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Magnesium in PDB 1dv6: Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+, PDB code: 1dv6 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) 27.52 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.517, 141.517, 278.506, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 26.5

Other elements in 1dv6:

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ (pdb code 1dv6). 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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+, PDB code: 1dv6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1dv6

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Magnesium binding site 1 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1002

b:39.3
occ:1.00
MG L:BCL1002 0.0 39.3 1.0
ND L:BCL1002 2.1 39.2 1.0
NB L:BCL1002 2.1 38.6 1.0
NA L:BCL1002 2.1 39.6 1.0
NC L:BCL1002 2.1 40.3 1.0
NE2 L:HIS173 2.2 38.3 1.0
CE1 L:HIS173 3.0 37.1 1.0
C4A L:BCL1002 3.0 38.4 1.0
C1B L:BCL1002 3.1 37.7 1.0
C4D L:BCL1002 3.1 39.6 1.0
C1D L:BCL1002 3.1 40.3 1.0
C4C L:BCL1002 3.1 40.6 1.0
C4B L:BCL1002 3.1 39.0 1.0
C1C L:BCL1002 3.1 39.5 1.0
C1A L:BCL1002 3.2 38.8 1.0
CHB L:BCL1002 3.3 37.6 1.0
CD2 L:HIS173 3.4 36.2 1.0
CHD L:BCL1002 3.4 40.5 1.0
CHC L:BCL1002 3.5 38.6 1.0
CHA L:BCL1002 3.5 39.7 1.0
CBB M:BCL1003 3.7 37.6 1.0
CAB M:BCL1003 3.8 39.0 1.0
OBB M:BCL1003 3.9 40.8 1.0
ND1 L:HIS173 4.2 35.5 1.0
C2B L:BCL1002 4.3 36.7 1.0
C2D L:BCL1002 4.3 40.6 1.0
C3B L:BCL1002 4.3 37.5 1.0
C3D L:BCL1002 4.4 40.2 1.0
C3A L:BCL1002 4.4 38.7 1.0
C3C L:BCL1002 4.4 40.6 1.0
C2C L:BCL1002 4.4 39.4 1.0
CG L:HIS173 4.4 36.0 1.0
C2A L:BCL1002 4.5 37.5 1.0
C3B M:BCL1003 4.5 38.3 1.0
CD2 L:PHE167 4.7 45.0 1.0
CBD L:BCL1002 5.0 39.7 1.0

Magnesium binding site 2 out of 8 in 1dv6

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Magnesium binding site 2 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1001

b:35.6
occ:1.00
MG M:BCL1001 0.0 35.6 1.0
ND M:BCL1001 2.0 34.7 1.0
NB M:BCL1001 2.1 34.3 1.0
NC M:BCL1001 2.1 35.1 1.0
NA M:BCL1001 2.1 35.4 1.0
NE2 M:HIS182 2.6 35.8 1.0
C4A M:BCL1001 3.0 35.5 1.0
C4D M:BCL1001 3.1 35.2 1.0
C1C M:BCL1001 3.1 35.0 1.0
C1D M:BCL1001 3.1 34.7 1.0
C4C M:BCL1001 3.1 34.9 1.0
C1B M:BCL1001 3.1 34.1 1.0
C4B M:BCL1001 3.1 34.4 1.0
C1A M:BCL1001 3.2 35.0 1.0
CD2 M:HIS182 3.3 36.4 1.0
CHB M:BCL1001 3.4 34.1 1.0
CHC M:BCL1001 3.4 34.2 1.0
CHD M:BCL1001 3.4 34.3 1.0
CHA M:BCL1001 3.5 35.6 1.0
CE1 M:HIS182 3.7 35.4 1.0
C2D M:BCL1001 4.2 34.8 1.0
C2B M:BCL1001 4.3 34.3 1.0
C3B M:BCL1001 4.3 33.7 1.0
C3D M:BCL1001 4.3 34.9 1.0
C3A M:BCL1001 4.4 36.3 1.0
C2C M:BCL1001 4.4 35.3 1.0
C3C M:BCL1001 4.4 35.3 1.0
C2A M:BCL1001 4.5 36.7 1.0
CG M:HIS182 4.6 36.3 1.0
CBB M:BPH1005 4.6 31.2 1.0
ND1 M:HIS182 4.8 35.4 1.0
CE2 L:PHE181 4.8 36.7 1.0
CBD M:BCL1001 5.0 36.4 1.0

Magnesium binding site 3 out of 8 in 1dv6

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Magnesium binding site 3 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1003

b:37.8
occ:1.00
MG M:BCL1003 0.0 37.8 1.0
ND M:BCL1003 2.0 36.5 1.0
NB M:BCL1003 2.1 37.6 1.0
NC M:BCL1003 2.1 37.3 1.0
NA M:BCL1003 2.1 36.5 1.0
NE2 M:HIS202 2.3 37.5 1.0
C4D M:BCL1003 3.0 35.3 1.0
C1C M:BCL1003 3.1 37.2 1.0
C4B M:BCL1003 3.1 38.3 1.0
C1D M:BCL1003 3.1 36.6 1.0
C4A M:BCL1003 3.1 36.3 1.0
C1B M:BCL1003 3.1 37.2 1.0
C1A M:BCL1003 3.1 35.5 1.0
CE1 M:HIS202 3.1 38.4 1.0
C4C M:BCL1003 3.1 36.5 1.0
CBB L:BCL1002 3.3 37.9 1.0
CD2 M:HIS202 3.4 38.1 1.0
CHC M:BCL1003 3.4 37.6 1.0
CHB M:BCL1003 3.4 36.2 1.0
CHA M:BCL1003 3.4 34.8 1.0
CHD M:BCL1003 3.5 37.2 1.0
CAB L:BCL1002 3.7 37.8 1.0
OBB L:BCL1002 4.0 36.0 1.0
C2D M:BCL1003 4.3 35.8 1.0
C3B M:BCL1003 4.3 38.3 1.0
C3D M:BCL1003 4.3 35.3 1.0
C2B M:BCL1003 4.3 37.3 1.0
ND1 M:HIS202 4.3 38.1 1.0
C3B L:BCL1002 4.4 37.5 1.0
C2C M:BCL1003 4.4 37.2 1.0
CG M:HIS202 4.4 38.4 1.0
C3C M:BCL1003 4.4 36.1 1.0
C3A M:BCL1003 4.4 35.7 1.0
C2A M:BCL1003 4.5 36.1 1.0
CBD M:BCL1003 4.9 33.6 1.0

Magnesium binding site 4 out of 8 in 1dv6

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Magnesium binding site 4 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1004

b:34.3
occ:1.00
MG M:BCL1004 0.0 34.3 1.0
ND M:BCL1004 2.0 31.9 1.0
NC M:BCL1004 2.1 31.5 1.0
NA M:BCL1004 2.1 32.8 1.0
NB M:BCL1004 2.1 30.7 1.0
NE2 L:HIS153 2.5 36.4 1.0
C4A M:BCL1004 3.0 32.7 1.0
C4D M:BCL1004 3.0 32.6 1.0
C4C M:BCL1004 3.0 31.1 1.0
C1D M:BCL1004 3.1 31.6 1.0
C1C M:BCL1004 3.1 31.1 1.0
C1B M:BCL1004 3.1 30.2 1.0
C1A M:BCL1004 3.1 33.5 1.0
C4B M:BCL1004 3.1 30.8 1.0
CHB M:BCL1004 3.3 30.8 1.0
CHD M:BCL1004 3.4 30.8 1.0
CD2 L:HIS153 3.4 40.0 1.0
CHA M:BCL1004 3.4 34.1 1.0
CHC M:BCL1004 3.4 29.9 1.0
CE1 L:HIS153 3.6 39.1 1.0
C2D M:BCL1004 4.2 30.9 1.0
C3D M:BCL1004 4.3 31.8 1.0
C2B M:BCL1004 4.3 30.6 1.0
C3C M:BCL1004 4.3 30.4 1.0
C3B M:BCL1004 4.3 30.6 1.0
C3A M:BCL1004 4.4 33.3 1.0
C2C M:BCL1004 4.4 31.2 1.0
CBB L:BPH1006 4.4 42.3 1.0
C2A M:BCL1004 4.4 33.8 1.0
CE2 M:TYR210 4.6 38.7 1.0
CG L:HIS153 4.6 42.2 1.0
ND1 L:HIS153 4.7 42.2 1.0
CBA M:BCL1004 4.8 35.9 1.0
CBC M:BCL1004 4.9 31.6 1.0
CBD M:BCL1004 4.9 35.4 1.0

Magnesium binding site 5 out of 8 in 1dv6

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Magnesium binding site 5 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2002

b:43.5
occ:1.00
MG R:BCL2002 0.0 43.5 1.0
ND R:BCL2002 2.1 44.6 1.0
NB R:BCL2002 2.1 43.7 1.0
NA R:BCL2002 2.1 44.6 1.0
NC R:BCL2002 2.1 44.7 1.0
NE2 R:HIS173 2.3 41.2 1.0
C4A R:BCL2002 3.0 44.7 1.0
C1B R:BCL2002 3.1 44.0 1.0
CE1 R:HIS173 3.1 40.0 1.0
C1D R:BCL2002 3.1 44.6 1.0
C4D R:BCL2002 3.1 44.9 1.0
C4C R:BCL2002 3.1 44.9 1.0
C1C R:BCL2002 3.1 44.4 1.0
C4B R:BCL2002 3.1 43.6 1.0
C1A R:BCL2002 3.2 43.9 1.0
CHB R:BCL2002 3.3 44.1 1.0
CHD R:BCL2002 3.4 45.1 1.0
CHC R:BCL2002 3.5 44.4 1.0
CD2 R:HIS173 3.5 39.7 1.0
CHA R:BCL2002 3.5 44.5 1.0
CBB S:BCL2003 3.7 43.8 1.0
OBB S:BCL2003 3.8 46.4 1.0
CAB S:BCL2003 3.8 45.1 1.0
C2D R:BCL2002 4.3 45.0 1.0
C2B R:BCL2002 4.3 43.9 1.0
ND1 R:HIS173 4.3 38.3 1.0
C3B R:BCL2002 4.3 43.3 1.0
C3D R:BCL2002 4.3 45.6 1.0
C3A R:BCL2002 4.4 45.1 1.0
C3C R:BCL2002 4.4 45.3 1.0
C2C R:BCL2002 4.4 44.9 1.0
C3B S:BCL2003 4.5 43.9 1.0
C2A R:BCL2002 4.5 43.8 1.0
CG R:HIS173 4.5 39.0 1.0
CD2 R:PHE167 4.8 45.9 1.0

Magnesium binding site 6 out of 8 in 1dv6

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Magnesium binding site 6 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg2004

b:40.4
occ:1.00
MG R:BCL2004 0.0 40.4 1.0
NA R:BCL2004 2.0 40.5 1.0
ND R:BCL2004 2.0 40.0 1.0
NC R:BCL2004 2.0 39.6 1.0
NB R:BCL2004 2.0 38.8 1.0
NE2 R:HIS153 2.6 40.7 1.0
C4A R:BCL2004 3.0 41.2 1.0
C1C R:BCL2004 3.0 39.9 1.0
C4D R:BCL2004 3.0 40.6 1.0
C4C R:BCL2004 3.1 39.3 1.0
C1B R:BCL2004 3.1 38.8 1.0
C4B R:BCL2004 3.1 39.0 1.0
C1D R:BCL2004 3.1 40.0 1.0
C1A R:BCL2004 3.1 41.6 1.0
CHB R:BCL2004 3.4 38.9 1.0
CHC R:BCL2004 3.4 39.5 1.0
CHD R:BCL2004 3.4 38.8 1.0
CHA R:BCL2004 3.4 41.5 1.0
CD2 R:HIS153 3.5 41.7 1.0
CE1 R:HIS153 3.7 41.0 1.0
C2D R:BCL2004 4.3 40.6 1.0
C2B R:BCL2004 4.3 38.5 1.0
C3B R:BCL2004 4.3 38.8 1.0
C3D R:BCL2004 4.3 40.4 1.0
C3A R:BCL2004 4.4 42.6 1.0
C2C R:BCL2004 4.4 39.9 1.0
C3C R:BCL2004 4.4 39.0 1.0
C2A R:BCL2004 4.4 42.6 1.0
CE2 S:TYR210 4.5 39.8 1.0
OBB R:BPH2006 4.6 61.6 1.0
CG R:HIS153 4.7 42.7 1.0
CBA R:BCL2004 4.7 46.8 1.0
ND1 R:HIS153 4.8 42.2 1.0
CBD R:BCL2004 4.9 42.5 1.0

Magnesium binding site 7 out of 8 in 1dv6

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Magnesium binding site 7 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2001

b:41.0
occ:1.00
MG S:BCL2001 0.0 41.0 1.0
NB S:BCL2001 2.1 42.1 1.0
ND S:BCL2001 2.1 42.0 1.0
NC S:BCL2001 2.1 42.2 1.0
NA S:BCL2001 2.1 42.4 1.0
NE2 S:HIS182 2.3 39.4 1.0
C4A S:BCL2001 3.1 42.1 1.0
C1C S:BCL2001 3.1 42.4 1.0
C4D S:BCL2001 3.1 42.5 1.0
C1D S:BCL2001 3.1 41.8 1.0
C1B S:BCL2001 3.1 42.7 1.0
C4B S:BCL2001 3.1 42.6 1.0
C4C S:BCL2001 3.1 41.8 1.0
CD2 S:HIS182 3.1 37.3 1.0
C1A S:BCL2001 3.2 42.1 1.0
CHC S:BCL2001 3.4 43.1 1.0
CHB S:BCL2001 3.4 42.3 1.0
CHD S:BCL2001 3.4 42.0 1.0
CE1 S:HIS182 3.5 37.8 1.0
CHA S:BCL2001 3.5 42.5 1.0
C2D S:BCL2001 4.2 42.3 1.0
C2B S:BCL2001 4.3 43.0 1.0
C3B S:BCL2001 4.3 43.7 1.0
C3D S:BCL2001 4.3 42.1 1.0
CG S:HIS182 4.4 37.1 1.0
C3A S:BCL2001 4.4 42.0 1.0
C2C S:BCL2001 4.4 41.9 1.0
C3C S:BCL2001 4.4 41.8 1.0
C2A S:BCL2001 4.5 42.6 1.0
ND1 S:HIS182 4.5 37.5 1.0
CBB S:BPH2005 4.7 41.3 1.0
CBD S:BCL2001 5.0 42.2 1.0
CE2 R:PHE181 5.0 38.2 1.0

Magnesium binding site 8 out of 8 in 1dv6

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Magnesium binding site 8 out of 8 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Charge-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+


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-Neutral Dqaqb State with the Proton Transfer Inhibitor ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg2003

b:42.1
occ:1.00
MG S:BCL2003 0.0 42.1 1.0
ND S:BCL2003 2.1 41.9 1.0
NC S:BCL2003 2.1 42.4 1.0
NB S:BCL2003 2.1 42.8 1.0
NA S:BCL2003 2.1 42.5 1.0
NE2 S:HIS202 2.3 41.1 1.0
C4D S:BCL2003 3.1 42.0 1.0
C1C S:BCL2003 3.1 42.5 1.0
C4C S:BCL2003 3.1 41.6 1.0
C1B S:BCL2003 3.1 43.2 1.0
C1D S:BCL2003 3.1 42.3 1.0
C4A S:BCL2003 3.1 42.8 1.0
C4B S:BCL2003 3.1 43.5 1.0
C1A S:BCL2003 3.1 42.2 1.0
CE1 S:HIS202 3.2 40.9 1.0
CBB R:BCL2002 3.4 41.1 1.0
CD2 S:HIS202 3.4 41.6 1.0
CHB S:BCL2003 3.4 43.0 1.0
CHD S:BCL2003 3.4 42.2 1.0
CHC S:BCL2003 3.4 42.5 1.0
CHA S:BCL2003 3.5 42.5 1.0
CAB R:BCL2002 3.6 43.2 1.0
OBB R:BCL2002 3.8 41.7 1.0
C2D S:BCL2003 4.3 42.2 1.0
C2B S:BCL2003 4.3 43.4 1.0
C3D S:BCL2003 4.3 42.0 1.0
C3B S:BCL2003 4.3 43.9 1.0
ND1 S:HIS202 4.4 41.1 1.0
C2C S:BCL2003 4.4 42.2 1.0
C3C S:BCL2003 4.4 41.3 1.0
C3B R:BCL2002 4.4 43.3 1.0
C2A S:BCL2003 4.4 43.6 1.0
CG S:HIS202 4.5 41.5 1.0
C3A S:BCL2003 4.5 43.4 1.0
CBD S:BCL2003 5.0 41.4 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: Mon Dec 14 05:50:56 2020

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