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Magnesium in PDB 7mha: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant

Protein crystallography data

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant, PDB code: 7mha was solved by S.G.Boxer, I.I.Mathews, J.B.Weaver, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.19 / 2.79
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 142.193, 142.193, 187.673, 90, 90, 120
R / Rfree (%) 15.6 / 17.8

Other elements in 7mha:

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant (pdb code 7mha). 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; W252V Mutant, PDB code: 7mha:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mha

Go back to Magnesium Binding Sites List in 7mha
Magnesium binding site 1 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant


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; W252V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:36.6
occ:1.00
MG L:BCL301 0.0 36.6 1.0
NA L:BCL301 2.0 37.2 1.0
NC L:BCL301 2.0 35.8 1.0
ND L:BCL301 2.0 34.5 1.0
NB L:BCL301 2.0 34.6 1.0
NE2 L:HIS153 2.5 50.8 1.0
C4D L:BCL301 2.9 35.2 1.0
C1A L:BCL301 3.0 37.9 1.0
C4A L:BCL301 3.0 36.9 1.0
C1C L:BCL301 3.0 37.8 1.0
C4C L:BCL301 3.0 37.1 1.0
C1B L:BCL301 3.0 35.0 1.0
C4B L:BCL301 3.1 35.3 1.0
C1D L:BCL301 3.1 35.5 1.0
CD2 L:HIS153 3.3 52.4 1.0
CHB L:BCL301 3.4 35.2 1.0
CHA L:BCL301 3.4 37.0 1.0
CHC L:BCL301 3.4 36.7 1.0
CHD L:BCL301 3.5 35.5 1.0
CE1 L:HIS153 3.6 51.9 1.0
C3D L:BCL301 4.1 35.1 1.0
C3A L:BCL301 4.3 38.5 1.0
C2A L:BCL301 4.3 39.5 1.0
C3C L:BCL301 4.3 40.3 1.0
C2C L:BCL301 4.3 39.7 1.0
C2B L:BCL301 4.4 34.8 1.0
C3B L:BCL301 4.4 35.5 1.0
C2D L:BCL301 4.4 34.8 1.0
OBB L:BPH302 4.5 51.7 1.0
CG L:HIS153 4.6 52.8 1.0
ND1 L:HIS153 4.6 52.0 1.0
CE2 M:TYR210 4.7 44.0 1.0
CBC L:BCL301 4.7 43.1 1.0
CBA L:BCL301 4.9 47.8 1.0
CBD L:BCL301 4.9 40.8 1.0
CD1 L:LEU154 5.0 53.5 1.0

Magnesium binding site 2 out of 4 in 7mha

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Magnesium binding site 2 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant


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; W252V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg304

b:43.4
occ:1.00
MG L:BCL304 0.0 43.4 1.0
NA L:BCL304 2.0 42.4 1.0
NC L:BCL304 2.0 42.7 1.0
ND L:BCL304 2.0 42.4 1.0
NB L:BCL304 2.0 39.8 1.0
NE2 L:HIS173 2.3 42.5 1.0
C4D L:BCL304 2.9 43.2 1.0
C4A L:BCL304 3.0 41.1 1.0
C1A L:BCL304 3.0 43.3 1.0
C1C L:BCL304 3.0 43.4 1.0
C4C L:BCL304 3.0 41.4 1.0
C4B L:BCL304 3.1 40.5 1.0
C1B L:BCL304 3.1 38.6 1.0
C1D L:BCL304 3.2 41.0 1.0
CE1 L:HIS173 3.3 43.5 1.0
CD2 L:HIS173 3.4 42.8 1.0
CHC L:BCL304 3.4 42.1 1.0
CHB L:BCL304 3.4 38.4 1.0
CHA L:BCL304 3.4 42.2 1.0
CHD L:BCL304 3.5 40.8 1.0
OBB M:BCL402 3.6 52.4 1.0
CAB M:BCL402 3.7 47.7 1.0
CBB M:BCL402 3.8 48.4 1.0
C3D L:BCL304 4.2 42.2 1.0
C3A L:BCL304 4.3 41.9 1.0
C3C L:BCL304 4.4 41.5 1.0
C2A L:BCL304 4.4 43.1 1.0
C3B L:BCL304 4.4 39.3 1.0
C2C L:BCL304 4.4 41.2 1.0
C2D L:BCL304 4.4 43.3 1.0
C2B L:BCL304 4.4 39.0 1.0
ND1 L:HIS173 4.4 43.7 1.0
CG L:HIS173 4.5 43.8 1.0
C3B M:BCL402 4.5 45.9 1.0
CD2 L:PHE167 4.8 49.8 1.0
CBD L:BCL304 4.9 42.1 1.0
CMA L:BCL304 5.0 42.0 1.0

Magnesium binding site 3 out of 4 in 7mha

Go back to Magnesium Binding Sites List in 7mha
Magnesium binding site 3 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant


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; W252V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg401

b:47.3
occ:1.00
MG M:BCL401 0.0 47.3 1.0
NA M:BCL401 2.0 46.7 1.0
ND M:BCL401 2.0 45.3 1.0
NC M:BCL401 2.0 48.1 1.0
NB M:BCL401 2.0 47.6 1.0
NE2 M:HIS182 2.4 54.3 1.0
C4D M:BCL401 2.9 46.0 1.0
C1A M:BCL401 3.0 45.8 1.0
C4A M:BCL401 3.0 46.2 1.0
C4C M:BCL401 3.0 47.1 1.0
C1B M:BCL401 3.0 47.8 1.0
C1C M:BCL401 3.0 46.1 1.0
C4B M:BCL401 3.1 47.9 1.0
C1D M:BCL401 3.2 45.4 1.0
CD2 M:HIS182 3.2 55.8 1.0
CHB M:BCL401 3.4 45.5 1.0
CHA M:BCL401 3.4 46.0 1.0
CHC M:BCL401 3.4 47.6 1.0
CE1 M:HIS182 3.5 55.8 1.0
CHD M:BCL401 3.6 46.4 1.0
C3D M:BCL401 4.2 45.4 1.0
C3A M:BCL401 4.3 45.5 1.0
C2A M:BCL401 4.3 47.4 1.0
C3B M:BCL401 4.4 49.0 1.0
C2B M:BCL401 4.4 49.5 1.0
C3C M:BCL401 4.4 46.1 1.0
C2C M:BCL401 4.4 44.8 1.0
C2D M:BCL401 4.4 45.1 1.0
CG M:HIS182 4.5 55.3 1.0
ND1 M:HIS182 4.6 55.5 1.0
CE2 L:PHE181 4.8 44.9 1.0
OBB L:BPH305 4.8 62.2 1.0
CBD M:BCL401 4.9 47.7 1.0
CBA M:BCL401 5.0 54.6 1.0

Magnesium binding site 4 out of 4 in 7mha

Go back to Magnesium Binding Sites List in 7mha
Magnesium binding site 4 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; W252V Mutant


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; W252V Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg402

b:44.0
occ:1.00
MG M:BCL402 0.0 44.0 1.0
NC M:BCL402 2.0 47.1 1.0
NA M:BCL402 2.0 45.6 1.0
ND M:BCL402 2.0 41.1 1.0
NB M:BCL402 2.0 42.9 1.0
NE2 M:HIS202 2.4 40.8 1.0
C4D M:BCL402 2.9 42.1 1.0
C4A M:BCL402 3.0 43.3 1.0
C1A M:BCL402 3.0 43.2 1.0
C1C M:BCL402 3.0 46.8 1.0
C4C M:BCL402 3.0 45.4 1.0
C1B M:BCL402 3.0 42.5 1.0
C4B M:BCL402 3.1 44.4 1.0
C1D M:BCL402 3.2 42.2 1.0
CHB M:BCL402 3.4 41.4 1.0
CHA M:BCL402 3.4 41.4 1.0
CD2 M:HIS202 3.4 42.3 1.0
CHC M:BCL402 3.4 44.6 1.0
CE1 M:HIS202 3.5 41.7 1.0
CBB L:BCL304 3.5 44.3 1.0
CHD M:BCL402 3.6 43.5 1.0
CAB L:BCL304 3.7 41.5 1.0
OBB L:BCL304 4.0 40.8 1.0
C3D M:BCL402 4.2 41.8 1.0
C3A M:BCL402 4.3 43.2 1.0
C2C M:BCL402 4.3 47.4 1.0
C2A M:BCL402 4.3 43.3 1.0
C3C M:BCL402 4.3 45.7 1.0
C2B M:BCL402 4.4 44.0 1.0
C3B M:BCL402 4.4 45.9 1.0
C2D M:BCL402 4.4 41.1 1.0
C3B L:BCL304 4.5 39.3 1.0
CG M:HIS202 4.6 43.2 1.0
ND1 M:HIS202 4.6 41.9 1.0
CBD M:BCL402 4.8 43.4 1.0

Reference:

J.B.Weaver, C.Y.Lin, K.M.Faries, I.I.Mathews, S.Russi, D.Holten, C.Kirmaier, S.G.Boxer. Photosynthetic Reaction Center Variants Made Via Genetic Code Expansion Indicate Tyrosine at M210 Tunes the Mechanism For Primary Electron Transfer Thesis pH.D. Stanford 294 2022UNIVERSITY.
Page generated: Thu Aug 14 10:17:51 2025

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