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Magnesium in PDB 7mh9: Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine

Protein crystallography data

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine, PDB code: 7mh9 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) 39.07 / 3.10
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 141.21, 141.21, 187.59, 90, 90, 120
R / Rfree (%) 16.9 / 20.5

Other elements in 7mh9:

The structure of Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine 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; Y(M210)3-Nitrotyrosine (pdb code 7mh9). 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-Nitrotyrosine, PDB code: 7mh9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7mh9

Go back to Magnesium Binding Sites List in 7mh9
Magnesium binding site 1 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine


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-Nitrotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg401

b:48.6
occ:1.00
MG L:BCL401 0.0 48.6 1.0
NA L:BCL401 2.0 47.4 1.0
NC L:BCL401 2.0 49.5 1.0
ND L:BCL401 2.0 48.6 1.0
NB L:BCL401 2.0 49.5 1.0
NE2 L:HIS153 2.4 53.3 1.0
C4D L:BCL401 2.9 48.3 1.0
C1A L:BCL401 2.9 48.3 1.0
C4A L:BCL401 3.0 47.1 1.0
C1C L:BCL401 3.0 52.0 1.0
C4C L:BCL401 3.0 49.0 1.0
C1B L:BCL401 3.0 48.6 1.0
C4B L:BCL401 3.1 50.6 1.0
C1D L:BCL401 3.2 48.0 1.0
CD2 L:HIS153 3.4 56.4 1.0
CHA L:BCL401 3.4 49.1 1.0
CHB L:BCL401 3.4 47.4 1.0
CHC L:BCL401 3.4 52.5 1.0
CE1 L:HIS153 3.4 53.6 1.0
CHD L:BCL401 3.6 48.3 1.0
C3D L:BCL401 4.2 47.9 1.0
C2A L:BCL401 4.3 48.5 1.0
C3A L:BCL401 4.3 47.4 1.0
C3C L:BCL401 4.3 50.6 1.0
C2C L:BCL401 4.4 51.4 1.0
C3B L:BCL401 4.4 50.9 1.0
C2B L:BCL401 4.4 48.9 1.0
C2D L:BCL401 4.4 49.0 1.0
ND1 L:HIS153 4.5 54.3 1.0
CG L:HIS153 4.6 57.1 1.0
OBB L:BPH402 4.6 52.9 1.0
CBC L:BCL401 4.8 53.0 1.0
CBA L:BCL401 4.8 51.5 1.0
CBD L:BCL401 4.8 49.8 1.0
CD1 L:LEU154 4.9 57.3 1.0
CE2 M:NIY210 4.9 50.2 1.0

Magnesium binding site 2 out of 4 in 7mh9

Go back to Magnesium Binding Sites List in 7mh9
Magnesium binding site 2 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine


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-Nitrotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg404

b:42.1
occ:1.00
MG L:BCL404 0.0 42.1 1.0
NC L:BCL404 2.0 46.1 1.0
NA L:BCL404 2.0 45.7 1.0
ND L:BCL404 2.0 46.1 1.0
NB L:BCL404 2.0 43.3 1.0
NE2 L:HIS173 2.2 41.3 1.0
C4D L:BCL404 2.9 48.8 1.0
C1A L:BCL404 3.0 46.2 1.0
C1C L:BCL404 3.0 45.9 1.0
C4C L:BCL404 3.0 46.9 1.0
C4A L:BCL404 3.0 43.2 1.0
C4B L:BCL404 3.0 44.4 1.0
C1B L:BCL404 3.1 41.2 1.0
C1D L:BCL404 3.2 46.8 1.0
CD2 L:HIS173 3.2 43.0 1.0
CE1 L:HIS173 3.2 42.1 1.0
OBB M:BCL401 3.3 66.3 1.0
CHC L:BCL404 3.4 45.5 1.0
CHA L:BCL404 3.4 48.9 1.0
CHB L:BCL404 3.5 40.2 1.0
CHD L:BCL404 3.5 47.2 1.0
CAB M:BCL401 3.8 58.6 1.0
C3D L:BCL404 4.2 48.5 1.0
CBB M:BCL401 4.3 58.8 1.0
C3A L:BCL404 4.3 44.6 1.0
ND1 L:HIS173 4.3 41.4 1.0
C2A L:BCL404 4.3 45.7 1.0
C3C L:BCL404 4.4 44.3 1.0
CG L:HIS173 4.4 43.3 1.0
C2C L:BCL404 4.4 43.9 1.0
C3B L:BCL404 4.4 42.9 1.0
C2D L:BCL404 4.4 48.0 1.0
C2B L:BCL404 4.4 42.4 1.0
C3B M:BCL401 4.7 54.1 1.0
CD2 L:PHE167 4.7 55.2 1.0
CBD L:BCL404 4.9 48.4 1.0
CMA L:BCL404 5.0 45.0 1.0

Magnesium binding site 3 out of 4 in 7mh9

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


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-Nitrotyrosine within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg405

b:47.3
occ:1.00
MG L:BCL405 0.0 47.3 1.0
NA L:BCL405 2.0 48.2 1.0
NC L:BCL405 2.0 49.8 1.0
ND L:BCL405 2.0 48.7 1.0
NB L:BCL405 2.0 48.0 1.0
NE2 M:HIS182 2.4 55.4 1.0
C4D L:BCL405 2.9 48.8 1.0
C1A L:BCL405 3.0 49.5 1.0
C4A L:BCL405 3.0 47.4 1.0
C1C L:BCL405 3.0 49.6 1.0
C4C L:BCL405 3.0 49.4 1.0
C1B L:BCL405 3.0 48.2 1.0
C4B L:BCL405 3.1 47.0 1.0
C1D L:BCL405 3.2 49.0 1.0
CD2 M:HIS182 3.3 54.5 1.0
CHB L:BCL405 3.4 45.7 1.0
CHA L:BCL405 3.4 51.0 1.0
CHC L:BCL405 3.4 48.2 1.0
CE1 M:HIS182 3.5 56.9 1.0
CHD L:BCL405 3.5 49.8 1.0
C3D L:BCL405 4.2 49.0 1.0
C3A L:BCL405 4.3 48.2 1.0
C2A L:BCL405 4.3 50.2 1.0
C2C L:BCL405 4.4 48.8 1.0
C3C L:BCL405 4.4 47.6 1.0
C2B L:BCL405 4.4 49.2 1.0
C3B L:BCL405 4.4 49.3 1.0
C2D L:BCL405 4.4 49.0 1.0
CG M:HIS182 4.5 54.9 1.0
ND1 M:HIS182 4.6 56.4 1.0
CE2 L:PHE181 4.8 52.9 1.0
OBB L:BPH406 4.8 64.2 1.0
CBA L:BCL405 4.8 58.2 1.0
CBD L:BCL405 4.9 52.9 1.0

Magnesium binding site 4 out of 4 in 7mh9

Go back to Magnesium Binding Sites List in 7mh9
Magnesium binding site 4 out of 4 in the Crystal Structure of R. Sphaeroides Photosynthetic Reaction Center Variant; Y(M210)3-Nitrotyrosine


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

b:49.6
occ:1.00
MG M:BCL401 0.0 49.6 1.0
NA M:BCL401 2.0 51.5 1.0
NC M:BCL401 2.0 54.0 1.0
ND M:BCL401 2.0 50.5 1.0
NB M:BCL401 2.0 49.4 1.0
NE2 M:HIS202 2.4 41.5 1.0
C4D M:BCL401 2.9 49.7 1.0
C4A M:BCL401 3.0 50.9 1.0
C1A M:BCL401 3.0 49.5 1.0
C4C M:BCL401 3.0 53.6 1.0
C1C M:BCL401 3.0 53.8 1.0
C1B M:BCL401 3.0 50.0 1.0
C4B M:BCL401 3.1 49.8 1.0
C1D M:BCL401 3.2 50.6 1.0
CD2 M:HIS202 3.3 44.1 1.0
CHB M:BCL401 3.4 49.8 1.0
CE1 M:HIS202 3.4 43.6 1.0
CHA M:BCL401 3.4 48.3 1.0
CHC M:BCL401 3.4 50.4 1.0
CHD M:BCL401 3.5 52.6 1.0
CBB L:BCL404 3.6 46.0 1.0
CAB L:BCL404 3.8 43.7 1.0
OBB L:BCL404 3.9 42.6 1.0
C3D M:BCL401 4.2 49.0 1.0
C3A M:BCL401 4.3 50.2 1.0
C2A M:BCL401 4.3 49.2 1.0
C2C M:BCL401 4.3 53.3 1.0
C3C M:BCL401 4.3 53.1 1.0
C2B M:BCL401 4.4 52.0 1.0
C3B M:BCL401 4.4 54.1 1.0
C2D M:BCL401 4.4 49.6 1.0
ND1 M:HIS202 4.5 43.0 1.0
CG M:HIS202 4.5 44.2 1.0
C3B L:BCL404 4.6 42.9 1.0
CBD M:BCL401 4.8 49.5 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 00:54:36 2024

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