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Magnesium in PDB 7mh4: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine

Protein crystallography data

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine, PDB code: 7mh4 was solved by I.Mathews, J.Weaver, S.G.Boxer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 2.48
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.337, 141.337, 186.87, 90, 90, 120
R / Rfree (%) 16.8 / 19.3

Other elements in 7mh4:

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Bromine (Br) 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)3-Bromotyrosine (pdb code 7mh4). 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)3-Bromotyrosine, PDB code: 7mh4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mh4

Go back to Magnesium Binding Sites List in 7mh4
Magnesium binding site 1 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine


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)3-Bromotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg301

b:37.6
occ:1.00
MG L:BCL301 0.0 37.6 1.0
NC L:BCL301 2.0 37.5 1.0
NA L:BCL301 2.0 37.1 1.0
ND L:BCL301 2.0 35.9 1.0
NB L:BCL301 2.0 36.9 1.0
NE2 L:HIS153 2.4 45.0 1.0
C4D L:BCL301 2.9 36.2 1.0
C1A L:BCL301 3.0 37.7 1.0
C4A L:BCL301 3.0 35.5 1.0
C1C L:BCL301 3.0 38.3 1.0
C4C L:BCL301 3.0 36.5 1.0
C1B L:BCL301 3.1 35.9 1.0
C4B L:BCL301 3.1 38.2 1.0
C1D L:BCL301 3.2 36.8 1.0
CD2 L:HIS153 3.3 45.5 1.0
BR2 M:DBY210 3.3 32.6 0.5
CHC L:BCL301 3.4 38.6 1.0
CHB L:BCL301 3.4 35.6 1.0
CHA L:BCL301 3.4 38.1 1.0
CE1 L:HIS153 3.5 46.4 1.0
CHD L:BCL301 3.5 35.7 1.0
C3D L:BCL301 4.2 34.8 1.0
C2A L:BCL301 4.3 39.0 1.0
C3A L:BCL301 4.3 36.9 1.0
C3C L:BCL301 4.3 38.1 1.0
C2C L:BCL301 4.3 38.8 1.0
C3B L:BCL301 4.4 36.4 1.0
C2B L:BCL301 4.4 35.1 1.0
C2D L:BCL301 4.4 34.7 1.0
CG L:HIS153 4.5 46.2 1.0
ND1 L:HIS153 4.5 45.3 1.0
CBC L:BCL301 4.8 38.4 1.0
CBA L:BCL301 4.8 42.1 1.0
OBB L:BPH302 4.8 46.6 1.0
CBD L:BCL301 4.9 39.1 1.0
CD1 L:LEU154 4.9 47.1 1.0

Magnesium binding site 2 out of 4 in 7mh4

Go back to Magnesium Binding Sites List in 7mh4
Magnesium binding site 2 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine


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)3-Bromotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg304

b:37.5
occ:1.00
MG L:BCL304 0.0 37.5 1.0
NC L:BCL304 2.0 38.7 1.0
ND L:BCL304 2.0 38.6 1.0
NA L:BCL304 2.0 38.7 1.0
NB L:BCL304 2.1 37.5 1.0
NE2 L:HIS173 2.3 34.7 1.0
C4D L:BCL304 2.9 39.4 1.0
C4A L:BCL304 3.0 35.0 1.0
C4C L:BCL304 3.0 36.1 1.0
C1A L:BCL304 3.0 38.2 1.0
C1C L:BCL304 3.0 37.9 1.0
C4B L:BCL304 3.1 38.0 1.0
C1B L:BCL304 3.1 35.4 1.0
C1D L:BCL304 3.1 37.1 1.0
CE1 L:HIS173 3.2 34.6 1.0
CD2 L:HIS173 3.3 35.4 1.0
CHB L:BCL304 3.4 35.5 1.0
CHC L:BCL304 3.4 38.2 1.0
CHA L:BCL304 3.4 37.5 1.0
CHD L:BCL304 3.5 36.2 1.0
OBB M:BCL402 3.6 48.7 1.0
CAB M:BCL402 3.8 42.4 1.0
CBB M:BCL402 4.0 41.2 1.0
C3D L:BCL304 4.2 37.5 1.0
C3A L:BCL304 4.3 37.2 1.0
C3C L:BCL304 4.3 36.5 1.0
C2A L:BCL304 4.4 39.5 1.0
C2C L:BCL304 4.4 36.4 1.0
C3B L:BCL304 4.4 36.9 1.0
ND1 L:HIS173 4.4 33.8 1.0
C2D L:BCL304 4.4 38.4 1.0
C2B L:BCL304 4.4 36.2 1.0
CG L:HIS173 4.4 34.6 1.0
C3B M:BCL402 4.5 38.5 1.0
CD2 L:PHE167 4.7 39.4 1.0
CMA L:BCL304 4.9 37.4 1.0
CBD L:BCL304 4.9 38.2 1.0

Magnesium binding site 3 out of 4 in 7mh4

Go back to Magnesium Binding Sites List in 7mh4
Magnesium binding site 3 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine


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)3-Bromotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg401

b:36.6
occ:1.00
MG M:BCL401 0.0 36.6 1.0
NA M:BCL401 2.0 36.7 1.0
NC M:BCL401 2.0 37.4 1.0
ND M:BCL401 2.0 36.0 1.0
NB M:BCL401 2.0 37.7 1.0
NE2 M:HIS182 2.4 46.3 1.0
C4D M:BCL401 2.9 35.8 1.0
C1A M:BCL401 3.0 37.4 1.0
C4A M:BCL401 3.0 37.9 1.0
C1C M:BCL401 3.0 36.4 1.0
C4C M:BCL401 3.0 37.2 1.0
C1B M:BCL401 3.0 38.3 1.0
C4B M:BCL401 3.1 36.8 1.0
C1D M:BCL401 3.2 35.2 1.0
CD2 M:HIS182 3.3 47.6 1.0
CHB M:BCL401 3.4 37.6 1.0
CHA M:BCL401 3.4 37.4 1.0
CHC M:BCL401 3.4 36.7 1.0
CE1 M:HIS182 3.5 46.3 1.0
CHD M:BCL401 3.5 35.5 1.0
C3D M:BCL401 4.1 36.2 1.0
C3A M:BCL401 4.3 40.3 1.0
C2A M:BCL401 4.3 40.6 1.0
C3C M:BCL401 4.3 38.7 1.0
C2C M:BCL401 4.3 37.3 1.0
C3B M:BCL401 4.4 38.8 1.0
C2B M:BCL401 4.4 38.9 1.0
C2D M:BCL401 4.4 36.0 1.0
CG M:HIS182 4.5 45.6 1.0
ND1 M:HIS182 4.6 46.4 1.0
CE2 L:PHE181 4.7 39.6 1.0
CBA M:BCL401 4.8 49.5 1.0
CBD M:BCL401 4.8 39.6 1.0
OBB L:BPH305 4.9 54.0 1.0

Magnesium binding site 4 out of 4 in 7mh4

Go back to Magnesium Binding Sites List in 7mh4
Magnesium binding site 4 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Bromotyrosine


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)3-Bromotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg402

b:35.7
occ:1.00
MG M:BCL402 0.0 35.7 1.0
NC M:BCL402 2.0 38.4 1.0
NA M:BCL402 2.0 37.1 1.0
ND M:BCL402 2.0 36.1 1.0
NB M:BCL402 2.0 36.0 1.0
NE2 M:HIS202 2.4 38.2 1.0
C4D M:BCL402 2.9 36.5 1.0
C4A M:BCL402 3.0 35.9 1.0
C1A M:BCL402 3.0 37.3 1.0
C1C M:BCL402 3.0 37.7 1.0
C4C M:BCL402 3.0 36.6 1.0
C1B M:BCL402 3.0 35.9 1.0
C4B M:BCL402 3.1 37.9 1.0
C1D M:BCL402 3.2 36.6 1.0
CD2 M:HIS202 3.3 38.7 1.0
CHB M:BCL402 3.4 35.4 1.0
CHC M:BCL402 3.4 38.2 1.0
CHA M:BCL402 3.4 35.8 1.0
CE1 M:HIS202 3.5 39.1 1.0
CBB L:BCL304 3.5 39.6 1.0
CHD M:BCL402 3.5 35.9 1.0
CAB L:BCL304 3.7 38.7 1.0
OBB L:BCL304 3.8 41.0 1.0
C3D M:BCL402 4.2 36.7 1.0
C3A M:BCL402 4.3 38.6 1.0
C2C M:BCL402 4.3 38.2 1.0
C3C M:BCL402 4.3 38.3 1.0
C2A M:BCL402 4.4 38.7 1.0
C2B M:BCL402 4.4 36.5 1.0
C3B M:BCL402 4.4 38.5 1.0
C2D M:BCL402 4.4 36.4 1.0
C3B L:BCL304 4.5 36.9 1.0
CG M:HIS202 4.5 39.3 1.0
ND1 M:HIS202 4.6 38.3 1.0
CBD M:BCL402 4.9 36.7 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 Show Tyr at M210 Tunes the Initial Electron Transfer Mechanism. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34907018
DOI: 10.1073/PNAS.2116439118
Page generated: Thu Mar 31 04:07:14 2022

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