Fluorine in PDB 8wf5: Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))

The structure of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)), PDB code: 8wf5 was solved by Y.Kagawa, K.Oohora, T.Himiyama, A.Suzuki, T.Hayashi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.26, 28.74, 63.65, 90, 105.47, 90
R / Rfree (%)	15.7 / 21.6

The structure of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Fluorine atom in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) (pdb code 8wf5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)), PDB code: 8wf5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:25.2 occ:1.00 F3 A:WC5401 0.0 25.2 1.0 C22 A:WC5401 1.3 23.4 1.0 F1 A:WC5401 2.1 26.3 1.0 F2 A:WC5401 2.1 26.5 1.0 C4 A:WC5401 2.2 16.3 1.0 C5 A:WC5401 2.9 14.4 1.0 C6 A:WC5401 3.0 12.5 1.0 O A:VAL68 3.0 12.5 1.0 CB A:ALA71 3.5 14.3 1.0 C3 A:WC5401 3.5 14.8 1.0 N A:LEU72 3.6 14.7 1.0 CG1 A:VAL68 3.7 13.5 1.0 C A:VAL68 3.9 12.8 1.0 CA A:VAL68 4.0 12.8 1.0 CB A:LEU72 4.1 14.3 1.0 CA A:LEU72 4.2 14.9 1.0 C A:ALA71 4.2 14.8 1.0 N1 A:WC5401 4.2 14.4 1.0 C21 A:WC5401 4.3 15.4 1.0 C7 A:WC5401 4.3 13.4 1.0 CA A:ALA71 4.4 14.9 1.0 C2 A:WC5401 4.4 15.0 1.0 CB A:VAL68 4.4 12.7 1.0 CD1 A:LEU89 4.6 20.1 1.0 C23 A:WC5401 4.7 13.9 1.0 N A:ALA71 4.9 14.7 1.0 O A:ALA71 5.0 15.4 1.0 C8 A:WC5401 5.0 13.7 1.0

Fluorine binding site 2 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.3 occ:1.00 F1 A:WC5401 0.0 26.3 1.0 C22 A:WC5401 1.3 23.4 1.0 F2 A:WC5401 2.1 26.5 1.0 F3 A:WC5401 2.1 25.2 1.0 C4 A:WC5401 2.3 16.3 1.0 C21 A:WC5401 2.8 15.4 1.0 C3 A:WC5401 2.8 14.8 1.0 CB A:LEU72 3.6 14.3 1.0 CD1 A:LEU72 3.6 14.7 1.0 C5 A:WC5401 3.7 14.4 1.0 CZ A:PHE138 3.9 23.0 1.0 CG A:LEU72 4.0 14.5 1.0 CA A:LEU72 4.1 14.9 1.0 C2 A:WC5401 4.2 15.0 1.0 O A:VAL68 4.2 12.5 1.0 CG1 A:VAL68 4.3 13.5 1.0 N A:LEU72 4.3 14.7 1.0 CD2 A:LEU72 4.3 15.2 1.0 CE2 A:PHE138 4.3 22.9 1.0 CE1 A:PHE138 4.4 20.3 1.0 C6 A:WC5401 4.4 12.5 1.0 N1 A:WC5401 4.6 14.4 1.0 CD1 A:ILE75 4.9 16.2 1.0

Fluorine binding site 3 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:26.5 occ:1.00 F2 A:WC5401 0.0 26.5 1.0 C22 A:WC5401 1.3 23.4 1.0 F1 A:WC5401 2.1 26.3 1.0 F3 A:WC5401 2.1 25.2 1.0 C4 A:WC5401 2.2 16.3 1.0 C5 A:WC5401 3.2 14.4 1.0 C3 A:WC5401 3.2 14.8 1.0 CD1 A:LEU89 3.4 20.1 1.0 C6 A:WC5401 3.5 12.5 1.0 CZ A:PHE138 3.6 23.0 1.0 C21 A:WC5401 3.7 15.4 1.0 CE1 A:PHE138 3.9 20.3 1.0 CD1 A:ILE75 4.1 16.2 1.0 C2 A:WC5401 4.2 15.0 1.0 N1 A:WC5401 4.3 14.4 1.0 CG A:LEU89 4.4 18.2 1.0 CD2 A:LEU89 4.6 17.6 1.0 CE2 A:PHE138 4.6 22.9 1.0 CB A:ALA71 4.7 14.3 1.0 CB A:LEU89 4.7 17.4 1.0 N A:LEU72 4.8 14.7 1.0 C7 A:WC5401 4.9 13.4 1.0 CA A:LEU72 5.0 14.9 1.0

Fluorine binding site 4 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:18.6 occ:1.00 F4 A:WC5401 0.0 18.6 1.0 C25 A:WC5401 1.3 16.4 1.0 F5 A:WC5401 2.1 17.1 1.0 F6 A:WC5401 2.1 17.2 1.0 C18 A:WC5401 2.3 15.3 1.0 C16 A:WC5401 2.9 12.4 1.0 C17 A:WC5401 3.0 13.3 1.0 CD1 A:ILE99 3.2 17.9 1.0 CE1 A:PHE43 3.5 17.9 1.0 CB A:LYS42 3.5 18.6 1.0 C19 A:WC5401 3.7 15.2 1.0 O A:THR39 3.7 15.5 1.0 CG A:LYS42 3.9 20.2 1.0 CG1 A:ILE99 4.1 16.5 1.0 CD1 A:PHE43 4.1 18.0 1.0 CZ A:PHE43 4.2 17.9 1.0 N4 A:WC5401 4.3 14.0 1.0 C15 A:WC5401 4.3 12.9 1.0 CG2 A:ILE99 4.5 17.8 1.0 CD2 A:TYR103 4.5 18.6 1.0 C20 A:WC5401 4.5 14.4 1.0 C A:THR39 4.5 15.7 1.0 C24 A:WC5401 4.5 12.9 1.0 CB A:THR39 4.5 14.8 1.0 C26 A:WC5401 4.6 14.9 1.0 CA A:THR39 4.6 15.8 1.0 C14 A:WC5401 4.8 13.6 1.0 CA A:LYS42 4.8 18.5 1.0 CB A:ILE99 4.9 17.1 1.0

Fluorine binding site 5 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:17.1 occ:1.00 F5 A:WC5401 0.0 17.1 1.0 C25 A:WC5401 1.4 16.4 1.0 F6 A:WC5401 2.1 17.2 1.0 F4 A:WC5401 2.1 18.6 1.0 C18 A:WC5401 2.2 15.3 1.0 C19 A:WC5401 3.0 15.2 1.0 C17 A:WC5401 3.3 13.3 1.0 CE1 A:PHE43 3.4 17.9 1.0 CD2 A:LEU32 3.4 15.8 1.0 C26 A:WC5401 3.5 14.9 1.0 CB A:THR39 3.7 14.8 1.0 C16 A:WC5401 3.8 12.4 1.0 O A:THR39 4.0 15.5 1.0 CZ A:PHE43 4.1 17.9 1.0 C20 A:WC5401 4.1 14.4 1.0 N4 A:WC5401 4.2 14.0 1.0 CG2 A:THR39 4.3 15.2 1.0 CD1 A:PHE43 4.4 18.0 1.0 CE1 A:PHE33 4.4 16.2 1.0 CA A:THR39 4.4 15.8 1.0 OG1 A:THR39 4.4 15.2 1.0 C A:THR39 4.5 15.7 1.0 CG A:LEU32 4.5 14.8 1.0 CD2 A:TYR103 5.0 18.6 1.0

Fluorine binding site 6 out of 6 in the Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2))


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Horse Heart Myoglobin Reconstituted with An Iron Complex of Porphyrin Bearing Two CF3 Groups (Rmb(Fepor(CF3)2)) within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:17.2 occ:1.00 F6 A:WC5401 0.0 17.2 1.0 C25 A:WC5401 1.3 16.4 1.0 F5 A:WC5401 2.1 17.1 1.0 F4 A:WC5401 2.1 18.6 1.0 C18 A:WC5401 2.3 15.3 1.0 C19 A:WC5401 2.9 15.2 1.0 C26 A:WC5401 3.1 14.9 1.0 CD2 A:TYR103 3.2 18.6 1.0 CB A:TYR103 3.4 16.7 1.0 CG2 A:ILE99 3.6 17.8 1.0 C17 A:WC5401 3.7 13.3 1.0 CG A:TYR103 3.7 18.6 1.0 CG2 A:THR39 3.9 15.2 1.0 CB A:THR39 3.9 14.8 1.0 CD1 A:ILE99 4.0 17.9 1.0 CE2 A:TYR103 4.2 21.2 1.0 C20 A:WC5401 4.2 14.4 1.0 C16 A:WC5401 4.4 12.4 1.0 CA A:THR39 4.5 15.8 1.0 CG1 A:ILE99 4.5 16.5 1.0 CB A:ILE99 4.6 17.1 1.0 N4 A:WC5401 4.6 14.0 1.0 O A:THR39 4.7 15.5 1.0 CA A:TYR103 4.7 16.0 1.0 CD2 A:LEU32 4.7 15.8 1.0 O A:TYR103 4.8 13.2 1.0 CG A:LYS42 4.9 20.2 1.0 C A:TYR103 4.9 14.8 1.0

Y.Kagawa, K.Oohora, T.Himiyama, A.Suzuki, T.Hayashi. Redox Engineering of Myoglobin By Cofactor Substitution to Enhance Cyclopropanation Reactivity. Angew.Chem.Int.Ed.Engl. 03485 2024.
ISSN: ESSN 1521-3773
PubMed: 38780472
DOI: 10.1002/ANIE.202403485