Magnesium in PDB 8vtk: Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine

Protein crystallography data

The structure of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine, PDB code: 8vtk was solved by K.Tran, I.Mathews, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.76 / 3.07
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.95, 140.95, 186.72, 90, 90, 120
R / Rfree (%) 17.7 / 21.3

Other elements in 8vtk:

The structure of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Iron (Fe) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine (pdb code 8vtk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine, PDB code: 8vtk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8vtk

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Magnesium binding site 1 out of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg303

b:46.0
occ:1.00
MG L:BCL303 0.0 46.0 1.0
NE2 L:HIS153 1.9 57.5 1.0
ND L:BCL303 2.0 43.8 1.0
NB L:BCL303 2.1 49.7 1.0
NC L:BCL303 2.2 49.5 1.0
NA L:BCL303 2.2 48.9 1.0
CE1 L:HIS153 2.9 54.7 1.0
CD2 L:HIS153 3.0 52.1 1.0
C4D L:BCL303 3.0 46.4 1.0
C1B L:BCL303 3.1 49.2 1.0
C4B L:BCL303 3.1 49.4 1.0
C1D L:BCL303 3.1 49.8 1.0
C1C L:BCL303 3.1 50.8 1.0
C4A L:BCL303 3.2 47.6 1.0
C4C L:BCL303 3.2 45.3 1.0
C1A L:BCL303 3.2 51.4 1.0
CHB L:BCL303 3.4 49.5 1.0
CHC L:BCL303 3.4 49.0 1.0
CHD L:BCL303 3.5 49.8 1.0
CHA L:BCL303 3.5 51.0 1.0
ND1 L:HIS153 4.0 56.8 1.0
CG L:HIS153 4.1 58.8 1.0
C3D L:BCL303 4.2 46.3 1.0
C2D L:BCL303 4.3 45.3 1.0
C2B L:BCL303 4.3 44.8 1.0
C3B L:BCL303 4.4 51.0 1.0
C3A L:BCL303 4.4 42.8 1.0
C2C L:BCL303 4.4 47.6 1.0
C3C L:BCL303 4.5 47.5 1.0
C2A L:BCL303 4.5 48.2 1.0
OBB L:BPH304 4.6 53.4 1.0
CD1 L:LEU154 4.7 51.8 1.0
CMA L:BCL303 4.9 44.6 1.0
CL M:2L5210 4.9 53.5 1.0
CBD L:BCL303 5.0 48.0 1.0

Magnesium binding site 2 out of 4 in 8vtk

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Magnesium binding site 2 out of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg306

b:47.3
occ:1.00
MG L:BCL306 0.0 47.3 1.0
NE2 L:HIS173 1.9 54.5 1.0
ND L:BCL306 2.0 47.0 1.0
NB L:BCL306 2.1 47.9 1.0
NC L:BCL306 2.1 49.6 1.0
NA L:BCL306 2.2 49.8 1.0
CE1 L:HIS173 2.7 48.3 1.0
C4D L:BCL306 3.0 54.5 1.0
CD2 L:HIS173 3.1 47.5 1.0
C1B L:BCL306 3.1 49.8 1.0
C4B L:BCL306 3.1 49.4 1.0
C4A L:BCL306 3.1 49.4 1.0
C1C L:BCL306 3.1 50.1 1.0
C1D L:BCL306 3.1 48.2 1.0
C4C L:BCL306 3.2 51.5 1.0
C1A L:BCL306 3.2 49.7 1.0
CHB L:BCL306 3.4 47.4 1.0
CHC L:BCL306 3.4 48.4 1.0
CHD L:BCL306 3.5 50.6 1.0
CHA L:BCL306 3.5 54.5 1.0
CBB M:BCL401 3.7 51.8 1.0
ND1 L:HIS173 3.9 48.8 1.0
CAB M:BCL401 3.9 58.3 1.0
OBB M:BCL401 4.0 61.7 1.0
CG L:HIS173 4.1 47.8 1.0
C3D L:BCL306 4.2 50.8 1.0
C2D L:BCL306 4.3 48.2 1.0
C2B L:BCL306 4.3 52.9 1.0
C3B L:BCL306 4.3 49.9 1.0
C3A L:BCL306 4.4 46.0 1.0
C2C L:BCL306 4.5 45.7 1.0
C3C L:BCL306 4.5 50.2 1.0
C2A L:BCL306 4.5 51.0 1.0
CD2 L:PHE167 4.6 48.9 1.0
C3B M:BCL401 4.7 52.6 1.0
CMA L:BCL306 4.8 43.0 1.0
CBD L:BCL306 5.0 55.8 1.0

Magnesium binding site 3 out of 4 in 8vtk

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Magnesium binding site 3 out of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg401

b:49.9
occ:1.00
MG M:BCL401 0.0 49.9 1.0
NE2 M:HIS202 1.9 51.9 1.0
ND M:BCL401 2.1 51.7 1.0
NB M:BCL401 2.1 50.3 1.0
NC M:BCL401 2.1 47.9 1.0
NA M:BCL401 2.2 43.9 1.0
CE1 M:HIS202 2.8 47.1 1.0
C4D M:BCL401 3.0 50.7 1.0
CD2 M:HIS202 3.0 48.2 1.0
C4B M:BCL401 3.1 48.8 1.0
C1B M:BCL401 3.1 48.8 1.0
C4A M:BCL401 3.1 46.7 1.0
C1C M:BCL401 3.1 54.7 1.0
C1D M:BCL401 3.2 46.0 1.0
C4C M:BCL401 3.2 47.8 1.0
C1A M:BCL401 3.2 48.1 1.0
CHC M:BCL401 3.4 52.0 1.0
CHB M:BCL401 3.4 45.2 1.0
CHA M:BCL401 3.5 46.9 1.0
CHD M:BCL401 3.5 49.0 1.0
CBB L:BCL306 3.6 47.6 1.0
ND1 M:HIS202 4.0 47.5 1.0
CAB L:BCL306 4.1 50.2 1.0
CG M:HIS202 4.1 45.9 1.0
C3D M:BCL401 4.2 49.9 1.0
C2B M:BCL401 4.3 47.8 1.0
C2D M:BCL401 4.3 47.5 1.0
C3B M:BCL401 4.3 52.6 1.0
C2C M:BCL401 4.4 46.5 1.0
OBB L:BCL306 4.4 51.0 1.0
C3A M:BCL401 4.5 47.2 1.0
C3C M:BCL401 4.5 45.8 1.0
C2A M:BCL401 4.5 46.3 1.0
C3B L:BCL306 4.7 49.9 1.0
CMC M:BCL401 4.8 46.8 1.0
CD1 M:LEU196 4.9 47.8 1.0
CD1 M:ILE206 4.9 49.7 1.0
CBD M:BCL401 4.9 46.7 1.0

Magnesium binding site 4 out of 4 in 8vtk

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Magnesium binding site 4 out of 4 in the Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg406

b:46.8
occ:1.00
MG M:BCL406 0.0 46.8 1.0
NE2 M:HIS182 1.9 56.3 1.0
ND M:BCL406 2.0 45.9 1.0
NB M:BCL406 2.1 50.5 1.0
NC M:BCL406 2.1 52.3 1.0
NA M:BCL406 2.2 47.9 1.0
CE1 M:HIS182 2.9 50.4 1.0
CD2 M:HIS182 3.0 52.5 1.0
C4D M:BCL406 3.0 50.6 1.0
C1B M:BCL406 3.1 49.6 1.0
C4B M:BCL406 3.1 49.4 1.0
C1C M:BCL406 3.1 52.0 1.0
C4A M:BCL406 3.1 47.1 1.0
C1D M:BCL406 3.2 47.0 1.0
C4C M:BCL406 3.2 53.2 1.0
C1A M:BCL406 3.2 51.8 1.0
CHC M:BCL406 3.4 48.7 1.0
CHB M:BCL406 3.4 44.8 1.0
CHA M:BCL406 3.5 54.2 1.0
CHD M:BCL406 3.5 51.0 1.0
ND1 M:HIS182 4.0 50.9 1.0
CG M:HIS182 4.1 54.3 1.0
C3D M:BCL406 4.2 51.1 1.0
C2B M:BCL406 4.3 49.4 1.0
C2D M:BCL406 4.3 50.2 1.0
C3B M:BCL406 4.4 52.9 1.0
C2C M:BCL406 4.4 48.7 1.0
C3A M:BCL406 4.5 44.8 1.0
C3C M:BCL406 4.5 50.8 1.0
C2A M:BCL406 4.5 49.5 1.0
C18 M:SPO404 4.9 49.7 1.0
CBD M:BCL406 5.0 54.0 1.0

Reference:

K.Tran, I.Mathews, S.G.Boxer. Crystal Structure of R.Sphaeroides Photosynthetic Reaction Center Variant Y(M210)2-Chlorophenylalanine To Be Published.
Page generated: Fri Oct 4 22:14:49 2024

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