5 1.0
C4B S:BCL2003 2.9 50.5 1.0
C1B S:BCL2003 3.0 49.4 1.0
C1C S:BCL2003 3.0 47.9 1.0
C4D S:BCL2003 3.0 47.2 1.0
C4A S:BCL2003 3.1 48.6 1.0
C4C S:BCL2003 3.1 47.3 1.0
CE1 S:HIS202 3.2 45.9 1.0
C1D S:BCL2003 3.2 46.4 1.0
C1A S:BCL2003 3.2 47.8 1.0
CHC S:BCL2003 3.3 48.5 1.0
CHB S:BCL2003 3.3 49.6 1.0
CBB R:BCL2002 3.4 49.4 1.0
CD2 S:HIS202 3.4 46.2 1.0
CHA S:BCL2003 3.5 48.2 1.0
CHD S:BCL2003 3.5 46.5 1.0
CAB R:BCL2002 3.7 52.2 1.0
OBB R:BCL2002 4.0 50.9 1.0
C3B S:BCL2003 4.2 50.7 1.0
C3D S:BCL2003 4.2 46.2 1.0
C2B S:BCL2003 4.2 50.3 1.0
C2C S:BCL2003 4.3 49.0 1.0
C3B R:BCL2002 4.3 53.7 1.0
C3C S:BCL2003 4.4 47.2 1.0
ND1 S:HIS202 4.4 45.6 1.0
C2D S:BCL2003 4.4 46.2 1.0
CG S:HIS202 4.5 46.8 1.0
C3A S:BCL2003 4.5 47.8 1.0
C2A S:BCL2003 4.5 48.4 1.0
CBD S:BCL2003 5.0 48.4 1.0
C2B R:BCL2002 5.0 54.1 1.0

Magnesium binding site 8 out of 8 in 1s00

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Magnesium binding site 8 out of 8 in the Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Photosynthetic Reaction Center Double Mutant From Rhodobacter Sphaeroides with Asp L213 Replaced with Asn and Arg M233 Replaced with Cys in the Charge-Separated D+Qaqb- State within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2004

b:46.9
occ:1.00
 MG S:BCL2004 0.0 46.9 1.0
NB S:BCL2004 1.9 46.0 1.0
NC S:BCL2004 2.0 46.5 1.0
NA S:BCL2004 2.1 48.1 1.0
ND S:BCL2004 2.2 46.5 1.0
NE2 R:HIS153 2.5 48.2 1.0
C4B S:BCL2004 2.9 46.3 1.0
C1B S:BCL2004 3.0 46.2 1.0
C1C S:BCL2004 3.0 46.0 1.0
C4D S:BCL2004 3.0 47.7 1.0
C4C S:BCL2004 3.1 47.3 1.0
C4A S:BCL2004 3.1 50.1 1.0
C1D S:BCL2004 3.2 45.7 1.0
C1A S:BCL2004 3.2 50.3 1.0
CHC S:BCL2004 3.3 45.1 1.0
CD2 R:HIS153 3.3 48.4 1.0
CHB S:BCL2004 3.3 47.4 1.0
CHA S:BCL2004 3.5 49.6 1.0
CHD S:BCL2004 3.5 44.5 1.0
CE1 R:HIS153 3.6 50.0 1.0
C3B S:BCL2004 4.2 46.7 1.0
C3D S:BCL2004 4.2 47.4 1.0
C2B S:BCL2004 4.3 46.8 1.0
C2C S:BCL2004 4.3 47.4 1.0
C3C S:BCL2004 4.3 49.1 1.0
C2D S:BCL2004 4.4 46.3 1.0
C3A S:BCL2004 4.5 52.9 1.0
CG R:HIS153 4.5 50.5 1.0
CBB R:BPH2006 4.5 58.1 1.0
C2A S:BCL2004 4.5 52.9 1.0
ND1 R:HIS153 4.7 51.3 1.0
C19 R:BPH2006 4.7 47.5 1.0
CE2 S:TYR210 4.7 44.2 1.0
CBA S:BCL2004 4.8 63.6 1.0
CD2 R:LEU154 5.0 43.8 1.0

Reference:

Q.Xu, H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher. X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers From Rb. Sphaeroides; Altered Proton Transfer Pathways. Structure V. 12 703 2004.
ISSN: ISSN 0969-2126
PubMed: 15062092
DOI: 10.1016/J.STR.2004.03.001
Page generated: Tue Aug 13 13:10:55 2024

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