Magnesium in PDB 3v3z: I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides

The structure of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 3v3z 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)	28.90 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	140.130, 140.130, 186.030, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 25.1

The structure of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides also contains other interesting chemical elements:

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

The binding sites of Magnesium atom in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides (pdb code 3v3z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides, PDB code: 3v3z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg301 b:67.9 occ:1.00 MG L:BCL301 0.0 67.9 1.0 ND L:BCL301 1.9 69.0 1.0 NB L:BCL301 2.0 67.7 1.0 NA L:BCL301 2.0 69.2 1.0 NC L:BCL301 2.0 66.3 1.0 NE2 M:HIS182 2.4 63.0 1.0 C4A L:BCL301 2.9 69.4 1.0 C4D L:BCL301 3.0 70.0 1.0 C4C L:BCL301 3.0 66.1 1.0 C1C L:BCL301 3.0 64.9 1.0 C1B L:BCL301 3.0 67.9 1.0 C1D L:BCL301 3.0 68.9 1.0 C4B L:BCL301 3.0 66.4 1.0 C1A L:BCL301 3.1 70.9 1.0 CE1 M:HIS182 3.3 63.2 1.0 CHB L:BCL301 3.3 68.3 1.0 CHC L:BCL301 3.4 64.8 1.0 CD2 M:HIS182 3.4 63.4 1.0 CHD L:BCL301 3.4 67.3 1.0 CHA L:BCL301 3.5 70.6 1.0 C3D L:BCL301 4.2 70.6 1.0 C2D L:BCL301 4.2 70.0 1.0 C2B L:BCL301 4.2 67.8 1.0 C3B L:BCL301 4.2 67.6 1.0 C3A L:BCL301 4.3 71.0 1.0 C3C L:BCL301 4.3 63.9 1.0 C2C L:BCL301 4.3 63.7 1.0 C2A L:BCL301 4.4 72.8 1.0 ND1 M:HIS182 4.4 64.1 1.0 CG M:HIS182 4.5 64.5 1.0 CMA L:BCL301 4.8 71.3 1.0 CM5 M:SPN600 4.9 67.1 1.0 CBD L:BCL301 4.9 71.5 1.0 OBB M:BPH401 5.0 76.2 1.0

Magnesium binding site 2 out of 4 in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg302 b:63.8 occ:1.00 MG L:BCL302 0.0 63.8 1.0 ND L:BCL302 1.9 64.8 1.0 NB L:BCL302 2.0 63.9 1.0 NA L:BCL302 2.0 63.4 1.0 NC L:BCL302 2.0 63.7 1.0 NE2 L:HIS173 2.4 49.8 1.0 C4A L:BCL302 3.0 63.1 1.0 C1C L:BCL302 3.0 63.2 1.0 C4D L:BCL302 3.0 64.7 1.0 C4C L:BCL302 3.0 62.1 1.0 C4B L:BCL302 3.0 64.0 1.0 C1B L:BCL302 3.0 64.0 1.0 C1D L:BCL302 3.1 64.2 1.0 C1A L:BCL302 3.1 63.2 1.0 CD2 L:HIS173 3.1 50.6 1.0 CHC L:BCL302 3.3 63.8 1.0 CBB M:BCL303 3.3 63.9 1.0 CHB L:BCL302 3.4 63.5 1.0 CHD L:BCL302 3.4 62.7 1.0 CHA L:BCL302 3.5 64.0 1.0 CE1 L:HIS173 3.5 49.4 1.0 CAB M:BCL303 4.1 63.5 1.0 C2B L:BCL302 4.2 64.1 1.0 C2D L:BCL302 4.2 64.8 1.0 C3B L:BCL302 4.2 64.2 1.0 C3D L:BCL302 4.2 64.9 1.0 C3A L:BCL302 4.3 62.4 1.0 C2C L:BCL302 4.3 61.2 1.0 CG L:HIS173 4.3 52.5 1.0 C3C L:BCL302 4.4 60.6 1.0 C2A L:BCL302 4.4 62.2 1.0 CD2 L:PHE167 4.5 57.9 1.0 ND1 L:HIS173 4.5 50.8 1.0 OBB M:BCL303 4.7 63.9 1.0 C3B M:BCL303 4.8 62.1 1.0 CMA L:BCL302 4.8 61.4 1.0 CBD L:BCL302 5.0 64.2 1.0

Magnesium binding site 3 out of 4 in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg304 b:39.0 occ:1.00 MG L:BCL304 0.0 39.0 1.0 ND L:BCL304 2.0 37.7 1.0 NB L:BCL304 2.0 38.0 1.0 NC L:BCL304 2.0 38.1 1.0 NA L:BCL304 2.0 39.4 1.0 NE2 L:HIS153 2.3 68.6 1.0 C4A L:BCL304 2.9 39.6 1.0 C4D L:BCL304 3.0 38.2 1.0 C1C L:BCL304 3.0 39.6 1.0 C4C L:BCL304 3.0 38.2 1.0 C1B L:BCL304 3.0 38.9 1.0 C4B L:BCL304 3.0 39.1 1.0 C1D L:BCL304 3.1 37.8 1.0 C1A L:BCL304 3.1 40.4 1.0 CE1 L:HIS153 3.3 68.6 1.0 CD2 L:HIS153 3.3 67.7 1.0 CHB L:BCL304 3.3 38.1 1.0 CHC L:BCL304 3.4 38.4 1.0 CHD L:BCL304 3.4 37.7 1.0 CHA L:BCL304 3.5 40.2 1.0 C3D L:BCL304 4.2 38.3 1.0 C2B L:BCL304 4.2 39.8 1.0 C2D L:BCL304 4.2 37.8 1.0 C3B L:BCL304 4.2 40.4 1.0 C3A L:BCL304 4.3 41.4 1.0 C2C L:BCL304 4.3 39.9 1.0 C3C L:BCL304 4.3 39.4 1.0 C2A L:BCL304 4.4 41.5 1.0 ND1 L:HIS153 4.4 69.2 1.0 CG L:HIS153 4.5 68.6 1.0 OBB L:BPH402 4.6 61.8 1.0 C19 L:BPH402 4.6 54.2 1.0 CD2 L:LEU154 4.7 65.5 1.0 CE2 M:TYR210 4.8 57.7 1.0 CBA L:BCL304 4.8 47.7 1.0 CBD L:BCL304 4.9 43.4 1.0 CMA L:BCL304 5.0 42.9 1.0

Magnesium binding site 4 out of 4 in the I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of I(L177)H Mutant Structure of Photosynthetic Reaction Center From Rhodobacter Sphaeroides within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg303 b:60.6 occ:1.00 MG M:BCL303 0.0 60.6 1.0 ND M:BCL303 1.9 60.5 1.0 NB M:BCL303 2.0 60.7 1.0 NA M:BCL303 2.0 60.9 1.0 NC M:BCL303 2.0 61.1 1.0 NE2 M:HIS202 2.2 55.5 1.0 C4D M:BCL303 3.0 60.2 1.0 C1C M:BCL303 3.0 60.2 1.0 C4B M:BCL303 3.0 61.2 1.0 C4A M:BCL303 3.0 59.8 1.0 C1B M:BCL303 3.0 59.9 1.0 C4C M:BCL303 3.0 60.0 1.0 C1A M:BCL303 3.1 60.1 1.0 C1D M:BCL303 3.1 60.9 1.0 CE1 M:HIS202 3.1 56.1 1.0 CD2 M:HIS202 3.3 56.4 1.0 CHC M:BCL303 3.3 60.5 1.0 CHB M:BCL303 3.4 59.2 1.0 CHA M:BCL303 3.4 60.0 1.0 CHD M:BCL303 3.5 60.7 1.0 OBB L:BCL302 3.8 63.9 1.0 CAB L:BCL302 4.0 64.6 1.0 CBB L:BCL302 4.0 64.2 1.0 C3B M:BCL303 4.2 62.1 1.0 C2B M:BCL303 4.2 60.5 1.0 C3D M:BCL303 4.2 60.6 1.0 C2D M:BCL303 4.2 61.0 1.0 C2C M:BCL303 4.2 58.2 1.0 ND1 M:HIS202 4.3 56.6 1.0 C3A M:BCL303 4.3 59.8 1.0 C3C M:BCL303 4.3 58.1 1.0 C2A M:BCL303 4.4 60.0 1.0 CG M:HIS202 4.4 56.7 1.0 C3B L:BCL302 4.8 64.2 1.0 CMC M:BCL303 4.8 57.4 1.0 CBD M:BCL303 4.9 60.2 1.0

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