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Magnesium in PDB 1dv3: Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+, PDB code: 1dv3 was solved by 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) 27.80 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.250, 141.250, 275.330, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 25.2

Other elements in 1dv3:

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ also contains other interesting chemical elements:

Cadmium (Cd) 2 atoms
Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ (pdb code 1dv3). 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 From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+, PDB code: 1dv3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1dv3

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Magnesium binding site 1 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1001

b:27.8
occ:1.00
MG L:BCL1001 0.0 27.8 1.0
ND L:BCL1001 2.0 26.5 1.0
NB L:BCL1001 2.1 26.8 1.0
NC L:BCL1001 2.1 26.8 1.0
NA L:BCL1001 2.1 27.5 1.0
NE2 M:HIS182 2.6 27.2 1.0
C4D L:BCL1001 3.0 27.3 1.0
C4A L:BCL1001 3.0 27.9 1.0
C1C L:BCL1001 3.1 27.0 1.0
C1D L:BCL1001 3.1 26.4 1.0
C4C L:BCL1001 3.1 26.4 1.0
C4B L:BCL1001 3.1 28.2 1.0
C1B L:BCL1001 3.1 26.9 1.0
C1A L:BCL1001 3.1 28.1 1.0
CD2 M:HIS182 3.4 28.3 1.0
CHC L:BCL1001 3.4 26.6 1.0
CHB L:BCL1001 3.4 26.8 1.0
CHD L:BCL1001 3.4 26.8 1.0
CHA L:BCL1001 3.4 27.7 1.0
CE1 M:HIS182 3.7 26.8 1.0
C2D L:BCL1001 4.2 26.8 1.0
C3D L:BCL1001 4.3 27.3 1.0
C3B L:BCL1001 4.3 28.1 1.0
C2B L:BCL1001 4.3 27.4 1.0
C3A L:BCL1001 4.4 29.2 1.0
C2C L:BCL1001 4.4 26.8 1.0
C3C L:BCL1001 4.4 26.6 1.0
C2A L:BCL1001 4.5 29.4 1.0
CG M:HIS182 4.6 28.4 1.0
CBB M:BPH1005 4.6 22.7 1.0
ND1 M:HIS182 4.8 26.8 1.0
CE2 L:PHE181 4.8 28.1 1.0
CBD L:BCL1001 4.9 28.0 1.0

Magnesium binding site 2 out of 8 in 1dv3

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Magnesium binding site 2 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1002

b:31.9
occ:1.00
MG L:BCL1002 0.0 31.9 1.0
ND L:BCL1002 2.1 31.5 1.0
NB L:BCL1002 2.1 31.5 1.0
NA L:BCL1002 2.1 32.9 1.0
NC L:BCL1002 2.1 32.6 1.0
NE2 L:HIS173 2.3 30.1 1.0
C4A L:BCL1002 3.1 32.0 1.0
CE1 L:HIS173 3.1 29.1 1.0
C1B L:BCL1002 3.1 31.3 1.0
C4D L:BCL1002 3.1 32.3 1.0
C1D L:BCL1002 3.1 32.6 1.0
C4C L:BCL1002 3.1 32.8 1.0
C4B L:BCL1002 3.1 32.3 1.0
C1C L:BCL1002 3.1 31.4 1.0
C1A L:BCL1002 3.2 31.9 1.0
CHB L:BCL1002 3.3 31.3 1.0
CHD L:BCL1002 3.4 32.7 1.0
CHC L:BCL1002 3.5 31.6 1.0
CD2 L:HIS173 3.5 28.5 1.0
CHA L:BCL1002 3.5 33.0 1.0
CBB M:BCL1003 3.6 28.8 1.0
OBB M:BCL1003 3.7 35.2 1.0
CAB M:BCL1003 3.7 31.7 1.0
C2D L:BCL1002 4.3 32.6 1.0
ND1 L:HIS173 4.3 26.6 1.0
C2B L:BCL1002 4.3 30.6 1.0
C3B L:BCL1002 4.3 31.1 1.0
C3D L:BCL1002 4.3 32.9 1.0
C3A L:BCL1002 4.4 32.5 1.0
C3C L:BCL1002 4.4 32.1 1.0
C2C L:BCL1002 4.4 31.1 1.0
C3B M:BCL1003 4.5 30.5 1.0
CG L:HIS173 4.5 27.9 1.0
C2A L:BCL1002 4.5 30.8 1.0
CD2 L:PHE167 4.8 35.8 1.0
CBD L:BCL1002 5.0 33.2 1.0

Magnesium binding site 3 out of 8 in 1dv3

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Magnesium binding site 3 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1003

b:30.0
occ:1.00
MG M:BCL1003 0.0 30.0 1.0
ND M:BCL1003 2.0 29.7 1.0
NB M:BCL1003 2.1 30.7 1.0
NA M:BCL1003 2.1 29.7 1.0
NC M:BCL1003 2.1 30.3 1.0
NE2 M:HIS202 2.2 29.2 1.0
C4D M:BCL1003 3.0 29.1 1.0
C1B M:BCL1003 3.1 30.3 1.0
C4A M:BCL1003 3.1 29.5 1.0
C1C M:BCL1003 3.1 29.8 1.0
C1D M:BCL1003 3.1 29.7 1.0
C4C M:BCL1003 3.1 30.2 1.0
C4B M:BCL1003 3.1 30.7 1.0
C1A M:BCL1003 3.1 28.4 1.0
CE1 M:HIS202 3.1 29.8 1.0
CD2 M:HIS202 3.3 29.4 1.0
CBB L:BCL1002 3.4 30.3 1.0
CHB M:BCL1003 3.4 29.2 1.0
CHC M:BCL1003 3.4 29.8 1.0
CHA M:BCL1003 3.4 28.3 1.0
CHD M:BCL1003 3.4 30.3 1.0
CAB L:BCL1002 3.7 30.8 1.0
OBB L:BCL1002 4.0 29.4 1.0
C2D M:BCL1003 4.3 28.8 1.0
C2B M:BCL1003 4.3 30.1 1.0
C3D M:BCL1003 4.3 28.9 1.0
C3B M:BCL1003 4.3 30.5 1.0
ND1 M:HIS202 4.3 29.7 1.0
CG M:HIS202 4.4 30.2 1.0
C3B L:BCL1002 4.4 31.1 1.0
C2C M:BCL1003 4.4 30.8 1.0
C3C M:BCL1003 4.4 30.6 1.0
C3A M:BCL1003 4.5 28.3 1.0
C2A M:BCL1003 4.5 29.2 1.0
CBD M:BCL1003 4.9 27.8 1.0

Magnesium binding site 4 out of 8 in 1dv3

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Magnesium binding site 4 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1004

b:25.1
occ:1.00
MG M:BCL1004 0.0 25.1 1.0
NC M:BCL1004 2.0 22.6 1.0
NA M:BCL1004 2.0 23.7 1.0
ND M:BCL1004 2.0 22.6 1.0
NB M:BCL1004 2.1 22.1 1.0
NE2 L:HIS153 2.6 26.6 1.0
C4A M:BCL1004 3.0 24.1 1.0
C4C M:BCL1004 3.0 22.6 1.0
C1C M:BCL1004 3.0 23.0 1.0
C4D M:BCL1004 3.0 22.7 1.0
C1B M:BCL1004 3.1 22.4 1.0
C1D M:BCL1004 3.1 21.4 1.0
C1A M:BCL1004 3.1 24.5 1.0
C4B M:BCL1004 3.1 22.4 1.0
CHB M:BCL1004 3.4 22.3 1.0
CHD M:BCL1004 3.4 20.6 1.0
CD2 L:HIS153 3.4 30.4 1.0
CHC M:BCL1004 3.4 23.0 1.0
CHA M:BCL1004 3.4 24.9 1.0
CE1 L:HIS153 3.7 30.1 1.0
C2D M:BCL1004 4.2 21.4 1.0
C2B M:BCL1004 4.3 23.7 1.0
CBB L:BPH1006 4.3 27.0 1.0
C3D M:BCL1004 4.3 22.9 1.0
C3B M:BCL1004 4.3 22.9 1.0
C3C M:BCL1004 4.3 22.7 1.0
C2C M:BCL1004 4.3 23.8 1.0
C3A M:BCL1004 4.4 25.1 1.0
C2A M:BCL1004 4.4 24.8 1.0
CG L:HIS153 4.6 33.5 1.0
CE2 M:TYR210 4.6 29.0 1.0
ND1 L:HIS153 4.8 33.5 1.0
CBA M:BCL1004 4.8 28.5 1.0
CBC M:BCL1004 4.9 24.2 1.0
CBD M:BCL1004 4.9 27.3 1.0

Magnesium binding site 5 out of 8 in 1dv3

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Magnesium binding site 5 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2002

b:33.5
occ:1.00
MG R:BCL2002 0.0 33.5 1.0
ND R:BCL2002 2.1 34.7 1.0
NB R:BCL2002 2.1 33.5 1.0
NC R:BCL2002 2.1 34.3 1.0
NA R:BCL2002 2.1 34.5 1.0
NE2 R:HIS173 2.3 32.1 1.0
C4A R:BCL2002 3.1 35.2 1.0
CE1 R:HIS173 3.1 30.9 1.0
C1B R:BCL2002 3.1 35.0 1.0
C4D R:BCL2002 3.1 35.1 1.0
C1D R:BCL2002 3.1 35.1 1.0
C4C R:BCL2002 3.1 34.5 1.0
C1C R:BCL2002 3.1 33.8 1.0
C4B R:BCL2002 3.1 33.1 1.0
C1A R:BCL2002 3.2 33.9 1.0
CHB R:BCL2002 3.4 35.0 1.0
CHD R:BCL2002 3.4 35.2 1.0
CHC R:BCL2002 3.5 33.2 1.0
CD2 R:HIS173 3.5 30.8 1.0
CHA R:BCL2002 3.5 34.7 1.0
CBB S:BCL2003 3.6 31.5 1.0
CAB S:BCL2003 3.7 33.3 1.0
OBB S:BCL2003 3.7 34.9 1.0
C2D R:BCL2002 4.3 35.7 1.0
ND1 R:HIS173 4.3 29.7 1.0
C2B R:BCL2002 4.3 34.5 1.0
C3D R:BCL2002 4.3 36.1 1.0
C3B R:BCL2002 4.4 33.5 1.0
C3A R:BCL2002 4.4 35.1 1.0
C2C R:BCL2002 4.4 33.6 1.0
C3C R:BCL2002 4.4 34.5 1.0
C3B S:BCL2003 4.4 32.1 1.0
CG R:HIS173 4.5 30.1 1.0
C2A R:BCL2002 4.5 33.7 1.0
CD2 R:PHE167 4.8 37.1 1.0

Magnesium binding site 6 out of 8 in 1dv3

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Magnesium binding site 6 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2004

b:27.0
occ:1.00
MG R:BCL2004 0.0 27.0 1.0
ND R:BCL2004 2.0 27.7 1.0
NC R:BCL2004 2.0 26.8 1.0
NA R:BCL2004 2.0 27.9 1.0
NB R:BCL2004 2.1 25.8 1.0
NE2 R:HIS153 2.5 29.6 1.0
C1C R:BCL2004 3.0 25.9 1.0
C4D R:BCL2004 3.0 28.6 1.0
C4A R:BCL2004 3.0 28.2 1.0
C4C R:BCL2004 3.1 26.1 1.0
C4B R:BCL2004 3.1 25.4 1.0
C1B R:BCL2004 3.1 25.3 1.0
C1D R:BCL2004 3.1 27.8 1.0
C1A R:BCL2004 3.1 29.0 1.0
CHC R:BCL2004 3.4 25.6 1.0
CD2 R:HIS153 3.4 32.0 1.0
CHB R:BCL2004 3.4 25.7 1.0
CHA R:BCL2004 3.4 29.8 1.0
CHD R:BCL2004 3.4 25.8 1.0
CE1 R:HIS153 3.6 30.6 1.0
C2D R:BCL2004 4.3 28.2 1.0
C3B R:BCL2004 4.3 25.3 1.0
C2B R:BCL2004 4.3 24.6 1.0
C3D R:BCL2004 4.3 28.9 1.0
C2C R:BCL2004 4.4 26.5 1.0
C3A R:BCL2004 4.4 30.0 1.0
C3C R:BCL2004 4.4 26.2 1.0
C2A R:BCL2004 4.4 29.6 1.0
CG R:HIS153 4.6 33.5 1.0
OBB R:BPH2006 4.6 44.7 1.0
CE2 S:TYR210 4.6 30.6 1.0
ND1 R:HIS153 4.7 32.9 1.0
CBA R:BCL2004 4.8 35.1 1.0
CBD R:BCL2004 4.9 31.3 1.0

Magnesium binding site 7 out of 8 in 1dv3

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Magnesium binding site 7 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2001

b:31.3
occ:1.00
MG S:BCL2001 0.0 31.3 1.0
ND S:BCL2001 2.1 31.4 1.0
NB S:BCL2001 2.1 31.6 1.0
NC S:BCL2001 2.1 32.0 1.0
NA S:BCL2001 2.1 31.5 1.0
NE2 S:HIS182 2.4 30.8 1.0
C4D S:BCL2001 3.1 31.3 1.0
C1C S:BCL2001 3.1 31.9 1.0
C1D S:BCL2001 3.1 31.1 1.0
C4A S:BCL2001 3.1 31.7 1.0
C4B S:BCL2001 3.1 31.3 1.0
C1B S:BCL2001 3.1 32.9 1.0
C4C S:BCL2001 3.1 31.6 1.0
C1A S:BCL2001 3.2 31.5 1.0
CD2 S:HIS182 3.2 30.1 1.0
CHC S:BCL2001 3.4 31.4 1.0
CHB S:BCL2001 3.4 31.4 1.0
CHD S:BCL2001 3.5 30.9 1.0
CE1 S:HIS182 3.5 30.3 1.0
CHA S:BCL2001 3.5 31.2 1.0
C2D S:BCL2001 4.2 31.6 1.0
C3D S:BCL2001 4.3 31.4 1.0
C3B S:BCL2001 4.3 32.4 1.0
C2B S:BCL2001 4.3 33.0 1.0
C2C S:BCL2001 4.4 31.3 1.0
C3C S:BCL2001 4.4 30.7 1.0
CG S:HIS182 4.4 30.5 1.0
C3A S:BCL2001 4.5 31.5 1.0
C2A S:BCL2001 4.5 31.8 1.0
ND1 S:HIS182 4.6 30.3 1.0
OBB S:BPH2005 4.9 32.3 1.0
CBD S:BCL2001 5.0 30.6 1.0

Magnesium binding site 8 out of 8 in 1dv3

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Magnesium binding site 8 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+


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 From Rhodobacter Sphaeroides in the Charge-Separated D+Qaqb-State with the Proton Transfer Inhibitor CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2003

b:31.5
occ:1.00
MG S:BCL2003 0.0 31.5 1.0
ND S:BCL2003 2.0 30.8 1.0
NC S:BCL2003 2.1 31.1 1.0
NB S:BCL2003 2.1 31.2 1.0
NA S:BCL2003 2.1 31.2 1.0
NE2 S:HIS202 2.3 30.1 1.0
C4D S:BCL2003 3.0 31.7 1.0
C1C S:BCL2003 3.1 31.0 1.0
C4A S:BCL2003 3.1 32.0 1.0
C1D S:BCL2003 3.1 31.5 1.0
C1B S:BCL2003 3.1 32.7 1.0
C4B S:BCL2003 3.1 32.0 1.0
C4C S:BCL2003 3.1 30.5 1.0
C1A S:BCL2003 3.1 31.5 1.0
CE1 S:HIS202 3.3 30.8 1.0
CD2 S:HIS202 3.4 31.4 1.0
CHC S:BCL2003 3.4 30.9 1.0
CHB S:BCL2003 3.4 31.6 1.0
CHA S:BCL2003 3.4 31.9 1.0
CHD S:BCL2003 3.5 30.9 1.0
CBB R:BCL2002 3.5 30.9 1.0
CAB R:BCL2002 3.7 32.9 1.0
OBB R:BCL2002 3.8 31.6 1.0
C2D S:BCL2003 4.3 31.3 1.0
C3D S:BCL2003 4.3 31.4 1.0
C2B S:BCL2003 4.3 32.3 1.0
C3B S:BCL2003 4.3 32.1 1.0
C2C S:BCL2003 4.4 30.9 1.0
C3B R:BCL2002 4.4 33.5 1.0
C3C S:BCL2003 4.4 29.3 1.0
ND1 S:HIS202 4.4 31.2 1.0
C3A S:BCL2003 4.4 32.7 1.0
C2A S:BCL2003 4.5 32.1 1.0
CG S:HIS202 4.5 32.0 1.0
CBD S:BCL2003 4.9 31.2 1.0

Reference:

H.L.Axelrod, E.C.Abresch, M.L.Paddock, M.Y.Okamura, G.Feher. Determination of the Binding Sites of the Proton Transfer Inhibitors CD2+ and ZN2+ in Bacterial Reaction Centers. Proc.Natl.Acad.Sci.Usa V. 97 1542 2000.
ISSN: ISSN 0027-8424
PubMed: 10677497
DOI: 10.1073/PNAS.97.4.1542
Page generated: Tue Aug 13 02:45:52 2024

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