Fluorine in PDB 2gyd: Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent

The structure of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent, PDB code: 2gyd was solved by P.J.Loll, M.J.Rossi, R.Eckenhoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.13 / 1.72
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.890, 181.890, 181.890, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 21.7

The structure of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent also contains other interesting chemical elements:

Cadmium

(Cd)

7 atoms

The binding sites of Fluorine atom in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent (pdb code 2gyd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent, PDB code: 2gyd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:F172 b:36.2 occ:0.50 FAB A:DFE172 0.0 36.2 0.5 CAI A:DFE172 1.3 36.0 0.5 FAC A:DFE172 2.2 37.3 0.5 OAH A:DFE172 2.3 37.0 0.5 CAA A:DFE172 2.3 29.9 0.5 OG A:SER27 3.2 18.5 1.0 N A:TYR28 3.4 14.9 1.0 CA A:TYR28 3.4 13.6 1.0 C A:SER27 3.4 15.4 1.0 O A:SER27 3.5 15.1 1.0 CAG A:DFE172 3.5 38.2 0.5 CB A:SER27 3.9 15.7 1.0 CB A:LEU31 4.0 15.3 1.0 CD2 A:LEU31 4.1 21.7 1.0 CB A:TYR28 4.1 13.4 1.0 CD1 A:TYR28 4.3 15.0 1.0 CA A:SER27 4.3 15.6 1.0 CG A:LEU31 4.6 18.9 1.0 CG A:TYR28 4.6 13.5 1.0 CAJ A:DFE172 4.6 39.0 0.5 C A:TYR28 4.6 14.1 1.0 FAE A:DFE172 4.7 38.7 0.5 O A:LEU24 4.8 15.6 1.0 O A:TYR28 5.0 13.8 1.0 FAD A:DFE172 5.0 39.3 0.5

Fluorine binding site 2 out of 5 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:F172 b:37.3 occ:0.50 FAC A:DFE172 0.0 37.3 0.5 CAI A:DFE172 1.3 36.0 0.5 FAB A:DFE172 2.2 36.2 0.5 OAH A:DFE172 2.3 37.0 0.5 CAA A:DFE172 2.4 29.9 0.5 CAG A:DFE172 2.6 38.2 0.5 O A:LEU24 2.9 15.6 1.0 N A:TYR28 2.9 14.9 1.0 CB A:SER27 3.3 15.7 1.0 CA A:TYR28 3.3 13.6 1.0 OG A:SER27 3.3 18.5 1.0 CB A:TYR28 3.4 13.4 1.0 C A:SER27 3.4 15.4 1.0 CA A:SER27 3.9 15.6 1.0 C A:LEU24 3.9 15.4 1.0 CAJ A:DFE172 4.1 39.0 0.5 O A:SER27 4.2 15.1 1.0 CG A:TYR28 4.2 13.5 1.0 CA A:LEU24 4.4 15.2 1.0 FAD A:DFE172 4.5 39.3 0.5 CD1 A:TYR28 4.5 15.0 1.0 N A:SER27 4.5 15.4 1.0 FAE A:DFE172 4.7 38.7 0.5 CB A:LEU24 4.8 14.8 1.0 CD1 A:LEU81 4.8 23.8 1.0 C A:TYR28 4.8 14.1 1.0 FAF A:DFE172 4.9 38.7 0.5 CD2 A:LEU24 5.0 17.7 1.0

Fluorine binding site 3 out of 5 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:F172 b:38.7 occ:0.50 FAE A:DFE172 0.0 38.7 0.5 CAJ A:DFE172 1.3 39.0 0.5 FAD A:DFE172 2.2 39.3 0.5 FAF A:DFE172 2.2 38.7 0.5 CAG A:DFE172 2.3 38.2 0.5 OAH A:DFE172 2.6 37.0 0.5 CAI A:DFE172 4.0 36.0 0.5 CAA A:DFE172 4.7 29.9 0.5 FAB A:DFE172 4.7 36.2 0.5 FAC A:DFE172 4.7 37.3 0.5 CD A:ARG59 5.0 26.1 1.0

Fluorine binding site 4 out of 5 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:F172 b:38.7 occ:0.50 FAF A:DFE172 0.0 38.7 0.5 CAJ A:DFE172 1.3 39.0 0.5 FAD A:DFE172 2.2 39.3 0.5 FAE A:DFE172 2.2 38.7 0.5 CAG A:DFE172 2.3 38.2 0.5 OAH A:DFE172 3.6 37.0 0.5 CD2 A:LEU24 4.3 17.7 1.0 CAI A:DFE172 4.8 36.0 0.5 CD1 A:LEU81 4.9 23.8 1.0 FAC A:DFE172 4.9 37.3 0.5

Fluorine binding site 5 out of 5 in the Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Equine Apoferritin with the H-Diaziflurane Photolabeling Reagent within 5.0Å range: probe atom residue distance (Å) B Occ A:F172 b:39.3 occ:0.50 FAD A:DFE172 0.0 39.3 0.5 CAJ A:DFE172 1.3 39.0 0.5 FAF A:DFE172 2.2 38.7 0.5 FAE A:DFE172 2.2 38.7 0.5 CAG A:DFE172 2.3 38.2 0.5 OAH A:DFE172 3.1 37.0 0.5 CAI A:DFE172 4.3 36.0 0.5 FAC A:DFE172 4.5 37.3 0.5 CD1 A:LEU81 4.6 23.8 1.0 FAB A:DFE172 5.0 36.2 0.5

J.Xi, R.Liu, M.J.Rossi, J.Yang, P.J.Loll, W.P.Dailey, R.G.Eckenhoff. Photoactive Analogues of the Haloether Anesthetics Provide High-Resolution Features From Low-Affinity Interactions. Acs Chem.Biol. V. 1 377 2006.
ISSN: ISSN 1554-8929
PubMed: 17163775
DOI: 10.1021/CB600207D