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Magnesium in PDB 1l9j: X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals

Protein crystallography data

The structure of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals, PDB code: 1l9j was solved by H.L.Axelrod, E.C.Abresch, M.Y.Okamura, A.P.Yeh, D.C.Rees, G.Feher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.32 / 3.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.930, 80.312, 246.575, 90.00, 92.41, 90.00
R / Rfree (%) 24.8 / 28.7

Other elements in 1l9j:

The structure of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals (pdb code 1l9j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals, PDB code: 1l9j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1l9j

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Magnesium binding site 1 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1002

b:34.0
occ:1.00
 MG L:BCL1002 0.0 34.0 1.0
NB L:BCL1002 1.9 35.3 1.0
NC L:BCL1002 2.0 33.7 1.0
NA L:BCL1002 2.1 35.4 1.0
ND L:BCL1002 2.1 36.4 1.0
NE2 L:HIS173 2.5 36.4 1.0
C4B L:BCL1002 2.9 35.4 1.0
C1B L:BCL1002 3.0 35.6 1.0
C1C L:BCL1002 3.0 33.0 1.0
C4D L:BCL1002 3.0 39.7 1.0
C4A L:BCL1002 3.1 35.9 1.0
C4C L:BCL1002 3.1 32.2 1.0
OBB M:BCL1003 3.2 43.7 1.0
C1D L:BCL1002 3.2 37.3 1.0
CE1 L:HIS173 3.2 37.6 1.0
C1A L:BCL1002 3.2 38.0 1.0
CHC L:BCL1002 3.3 34.3 1.0
CHB L:BCL1002 3.3 33.2 1.0
CAB M:BCL1003 3.5 42.3 1.0
CHA L:BCL1002 3.5 39.1 1.0
CHD L:BCL1002 3.5 35.2 1.0
CD2 L:HIS173 3.6 36.6 1.0
CBB M:BCL1003 3.8 44.6 1.0
C3B L:BCL1002 4.2 37.3 1.0
C2B L:BCL1002 4.2 37.6 1.0
C3D L:BCL1002 4.2 40.9 1.0
C3B M:BCL1003 4.3 40.9 1.0
C2C L:BCL1002 4.3 30.4 1.0
C3C L:BCL1002 4.4 31.1 1.0
C2D L:BCL1002 4.4 37.7 1.0
ND1 L:HIS173 4.5 38.8 1.0
C3A L:BCL1002 4.5 38.1 1.0
C2A L:BCL1002 4.5 40.8 1.0
CD2 L:PHE167 4.6 40.8 1.0
CG L:HIS173 4.7 36.6 1.0
C4B M:BCL1003 4.9 39.5 1.0
CBD L:BCL1002 5.0 42.3 1.0

Magnesium binding site 2 out of 8 in 1l9j

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Magnesium binding site 2 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1004

b:46.0
occ:1.00
 MG L:BCL1004 0.0 46.0 1.0
NB L:BCL1004 1.9 47.2 1.0
NC L:BCL1004 2.0 47.0 1.0
NA L:BCL1004 2.1 47.7 1.0
ND L:BCL1004 2.1 45.8 1.0
NE2 L:HIS153 2.4 47.4 1.0
C4B L:BCL1004 2.9 46.8 1.0
C1C L:BCL1004 3.0 46.1 1.0
C1B L:BCL1004 3.0 47.0 1.0
C4D L:BCL1004 3.0 46.9 1.0
C4C L:BCL1004 3.1 46.0 1.0
C4A L:BCL1004 3.1 46.9 1.0
C1D L:BCL1004 3.2 47.1 1.0
C1A L:BCL1004 3.2 47.1 1.0
CHC L:BCL1004 3.3 45.9 1.0
CHB L:BCL1004 3.3 46.7 1.0
CE1 L:HIS153 3.4 49.9 1.0
CD2 L:HIS153 3.4 48.1 1.0
CHA L:BCL1004 3.5 47.3 1.0
CHD L:BCL1004 3.5 46.0 1.0
C3D L:BCL1004 4.2 48.0 1.0
C3B L:BCL1004 4.3 48.6 1.0
C2B L:BCL1004 4.3 48.2 1.0
C2C L:BCL1004 4.3 44.5 1.0
C3C L:BCL1004 4.3 45.0 1.0
C2D L:BCL1004 4.4 47.1 1.0
C3A L:BCL1004 4.5 47.9 1.0
C2A L:BCL1004 4.5 47.9 1.0
CG L:HIS153 4.5 46.9 1.0
ND1 L:HIS153 4.5 48.7 1.0
CBB M:BPH1006 4.9 58.7 1.0
C19 M:BPH1006 4.9 59.7 1.0
CBD L:BCL1004 5.0 47.9 1.0

Magnesium binding site 3 out of 8 in 1l9j

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Magnesium binding site 3 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1001

b:42.8
occ:1.00
 MG M:BCL1001 0.0 42.8 1.0
NB M:BCL1001 1.9 45.3 1.0
NC M:BCL1001 2.0 43.5 1.0
NA M:BCL1001 2.1 44.3 1.0
ND M:BCL1001 2.2 43.1 1.0
NE2 M:HIS182 2.5 40.3 1.0
C4B M:BCL1001 2.9 46.5 1.0
C1B M:BCL1001 3.0 45.4 1.0
C1C M:BCL1001 3.0 43.7 1.0
C4D M:BCL1001 3.1 45.5 1.0
C4C M:BCL1001 3.1 42.0 1.0
C4A M:BCL1001 3.1 46.1 1.0
C1D M:BCL1001 3.2 41.7 1.0
C1A M:BCL1001 3.2 45.5 1.0
CHC M:BCL1001 3.3 45.3 1.0
CHB M:BCL1001 3.3 46.2 1.0
CD2 M:HIS182 3.3 39.0 1.0
CHD M:BCL1001 3.5 42.0 1.0
CE1 M:HIS182 3.5 39.9 1.0
CHA M:BCL1001 3.5 46.4 1.0
C3B M:BCL1001 4.2 48.0 1.0
C2B M:BCL1001 4.2 45.7 1.0
C3D M:BCL1001 4.3 45.1 1.0
C2C M:BCL1001 4.3 41.6 1.0
C3C M:BCL1001 4.3 41.0 1.0
C2D M:BCL1001 4.4 41.4 1.0
C3A M:BCL1001 4.5 48.6 1.0
C2A M:BCL1001 4.5 48.2 1.0
CG M:HIS182 4.5 39.4 1.0
CBB L:BPH1005 4.6 54.2 1.0
ND1 M:HIS182 4.6 40.2 1.0
CE1 L:PHE181 4.8 37.4 1.0

Magnesium binding site 4 out of 8 in 1l9j

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Magnesium binding site 4 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1003

b:38.2
occ:1.00
 MG M:BCL1003 0.0 38.2 1.0
NB M:BCL1003 1.9 40.1 1.0
NC M:BCL1003 2.0 38.6 1.0
NA M:BCL1003 2.1 39.2 1.0
ND M:BCL1003 2.2 37.7 1.0
NE2 M:HIS202 2.3 38.4 1.0
C4B M:BCL1003 2.9 39.5 1.0
C1B M:BCL1003 3.0 41.6 1.0
C1C M:BCL1003 3.0 40.1 1.0
C4D M:BCL1003 3.0 36.4 1.0
C4C M:BCL1003 3.1 38.5 1.0
C4A M:BCL1003 3.1 39.8 1.0
CE1 M:HIS202 3.2 41.8 1.0
C1D M:BCL1003 3.2 36.6 1.0
CHC M:BCL1003 3.2 40.0 1.0
C1A M:BCL1003 3.2 37.6 1.0
CBB L:BCL1002 3.3 35.3 1.0
CHB M:BCL1003 3.4 39.0 1.0
CD2 M:HIS202 3.4 39.7 1.0
CHA M:BCL1003 3.5 36.2 1.0
CHD M:BCL1003 3.6 37.9 1.0
CAB L:BCL1002 3.8 37.2 1.0
C3B M:BCL1003 4.2 40.9 1.0
C3D M:BCL1003 4.2 35.3 1.0
C2B M:BCL1003 4.2 43.5 1.0
OBB L:BCL1002 4.3 39.0 1.0
C2C M:BCL1003 4.3 39.9 1.0
C3C M:BCL1003 4.4 38.2 1.0
C2D M:BCL1003 4.4 35.5 1.0
ND1 M:HIS202 4.4 42.9 1.0
C3B L:BCL1002 4.4 37.3 1.0
CG M:HIS202 4.5 41.6 1.0
C3A M:BCL1003 4.5 38.8 1.0
C2A M:BCL1003 4.6 37.9 1.0
CD1 M:ILE206 4.7 35.0 1.0
CBD M:BCL1003 5.0 35.8 1.0

Magnesium binding site 5 out of 8 in 1l9j

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Magnesium binding site 5 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2002

b:41.3
occ:1.00
 MG R:BCL2002 0.0 41.3 1.0
NB R:BCL2002 1.9 41.7 1.0
NC R:BCL2002 2.0 41.4 1.0
NA R:BCL2002 2.1 41.2 1.0
ND R:BCL2002 2.2 41.9 1.0
NE2 R:HIS173 2.5 45.7 1.0
C4B R:BCL2002 2.9 40.8 1.0
C1B R:BCL2002 3.0 40.7 1.0
C1C R:BCL2002 3.0 41.6 1.0
C4D R:BCL2002 3.1 42.3 1.0
C4A R:BCL2002 3.1 40.3 1.0
C4C R:BCL2002 3.1 40.9 1.0
C1D R:BCL2002 3.2 42.5 1.0
C1A R:BCL2002 3.3 42.8 1.0
CHC R:BCL2002 3.3 42.2 1.0
CHB R:BCL2002 3.3 38.7 1.0
CE1 R:HIS173 3.4 47.3 1.0
CHA R:BCL2002 3.5 42.2 1.0
OBB S:BCL2003 3.5 39.6 1.0
CHD R:BCL2002 3.5 41.7 1.0
CAB S:BCL2003 3.6 37.9 1.0
CD2 R:HIS173 3.6 46.1 1.0
CBB S:BCL2003 3.7 37.5 1.0
C3B R:BCL2002 4.2 40.6 1.0
C2B R:BCL2002 4.3 40.4 1.0
C3D R:BCL2002 4.3 43.1 1.0
C3B S:BCL2003 4.3 37.5 1.0
C2C R:BCL2002 4.4 40.0 1.0
C3C R:BCL2002 4.4 40.4 1.0
C2D R:BCL2002 4.4 42.7 1.0
C3A R:BCL2002 4.5 41.4 1.0
C2A R:BCL2002 4.6 44.3 1.0
ND1 R:HIS173 4.6 48.1 1.0
CG R:HIS173 4.7 46.7 1.0
CD2 R:PHE167 4.8 43.5 1.0
C4B S:BCL2003 4.9 37.6 1.0

Magnesium binding site 6 out of 8 in 1l9j

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Magnesium binding site 6 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2004

b:51.0
occ:1.00
 MG R:BCL2004 0.0 51.0 1.0
NB R:BCL2004 2.0 52.3 1.0
NC R:BCL2004 2.0 51.6 1.0
NA R:BCL2004 2.1 52.6 1.0
ND R:BCL2004 2.1 49.5 1.0
NE2 R:HIS153 2.7 51.0 1.0
C4B R:BCL2004 2.9 52.3 1.0
C1B R:BCL2004 3.0 51.4 1.0
C1C R:BCL2004 3.0 52.3 1.0
C4D R:BCL2004 3.0 49.8 1.0
C4C R:BCL2004 3.1 51.6 1.0
C4A R:BCL2004 3.1 52.7 1.0
C1D R:BCL2004 3.2 50.4 1.0
C1A R:BCL2004 3.2 51.9 1.0
CHC R:BCL2004 3.3 51.5 1.0
CHB R:BCL2004 3.3 52.2 1.0
CHD R:BCL2004 3.5 50.6 1.0
CHA R:BCL2004 3.5 50.3 1.0
CD2 R:HIS153 3.5 51.8 1.0
CE1 R:HIS153 3.7 50.9 1.0
C3D R:BCL2004 4.2 50.8 1.0
C3B R:BCL2004 4.3 51.3 1.0
C2B R:BCL2004 4.3 50.5 1.0
C2C R:BCL2004 4.3 52.4 1.0
C3C R:BCL2004 4.3 52.1 1.0
C2D R:BCL2004 4.4 51.4 1.0
C3A R:BCL2004 4.5 53.7 1.0
C2A R:BCL2004 4.5 54.5 1.0
CG R:HIS153 4.7 50.8 1.0
ND1 R:HIS153 4.8 49.2 1.0
CD2 R:LEU154 4.8 45.2 1.0
C19 S:BPH2006 4.8 54.6 1.0

Magnesium binding site 7 out of 8 in 1l9j

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Magnesium binding site 7 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2001

b:56.3
occ:1.00
 MG S:BCL2001 0.0 56.3 1.0
NB S:BCL2001 1.9 57.1 1.0
NC S:BCL2001 2.0 56.0 1.0
NA S:BCL2001 2.1 56.7 1.0
ND S:BCL2001 2.1 58.0 1.0
NE2 S:HIS182 2.4 50.5 1.0
C4B S:BCL2001 2.9 57.5 1.0
C1B S:BCL2001 3.0 58.6 1.0
C1C S:BCL2001 3.0 54.7 1.0
C4D S:BCL2001 3.0 60.6 1.0
C4C S:BCL2001 3.1 55.3 1.0
C4A S:BCL2001 3.1 58.1 1.0
C1D S:BCL2001 3.2 58.1 1.0
CHC S:BCL2001 3.2 55.2 1.0
C1A S:BCL2001 3.2 58.9 1.0
CD2 S:HIS182 3.2 47.4 1.0
CHB S:BCL2001 3.3 58.6 1.0
CE1 S:HIS182 3.4 49.2 1.0
CHD S:BCL2001 3.5 57.0 1.0
CHA S:BCL2001 3.5 61.1 1.0
C3B S:BCL2001 4.2 60.2 1.0
C2B S:BCL2001 4.2 59.4 1.0
C3D S:BCL2001 4.2 61.5 1.0
C2C S:BCL2001 4.3 53.2 1.0
C3C S:BCL2001 4.3 53.4 1.0
C2D S:BCL2001 4.4 60.1 1.0
CG S:HIS182 4.4 48.4 1.0
C3A S:BCL2001 4.5 61.4 1.0
C2A S:BCL2001 4.5 60.3 1.0
ND1 S:HIS182 4.5 49.2 1.0
CBB R:BPH2005 4.6 76.0 1.0
CE1 R:PHE181 4.9 43.7 1.0

Magnesium binding site 8 out of 8 in 1l9j

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Magnesium binding site 8 out of 8 in the X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Structure of the Cytochrome-C(2)-Photosynthetic Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides in Type I Co- Crystals within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2003

b:38.4
occ:1.00
 MG S:BCL2003 0.0 38.4 1.0
NB S:BCL2003 1.9 37.9 1.0
NC S:BCL2003 2.0 40.5 1.0
NA S:BCL2003 2.1 38.5 1.0
ND S:BCL2003 2.2 38.6 1.0
NE2 S:HIS202 2.5 41.6 1.0
C4B S:BCL2003 2.9 37.6 1.0
C1B S:BCL2003 3.0 37.5 1.0
C1C S:BCL2003 3.0 42.0 1.0
C4D S:BCL2003 3.0 39.7 1.0
C4C S:BCL2003 3.1 42.1 1.0
C4A S:BCL2003 3.1 37.6 1.0
C1D S:BCL2003 3.2 38.9 1.0
C1A S:BCL2003 3.2 38.3 1.0
CHC S:BCL2003 3.3 40.0 1.0
CHB S:BCL2003 3.3 36.2 1.0
CE1 S:HIS202 3.4 42.7 1.0
CBB R:BCL2002 3.5 41.0 1.0
CD2 S:HIS202 3.5 45.0 1.0
CHA S:BCL2003 3.5 40.2 1.0
CHD S:BCL2003 3.5 40.7 1.0
CAB R:BCL2002 3.7 42.0 1.0
OBB R:BCL2002 4.0 43.5 1.0
C3B S:BCL2003 4.2 37.5 1.0
C3D S:BCL2003 4.2 38.7 1.0
C2B S:BCL2003 4.2 39.0 1.0
C3B R:BCL2002 4.4 40.6 1.0
C2C S:BCL2003 4.4 42.2 1.0
C3C S:BCL2003 4.4 42.8 1.0
C2D S:BCL2003 4.4 38.7 1.0
C3A S:BCL2003 4.5 37.0 1.0
C2A S:BCL2003 4.6 36.9 1.0
ND1 S:HIS202 4.6 44.2 1.0
CG S:HIS202 4.6 47.1 1.0
CBD S:BCL2003 5.0 42.0 1.0
CD1 S:ILE206 5.0 30.5 1.0

Reference:

H.L.Axelrod, E.C.Abresch, M.Y.Okamura, A.P.Yeh, D.C.Rees, G.Feher. X-Ray Structure Determination of the Cytochrome C2: Reaction Center Electron Transfer Complex From Rhodobacter Sphaeroides. J.Mol.Biol. V. 319 501 2002.
ISSN: ISSN 0022-2836
PubMed: 12051924
DOI: 10.1016/S0022-2836(02)00168-7
Page generated: Tue Aug 13 08:28:01 2024

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