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Magnesium in PDB 2j8c: X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State

Protein crystallography data

The structure of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State, PDB code: 2j8c was solved by J.Koepke, R.Diehm, G.Fritzsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 119.52 / 1.87
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 138.690, 138.690, 184.613, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 19.6

Other elements in 2j8c:

The structure of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State also contains other interesting chemical elements:

Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State (pdb code 2j8c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State, PDB code: 2j8c:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2j8c

Go back to Magnesium Binding Sites List in 2j8c
Magnesium binding site 1 out of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1282

b:17.1
occ:1.00
MG L:BCL1282 0.0 17.1 1.0
ND L:BCL1282 2.0 16.8 1.0
NC L:BCL1282 2.1 15.2 1.0
NB L:BCL1282 2.1 17.6 1.0
NE2 L:HIS153 2.1 17.6 1.0
NA L:BCL1282 2.1 17.9 1.0
C4D L:BCL1282 2.9 16.8 1.0
CD2 L:HIS153 3.0 17.8 1.0
C4A L:BCL1282 3.0 17.6 1.0
C1C L:BCL1282 3.1 14.2 1.0
C4C L:BCL1282 3.1 14.9 1.0
C4B L:BCL1282 3.1 16.1 1.0
C1B L:BCL1282 3.1 17.0 1.0
CE1 L:HIS153 3.1 17.7 1.0
C1D L:BCL1282 3.1 17.1 1.0
C1A L:BCL1282 3.1 15.7 1.0
CHB L:BCL1282 3.4 16.6 1.0
CHA L:BCL1282 3.4 16.6 1.0
CHC L:BCL1282 3.4 14.2 1.0
CHD L:BCL1282 3.5 15.7 1.0
C3D L:BCL1282 4.1 16.9 1.0
CG L:HIS153 4.2 17.7 1.0
ND1 L:HIS153 4.2 19.2 1.0
C2D L:BCL1282 4.2 17.0 1.0
C2B L:BCL1282 4.3 16.8 1.0
C3B L:BCL1282 4.3 17.7 1.0
C3A L:BCL1282 4.4 18.3 1.0
C2C L:BCL1282 4.4 16.4 1.0
C3C L:BCL1282 4.4 15.7 1.0
OBB L:BPH1286 4.4 24.1 1.0
C2A L:BCL1282 4.4 16.8 1.0
CE2 M:TYR210 4.7 16.6 1.0
CD1 L:LEU154 4.8 23.8 1.0
CBA L:BCL1282 4.8 16.1 1.0
CBC L:BCL1282 4.8 15.8 1.0
C20 L:BPH1286 4.9 19.7 1.0
CBD L:BCL1282 4.9 18.5 1.0
CMA L:BCL1282 5.0 18.2 1.0

Magnesium binding site 2 out of 4 in 2j8c

Go back to Magnesium Binding Sites List in 2j8c
Magnesium binding site 2 out of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg1288

b:17.2
occ:1.00
MG L:BCL1288 0.0 17.2 1.0
NB L:BCL1288 2.0 16.2 1.0
ND L:BCL1288 2.0 16.5 1.0
NC L:BCL1288 2.1 17.3 1.0
NA L:BCL1288 2.1 16.3 1.0
NE2 L:HIS173 2.3 16.1 1.0
C4D L:BCL1288 3.0 16.2 1.0
C4C L:BCL1288 3.0 19.0 1.0
C1C L:BCL1288 3.0 17.2 1.0
C4A L:BCL1288 3.0 16.0 1.0
C1B L:BCL1288 3.1 16.3 1.0
C4B L:BCL1288 3.1 16.4 1.0
C1D L:BCL1288 3.1 16.7 1.0
CE1 L:HIS173 3.1 14.7 1.0
C1A L:BCL1288 3.2 15.4 1.0
CD2 L:HIS173 3.3 13.6 1.0
CHB L:BCL1288 3.4 15.4 1.0
CHC L:BCL1288 3.4 16.5 1.0
CHD L:BCL1288 3.4 16.4 1.0
CHA L:BCL1288 3.5 16.6 1.0
OBB M:BCL1304 3.6 22.6 1.0
CAB M:BCL1304 3.7 18.3 1.0
CBB M:BCL1304 3.9 12.4 1.0
C3D L:BCL1288 4.2 16.2 1.0
C2B L:BCL1288 4.2 16.6 1.0
C3B L:BCL1288 4.3 16.5 1.0
C2D L:BCL1288 4.3 16.6 1.0
ND1 L:HIS173 4.3 16.4 1.0
C3A L:BCL1288 4.4 15.6 1.0
C3C L:BCL1288 4.4 16.7 1.0
C2C L:BCL1288 4.4 17.7 1.0
CG L:HIS173 4.4 15.8 1.0
C3B M:BCL1304 4.4 15.0 1.0
C2A L:BCL1288 4.5 16.0 1.0
CD1 L:PHE167 4.7 18.6 1.0
CMA L:BCL1288 4.9 16.9 1.0
CBD L:BCL1288 4.9 16.0 1.0

Magnesium binding site 3 out of 4 in 2j8c

Go back to Magnesium Binding Sites List in 2j8c
Magnesium binding site 3 out of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1303

b:19.8
occ:1.00
MG M:BCL1303 0.0 19.8 1.0
ND M:BCL1303 2.0 17.3 1.0
NC M:BCL1303 2.1 19.6 1.0
NE2 M:HIS182 2.1 18.9 1.0
NB M:BCL1303 2.1 19.9 1.0
NA M:BCL1303 2.1 20.1 1.0
C4D M:BCL1303 3.0 16.1 1.0
CD2 M:HIS182 3.0 21.1 1.0
C4C M:BCL1303 3.0 19.0 1.0
C1C M:BCL1303 3.1 17.0 1.0
C4A M:BCL1303 3.1 21.2 1.0
C1D M:BCL1303 3.1 17.4 1.0
C1B M:BCL1303 3.1 19.2 1.0
C4B M:BCL1303 3.1 19.5 1.0
CE1 M:HIS182 3.1 20.1 1.0
C1A M:BCL1303 3.2 19.4 1.0
CHC M:BCL1303 3.4 18.1 1.0
CHD M:BCL1303 3.4 17.1 1.0
CHB M:BCL1303 3.4 19.8 1.0
CHA M:BCL1303 3.5 17.8 1.0
C3D M:BCL1303 4.1 17.5 1.0
C2D M:BCL1303 4.2 16.7 1.0
ND1 M:HIS182 4.2 20.9 1.0
CG M:HIS182 4.2 20.8 1.0
C2B M:BCL1303 4.3 21.3 1.0
C3B M:BCL1303 4.3 21.7 1.0
C3C M:BCL1303 4.4 20.2 1.0
C2C M:BCL1303 4.4 19.9 1.0
C3A M:BCL1303 4.4 19.7 1.0
C2A M:BCL1303 4.5 21.9 1.0
OBB M:BPH1308 4.5 29.0 1.0
CE2 L:PHE181 4.8 17.5 1.0
CBA M:BCL1303 4.9 25.2 1.0
CBD M:BCL1303 4.9 19.9 1.0

Magnesium binding site 4 out of 4 in 2j8c

Go back to Magnesium Binding Sites List in 2j8c
Magnesium binding site 4 out of 4 in the X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray High Resolution Structure of the Photosynthetic Reaction Center From Rb. Sphaeroides at pH 8 in the Neutral State within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg1304

b:17.6
occ:1.00
MG M:BCL1304 0.0 17.6 1.0
ND M:BCL1304 2.0 18.3 1.0
NB M:BCL1304 2.1 16.3 1.0
NE2 M:HIS202 2.1 16.1 1.0
NC M:BCL1304 2.1 16.1 1.0
NA M:BCL1304 2.1 15.3 1.0
C4D M:BCL1304 3.0 19.5 1.0
CE1 M:HIS202 3.0 14.6 1.0
C1C M:BCL1304 3.0 15.2 1.0
C4A M:BCL1304 3.1 14.7 1.0
C4C M:BCL1304 3.1 16.2 1.0
C4B M:BCL1304 3.1 16.1 1.0
C1B M:BCL1304 3.1 14.5 1.0
CD2 M:HIS202 3.1 16.1 1.0
C1D M:BCL1304 3.1 19.2 1.0
C1A M:BCL1304 3.2 17.4 1.0
CHC M:BCL1304 3.4 15.6 1.0
CHB M:BCL1304 3.4 15.6 1.0
CHA M:BCL1304 3.5 18.4 1.0
CHD M:BCL1304 3.5 18.0 1.0
CBB L:BCL1288 3.6 17.4 1.0
CAB L:BCL1288 3.8 18.5 1.0
OBB L:BCL1288 4.0 20.7 1.0
ND1 M:HIS202 4.1 16.3 1.0
C3D M:BCL1304 4.2 19.6 1.0
CG M:HIS202 4.2 16.5 1.0
C2D M:BCL1304 4.3 19.3 1.0
C2B M:BCL1304 4.3 16.1 1.0
C3B M:BCL1304 4.3 15.0 1.0
C2C M:BCL1304 4.3 17.6 1.0
C3C M:BCL1304 4.4 16.7 1.0
C3A M:BCL1304 4.4 15.5 1.0
C2A M:BCL1304 4.5 16.9 1.0
C3B L:BCL1288 4.5 16.5 1.0
CMC M:BCL1304 4.9 18.9 1.0
CBD M:BCL1304 4.9 19.2 1.0

Reference:

J.Koepke, E.M.Krammer, A.R.Klingen, P.Sebban, G.M.Ullmann, G.Fritzsch. pH Modulates the Quinone Position in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides in the Neutral and Charge Separated States. J.Mol.Biol. V. 371 396 2007.
ISSN: ISSN 0022-2836
PubMed: 17570397
DOI: 10.1016/J.JMB.2007.04.082
Page generated: Wed Aug 14 00:39:54 2024

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