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Magnesium in PDB 3v3y: Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv

Protein crystallography data

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv, PDB code: 3v3y was solved by A.G.Gabdulkhakov, T.Y.Fufina, L.G.Vasilieva, V.A.Shuvalov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.750, 139.750, 185.604, 90.00, 90.00, 120.00
R / Rfree (%) 24.4 / 28.4

Other elements in 3v3y:

The structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv (pdb code 3v3y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv, PDB code: 3v3y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3v3y

Go back to Magnesium Binding Sites List in 3v3y
Magnesium binding site 1 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv


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 Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg302

b:32.7
occ:1.00
MG L:BCL302 0.0 32.7 1.0
ND L:BCL302 1.9 29.4 1.0
NB L:BCL302 2.0 30.8 1.0
NA L:BCL302 2.0 33.8 1.0
NC L:BCL302 2.0 27.6 1.0
NE2 L:HIS173 2.5 24.8 1.0
C4D L:BCL302 3.0 29.4 1.0
C1C L:BCL302 3.0 31.0 1.0
C4A L:BCL302 3.0 28.3 1.0
C4C L:BCL302 3.0 25.2 1.0
C4B L:BCL302 3.0 29.6 1.0
C1A L:BCL302 3.0 33.6 1.0
C1B L:BCL302 3.1 28.4 1.0
C1D L:BCL302 3.1 27.6 1.0
CD2 L:HIS173 3.3 26.4 1.0
CHC L:BCL302 3.3 29.5 1.0
CBB M:BCL304 3.3 29.6 1.0
CHB L:BCL302 3.4 25.4 1.0
CHD L:BCL302 3.4 27.9 1.0
CHA L:BCL302 3.4 30.8 1.0
CE1 L:HIS173 3.6 26.0 1.0
CAB M:BCL304 3.8 33.5 1.0
OBB M:BCL304 4.2 36.5 1.0
C3D L:BCL302 4.2 31.5 1.0
C2D L:BCL302 4.2 29.7 1.0
C2B L:BCL302 4.2 25.6 1.0
C3B L:BCL302 4.3 28.0 1.0
C3A L:BCL302 4.3 27.5 1.0
C2C L:BCL302 4.3 23.2 1.0
C3C L:BCL302 4.3 22.2 1.0
C2A L:BCL302 4.4 34.3 1.0
CD2 L:PHE167 4.5 29.3 1.0
CG L:HIS173 4.5 27.4 1.0
C3B M:BCL304 4.6 29.5 1.0
ND1 L:HIS173 4.6 29.7 1.0
CMA L:BCL302 4.8 27.0 1.0
CBD L:BCL302 4.9 34.8 1.0
CE2 L:PHE167 5.0 28.9 1.0

Magnesium binding site 2 out of 4 in 3v3y

Go back to Magnesium Binding Sites List in 3v3y
Magnesium binding site 2 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv


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 Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg303

b:27.1
occ:1.00
MG M:BCL303 0.0 27.1 1.0
ND M:BCL303 1.9 22.2 1.0
NB M:BCL303 2.0 33.9 1.0
NA M:BCL303 2.0 22.8 1.0
NC M:BCL303 2.0 24.4 1.0
NE2 M:HIS182 2.6 29.0 1.0
C4A M:BCL303 2.9 21.2 1.0
C4D M:BCL303 2.9 23.8 1.0
C4C M:BCL303 3.0 28.1 1.0
C1C M:BCL303 3.0 28.9 1.0
C1A M:BCL303 3.0 27.8 1.0
C1B M:BCL303 3.0 28.6 1.0
C4B M:BCL303 3.0 28.5 1.0
C1D M:BCL303 3.0 28.0 1.0
CHB M:BCL303 3.3 23.4 1.0
CHC M:BCL303 3.3 26.9 1.0
CHA M:BCL303 3.4 27.8 1.0
CE1 M:HIS182 3.4 29.3 1.0
CHD M:BCL303 3.4 29.1 1.0
CD2 M:HIS182 3.6 35.8 1.0
C3D M:BCL303 4.2 27.3 1.0
C3A M:BCL303 4.2 26.3 1.0
C2D M:BCL303 4.2 31.1 1.0
C2B M:BCL303 4.2 26.9 1.0
C3B M:BCL303 4.2 27.9 1.0
C3C M:BCL303 4.2 23.6 1.0
C2C M:BCL303 4.3 26.8 1.0
C2A M:BCL303 4.3 31.4 1.0
CMA M:BCL303 4.5 27.2 1.0
ND1 M:HIS182 4.5 38.7 1.0
CG M:HIS182 4.7 35.8 1.0
CBD M:BCL303 4.8 31.1 1.0
CBA M:BCL303 4.8 24.8 1.0
CE2 L:PHE181 4.8 26.8 1.0
CM5 M:SPN600 4.9 30.0 1.0

Magnesium binding site 3 out of 4 in 3v3y

Go back to Magnesium Binding Sites List in 3v3y
Magnesium binding site 3 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv


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 Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg304

b:38.5
occ:1.00
MG M:BCL304 0.0 38.5 1.0
ND M:BCL304 2.0 33.9 1.0
NB M:BCL304 2.0 38.7 1.0
NC M:BCL304 2.0 31.7 1.0
NA M:BCL304 2.0 28.0 1.0
NE2 M:HIS202 2.6 26.9 1.0
C4D M:BCL304 2.9 31.6 1.0
C1C M:BCL304 3.0 37.8 1.0
C4A M:BCL304 3.0 25.9 1.0
C4C M:BCL304 3.0 29.0 1.0
C1A M:BCL304 3.0 28.0 1.0
C1B M:BCL304 3.0 30.4 1.0
C4B M:BCL304 3.0 30.3 1.0
C1D M:BCL304 3.1 33.3 1.0
CHC M:BCL304 3.3 32.0 1.0
CBB L:BCL302 3.3 33.9 1.0
CD2 M:HIS202 3.4 29.9 1.0
CHB M:BCL304 3.4 27.1 1.0
CHA M:BCL304 3.4 33.6 1.0
CHD M:BCL304 3.5 31.4 1.0
CE1 M:HIS202 3.7 30.6 1.0
CAB L:BCL302 3.8 30.7 1.0
OBB L:BCL302 4.0 28.7 1.0
C3D M:BCL304 4.2 28.7 1.0
C2D M:BCL304 4.2 30.1 1.0
C2B M:BCL304 4.2 28.1 1.0
C3B M:BCL304 4.2 29.5 1.0
C2C M:BCL304 4.3 30.8 1.0
C3A M:BCL304 4.3 27.0 1.0
C2A M:BCL304 4.3 27.6 1.0
C3C M:BCL304 4.3 30.2 1.0
C3B L:BCL302 4.6 28.0 1.0
CG M:HIS202 4.6 27.1 1.0
ND1 M:HIS202 4.7 30.9 1.0
CBD M:BCL304 4.9 30.0 1.0
CMC M:BCL304 4.9 28.4 1.0

Magnesium binding site 4 out of 4 in 3v3y

Go back to Magnesium Binding Sites List in 3v3y
Magnesium binding site 4 out of 4 in the Photosynthetic Reaction Center From Rhodobacter Sphaeroides Strain Rv


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 Strain Rv within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg305

b:25.7
occ:1.00
MG M:BCL305 0.0 25.7 1.0
ND M:BCL305 2.0 25.6 1.0
NB M:BCL305 2.0 28.5 1.0
NA M:BCL305 2.0 24.8 1.0
NC M:BCL305 2.0 27.2 1.0
NE2 L:HIS153 2.6 31.4 1.0
C4A M:BCL305 2.9 21.9 1.0
C4D M:BCL305 2.9 25.3 1.0
C1C M:BCL305 3.0 26.4 1.0
C1B M:BCL305 3.0 26.8 1.0
C4C M:BCL305 3.0 25.6 1.0
C1A M:BCL305 3.0 27.4 1.0
C4B M:BCL305 3.1 26.0 1.0
C1D M:BCL305 3.1 25.8 1.0
CHB M:BCL305 3.3 24.6 1.0
CHC M:BCL305 3.4 21.1 1.0
CHA M:BCL305 3.4 28.4 1.0
CHD M:BCL305 3.5 24.3 1.0
CD2 L:HIS153 3.6 34.1 1.0
CE1 L:HIS153 3.6 35.2 1.0
C3D M:BCL305 4.2 25.4 1.0
C2D M:BCL305 4.2 27.3 1.0
C2B M:BCL305 4.2 21.2 1.0
C3A M:BCL305 4.2 22.4 1.0
C3B M:BCL305 4.2 24.1 1.0
C2C M:BCL305 4.3 23.8 1.0
C2A M:BCL305 4.3 22.5 1.0
C3C M:BCL305 4.3 22.6 1.0
CE2 M:TYR210 4.7 22.7 1.0
CD2 L:LEU154 4.7 29.8 1.0
ND1 L:HIS153 4.7 41.8 1.0
CG L:HIS153 4.8 37.8 1.0
OBB L:BPH402 4.8 29.4 1.0
CBA M:BCL305 4.8 25.2 1.0
CBD M:BCL305 4.9 31.2 1.0
CMA M:BCL305 4.9 22.3 1.0
CMC M:BCL305 5.0 24.3 1.0
CBC M:BCL305 5.0 25.1 1.0

Reference:

L.G.Vasilieva, T.Y.Fufina, A.G.Gabdulkhakov, M.M.Leonova, R.A.Khatypov, V.A.Shuvalov. The Site-Directed Mutation I(L177)H in Rhodobacter Sphaeroides Reaction Center Affects Coordination of P(A) and B(B) Bacteriochlorophylls. Biochim.Biophys.Acta V.1817 1407 2012.
ISSN: ISSN 0006-3002
PubMed: 22365928
DOI: 10.1016/J.BBABIO.2012.02.008
Page generated: Thu Aug 15 12:42:53 2024

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