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Magnesium in PDB 7mh5: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine

Protein crystallography data

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine, PDB code: 7mh5 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) 38.95 / 2.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.414, 141.414, 186.502, 90, 90, 120
R / Rfree (%) 18 / 20.5

Other elements in 7mh5:

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

Iron (Fe) 1 atom
Iodine (I) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine (pdb code 7mh5). 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-Iodotyrosine, PDB code: 7mh5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mh5

Go back to Magnesium Binding Sites List in 7mh5
Magnesium binding site 1 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine


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-Iodotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg303

b:56.1
occ:1.00
MG L:BCL303 0.0 56.1 1.0
NC L:BCL303 2.0 58.0 1.0
NA L:BCL303 2.0 57.6 1.0
ND L:BCL303 2.0 58.9 1.0
NB L:BCL303 2.1 53.8 1.0
NE2 L:HIS173 2.3 56.7 1.0
C4D L:BCL303 2.9 60.5 1.0
C1C L:BCL303 3.0 58.8 1.0
C4A L:BCL303 3.0 54.4 1.0
C1A L:BCL303 3.0 59.3 1.0
C4C L:BCL303 3.0 57.0 1.0
C4B L:BCL303 3.1 52.9 1.0
C1B L:BCL303 3.1 51.1 1.0
C1D L:BCL303 3.2 58.7 1.0
CD2 L:HIS173 3.3 57.7 1.0
CE1 L:HIS173 3.3 57.4 1.0
CHC L:BCL303 3.4 57.1 1.0
CHB L:BCL303 3.4 50.3 1.0
CHA L:BCL303 3.4 58.7 1.0
CHD L:BCL303 3.5 55.9 1.0
OBB M:BCL403 3.6 75.9 1.0
CAB M:BCL403 3.8 66.3 1.0
CBB M:BCL403 3.8 66.4 1.0
C3D L:BCL303 4.2 60.9 1.0
C3A L:BCL303 4.3 56.8 1.0
C3C L:BCL303 4.3 57.2 1.0
C2A L:BCL303 4.3 58.7 1.0
C2C L:BCL303 4.3 55.6 1.0
C3B L:BCL303 4.4 51.0 1.0
C2D L:BCL303 4.4 62.9 1.0
ND1 L:HIS173 4.4 58.0 1.0
C2B L:BCL303 4.4 51.7 1.0
CG L:HIS173 4.4 57.4 1.0
CD2 L:PHE167 4.6 57.8 1.0
C3B M:BCL403 4.6 60.5 1.0
CBD L:BCL303 4.9 59.3 1.0
CMA L:BCL303 5.0 57.9 1.0

Magnesium binding site 2 out of 4 in 7mh5

Go back to Magnesium Binding Sites List in 7mh5
Magnesium binding site 2 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine


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

b:53.4
occ:1.00
MG M:BCL401 0.0 53.4 1.0
NA M:BCL401 2.0 54.4 1.0
NC M:BCL401 2.0 53.6 1.0
ND M:BCL401 2.0 55.9 1.0
NB M:BCL401 2.1 54.4 1.0
NE2 L:HIS153 2.5 71.5 1.0
I2 M:TYI210 2.9 62.6 0.2
C4D M:BCL401 2.9 55.9 1.0
C1A M:BCL401 3.0 56.8 1.0
C4A M:BCL401 3.0 52.8 1.0
C1C M:BCL401 3.0 57.4 1.0
C4C M:BCL401 3.0 54.9 1.0
C1B M:BCL401 3.1 51.2 1.0
C4B M:BCL401 3.1 54.4 1.0
C1D M:BCL401 3.2 56.1 1.0
CHB M:BCL401 3.4 51.6 1.0
CHA M:BCL401 3.4 58.0 1.0
CHC M:BCL401 3.4 55.9 1.0
CE1 L:HIS153 3.4 73.4 1.0
CD2 L:HIS153 3.5 73.8 1.0
CHD M:BCL401 3.6 54.8 1.0
C3D M:BCL401 4.2 55.7 1.0
C3A M:BCL401 4.3 54.2 1.0
C2A M:BCL401 4.3 57.2 1.0
C3C M:BCL401 4.3 58.0 1.0
C2C M:BCL401 4.3 58.7 1.0
C2B M:BCL401 4.4 49.5 1.0
C3B M:BCL401 4.4 52.2 1.0
C2D M:BCL401 4.4 55.5 1.0
ND1 L:HIS153 4.6 75.1 1.0
CG L:HIS153 4.6 76.2 1.0
OBB L:BPH301 4.7 62.5 1.0
CBA M:BCL401 4.8 63.0 1.0
CBC M:BCL401 4.8 59.9 1.0
CBD M:BCL401 4.9 59.3 1.0
CE2 M:TYI210 4.9 60.9 1.0

Magnesium binding site 3 out of 4 in 7mh5

Go back to Magnesium Binding Sites List in 7mh5
Magnesium binding site 3 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine


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

b:59.6
occ:1.00
MG M:BCL402 0.0 59.6 1.0
NA M:BCL402 2.0 56.6 1.0
NC M:BCL402 2.0 60.1 1.0
ND M:BCL402 2.0 56.8 1.0
NB M:BCL402 2.1 60.5 1.0
NE2 M:HIS182 2.4 68.1 1.0
C4D M:BCL402 2.9 57.1 1.0
C1A M:BCL402 3.0 57.0 1.0
C4A M:BCL402 3.0 57.2 1.0
C4C M:BCL402 3.0 59.5 1.0
C1C M:BCL402 3.0 61.3 1.0
C1B M:BCL402 3.1 60.5 1.0
C4B M:BCL402 3.1 61.5 1.0
C1D M:BCL402 3.2 57.4 1.0
CD2 M:HIS182 3.3 69.2 1.0
CHB M:BCL402 3.4 56.2 1.0
CHA M:BCL402 3.4 58.4 1.0
CHC M:BCL402 3.4 61.1 1.0
CHD M:BCL402 3.5 58.0 1.0
CE1 M:HIS182 3.5 69.7 1.0
C3D M:BCL402 4.2 56.4 1.0
C3A M:BCL402 4.3 59.0 1.0
C2A M:BCL402 4.3 59.4 1.0
C3C M:BCL402 4.3 58.8 1.0
C2C M:BCL402 4.3 58.3 1.0
C3B M:BCL402 4.4 65.4 1.0
C2D M:BCL402 4.4 56.5 1.0
C2B M:BCL402 4.4 63.2 1.0
CG M:HIS182 4.5 68.9 1.0
ND1 M:HIS182 4.6 69.8 1.0
CE2 L:PHE181 4.8 64.2 1.0
CBD M:BCL402 4.9 59.5 1.0
C18 M:SPO411 4.9 83.9 1.0
CBA M:BCL402 4.9 66.8 1.0

Magnesium binding site 4 out of 4 in 7mh5

Go back to Magnesium Binding Sites List in 7mh5
Magnesium binding site 4 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Iodotyrosine


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-Iodotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg403

b:56.9
occ:1.00
MG M:BCL403 0.0 56.9 1.0
NA M:BCL403 2.0 58.1 1.0
NC M:BCL403 2.0 58.8 1.0
ND M:BCL403 2.0 55.9 1.0
NB M:BCL403 2.1 55.6 1.0
NE2 M:HIS202 2.4 53.5 1.0
C4D M:BCL403 2.9 55.3 1.0
C4A M:BCL403 3.0 57.2 1.0
C1A M:BCL403 3.0 55.0 1.0
C1C M:BCL403 3.0 58.9 1.0
C4C M:BCL403 3.0 57.1 1.0
C1B M:BCL403 3.0 54.8 1.0
C4B M:BCL403 3.1 56.2 1.0
C1D M:BCL403 3.2 57.9 1.0
CD2 M:HIS202 3.3 55.0 1.0
CHB M:BCL403 3.4 54.8 1.0
CHA M:BCL403 3.4 53.4 1.0
CHC M:BCL403 3.4 56.2 1.0
CBB L:BCL303 3.5 51.4 1.0
CE1 M:HIS202 3.5 55.1 1.0
CHD M:BCL403 3.5 56.0 1.0
CAB L:BCL303 3.7 50.8 1.0
OBB L:BCL303 3.8 49.0 1.0
C3D M:BCL403 4.2 56.3 1.0
C3A M:BCL403 4.3 59.1 1.0
C2C M:BCL403 4.3 60.5 1.0
C2A M:BCL403 4.3 57.8 1.0
C3C M:BCL403 4.3 59.8 1.0
C2B M:BCL403 4.4 56.4 1.0
C2D M:BCL403 4.4 56.9 1.0
C3B M:BCL403 4.4 60.5 1.0
CG M:HIS202 4.5 56.4 1.0
C3B L:BCL303 4.5 51.0 1.0
ND1 M:HIS202 4.6 56.2 1.0
CBD M:BCL403 4.8 56.0 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 Oct 3 00:53:31 2024

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