Iodine in PDB 7vso: Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla

The structure of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla, PDB code: 7vso was solved by E.Mizohata, T.Nakane, S.Hanashima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.90 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	46.2, 103, 128.7, 90, 90, 90
R / Rfree (%)	15.8 / 21

The structure of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Iodine atom in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla (pdb code 7vso). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla, PDB code: 7vso:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:89.7 occ:0.30 I1 A:7YH302 0.0 89.7 0.3 BR1 A:7YH302 0.1 96.6 0.3 C4 A:7YH302 1.8 89.4 0.3 C2 A:7YH302 2.1 89.4 0.3 C3 A:7YH302 2.7 88.1 0.3 C5 A:7YH302 2.9 81.6 0.3 C3 A:7YH302 3.0 89.6 0.3 C1 A:7YH302 3.1 84.8 0.3 C2 A:7YH302 4.0 87.1 0.3 CD2 A:TYR26 4.1 72.5 1.0 C6 A:7YH302 4.1 85.8 0.3 CA A:GLY23 4.1 66.1 1.0 CG1 A:VAL217 4.2 69.4 1.0 CB A:TYR26 4.2 66.9 1.0 CG A:TYR26 4.3 74.9 1.0 C4 A:7YH302 4.3 88.6 0.3 CD1 A:LEU221 4.3 70.0 1.0 C6 A:7YH302 4.4 91.2 0.3 N A:GLY23 4.4 69.1 1.0 O A:LEU22 4.5 77.6 1.0 CD2 A:LEU221 4.6 73.1 1.0 C1 A:7YH302 4.6 86.4 0.3 C A:LEU22 4.7 70.1 1.0 CG A:LEU221 4.8 79.3 1.0 CE2 A:TYR26 4.8 70.7 1.0 C5 A:7YH302 4.9 89.2 0.3 CE1 A:PHE27 5.0 66.5 1.0

Iodine binding site 2 out of 3 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:94.2 occ:0.30 I1 A:7YH302 0.0 94.2 0.3 BR1 A:7YH302 0.2 106.4 0.3 C4 A:7YH302 1.7 88.6 0.3 C2 A:7YH302 2.1 87.1 0.3 C5 A:7YH302 2.6 89.2 0.3 C3 A:7YH302 2.7 89.6 0.3 C1 A:7YH302 3.0 86.4 0.3 C3 A:7YH302 3.0 88.1 0.3 CD1 A:LEU22 3.9 78.3 1.0 C6 A:7YH302 3.9 91.2 0.3 C2 A:7YH302 3.9 89.4 0.3 CG A:LEU22 4.3 84.7 1.0 C6 A:7YH302 4.3 85.8 0.3 C4 A:7YH302 4.3 89.4 0.3 C1 A:7YH302 4.4 84.8 0.3 O A:LEU22 4.5 77.6 1.0 CB A:TYR26 4.6 66.9 1.0 CB A:LEU22 4.7 70.5 1.0 O26 A:7YH302 4.8 70.4 0.3 C20 A:HP6314 4.8 138.6 0.7 C5 A:7YH302 4.8 81.6 0.3 CD1 A:TYR26 4.9 76.8 1.0 CA A:LEU22 5.0 68.5 1.0 CD2 A:LEU25 5.0 107.9 1.0

Iodine binding site 3 out of 3 in the Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Serial Femtosecond Crystallography (Sfx) of Ground State Bacteriorhodopsin Crystallized From Bicelles in Complex with HAD16 Determined Using 7-Kev X-Ray Free Electron Laser (Xfel) at Sacla within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:132.8 occ:0.40 C8 A:OCT305 3.9 94.7 1.0 O A:SER214 4.1 66.2 1.0 CA A:GLY218 4.2 65.2 1.0 CB A:SER214 4.2 66.2 1.0 C26 A:HP6306 4.4 126.3 1.0 C A:GLY218 4.5 69.2 1.0 CA A:SER214 4.6 64.1 1.0 CG1 A:VAL177 4.6 71.0 1.0 CD1 A:ILE222 4.6 67.2 1.0 CG2 A:VAL177 4.7 64.3 1.0 C A:SER214 4.7 62.5 1.0 CD1 A:LEU181 4.8 66.4 1.0 OG A:SER214 4.8 64.0 1.0 N A:PHE219 4.8 62.5 1.0 O A:GLY218 4.9 70.2 1.0 C38 A:R16308 4.9 115.4 1.0

S.Hanashima, T.Nakane, E.Mizohata. Heavy Atom Detergent/Lipid Combined X-Ray Crystallography For Elucidating the Structure-Function Relationships of Membrane Proteins. Membranes (Basel) V. 11 2021.
ISSN: ESSN 2077-0375
PubMed: 34832053
DOI: 10.3390/MEMBRANES11110823