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Iodine 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:

Magnesium (Mg) 4 atoms
Iron (Fe) 1 atom

Iodine Binding Sites:

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

Iodine binding site 1 out of 2 in 7mh5

Go back to Iodine Binding Sites List in 7mh5
Iodine binding site 1 out of 2 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 Iodine with other atoms in the I 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
M:I210

b:60.3
occ:0.80
I1 M:TYI210 0.0 60.3 0.8
CE1 M:TYI210 2.1 59.0 1.0
CD1 M:TYI210 3.0 58.5 1.0
CZ M:TYI210 3.1 60.5 1.0
OH M:TYI210 3.4 56.5 1.0
CMB M:BCL403 3.5 56.2 1.0
CBA L:BCL303 3.6 58.7 1.0
C3A L:BCL303 3.9 56.8 1.0
CAA L:BCL303 3.9 60.9 1.0
CE2 L:PHE180 3.9 61.2 1.0
CD2 M:LEU209 3.9 64.0 1.0
CZ L:PHE180 4.0 58.7 1.0
CD2 L:PHE180 4.0 61.4 1.0
CE1 L:PHE180 4.0 57.5 1.0
CG L:PHE180 4.1 60.5 1.0
CHB L:BCL303 4.1 50.3 1.0
CD1 L:PHE180 4.1 58.6 1.0
C4A L:BCL303 4.3 54.4 1.0
CG M:TYI210 4.3 59.3 1.0
CE2 M:TYI210 4.4 60.9 1.0
C2A L:BCL303 4.5 58.7 1.0
CG M:LEU209 4.7 62.3 1.0
CD2 M:TYI210 4.9 60.6 1.0
CMA L:BCL303 4.9 57.9 1.0
C2B M:BCL403 4.9 56.4 1.0
CGA L:BCL303 5.0 58.9 1.0
CB L:PHE180 5.0 60.2 1.0

Iodine binding site 2 out of 2 in 7mh5

Go back to Iodine Binding Sites List in 7mh5
Iodine binding site 2 out of 2 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 Iodine with other atoms in the I 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:I210

b:62.6
occ:0.20
I2 M:TYI210 0.0 62.6 0.2
CE2 M:TYI210 2.0 60.9 1.0
ND M:BCL401 2.3 55.9 1.0
C4D M:BCL401 2.8 55.9 1.0
CD2 M:TYI210 2.9 60.6 1.0
MG M:BCL401 2.9 53.4 1.0
C1D M:BCL401 2.9 56.1 1.0
CZ M:TYI210 3.0 60.5 1.0
OH M:TYI210 3.2 56.5 1.0
CHA M:BCL401 3.4 58.0 1.0
NC M:BCL401 3.4 53.6 1.0
C3D M:BCL401 3.5 55.7 1.0
NA M:BCL401 3.5 54.4 1.0
CHD M:BCL401 3.6 54.8 1.0
C4C M:BCL401 3.6 54.9 1.0
C2D M:BCL401 3.7 55.5 1.0
C1A M:BCL401 3.7 56.8 1.0
CG2 M:ILE206 4.0 55.0 1.0
CBC M:BCL401 4.0 59.9 1.0
CG M:TYI210 4.2 59.3 1.0
CBA M:BCL401 4.2 63.0 1.0
OBB L:BPH301 4.2 62.5 1.0
NB M:BCL401 4.3 54.4 1.0
CE1 M:TYI210 4.3 59.0 1.0
CAD M:BCL401 4.4 56.8 1.0
CBD M:BCL401 4.4 59.3 1.0
C1C M:BCL401 4.5 57.4 1.0
C4A M:BCL401 4.6 52.8 1.0
CBB L:BPH301 4.7 58.3 1.0
CAC M:BCL401 4.7 60.0 1.0
CD1 M:TYI210 4.8 58.5 1.0
CAA M:BCL401 4.8 61.4 1.0
C3C M:BCL401 4.8 58.0 1.0
C2A M:BCL401 4.8 57.2 1.0
CMD M:BCL401 4.9 57.0 1.0
CAB L:BPH301 4.9 58.7 1.0
CGA M:BCL401 4.9 60.1 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: Mon Aug 12 01:45:08 2024

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