Fluorine in PDB 5xl0: Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain

The structure of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain, PDB code: 5xl0 was solved by Y.Kanai, A.Harada, T.Shibata, R.Nishimura, K.Namiki, M.Watanabe, S.Nakamura, F.Yumoto, T.Senda, A.Suzuki, S.Neya, Y.Yamamoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.92 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	34.261, 30.854, 64.130, 90.00, 105.36, 90.00
R / Rfree (%)	16.3 / 17.3

The structure of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Fluorine atom in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain (pdb code 5xl0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain, PDB code: 5xl0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:6.6 occ:0.50 F A:89R201 0.0 6.6 0.5 C28 A:89R201 1.3 10.4 0.5 C33 A:89R201 1.3 7.8 0.5 C29 A:89R201 1.8 9.5 0.5 F2 A:89R201 2.2 6.5 0.5 F1 A:89R201 2.2 7.7 0.5 C14 A:89R201 2.3 6.5 0.5 C17 A:89R201 2.5 6.6 0.5 C13 A:89R201 2.8 6.3 0.5 C30 A:89R201 2.9 8.1 0.5 C18 A:89R201 3.1 6.8 0.5 C32 A:89R201 3.2 10.8 0.5 CZ A:PHE138 3.3 9.7 1.0 C31 A:89R201 3.3 4.2 0.5 CE2 A:PHE138 3.3 11.2 1.0 C15 A:89R201 3.7 5.2 0.5 C16 A:89R201 3.8 6.2 0.5 C12 A:89R201 4.2 5.4 0.5 CD1 A:LEU72 4.2 9.8 1.0 CE1 A:PHE138 4.3 9.3 1.0 CD2 A:PHE138 4.3 9.9 1.0 C2 A:89R201 4.4 5.6 0.5 C2 A:89R201 4.4 6.3 0.5 C19 A:89R201 4.5 6.0 0.5 N1 A:89R201 4.6 5.2 0.5 CD2 A:LEU72 4.7 8.6 1.0 CB A:LEU72 4.8 6.8 1.0 N2 A:89R201 4.8 5.3 0.5 CG A:LEU72 4.8 7.0 1.0 CG2 A:ILE107 4.9 8.4 1.0

Fluorine binding site 2 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:17.4 occ:0.50 F A:89R201 0.0 17.4 0.5 C29 A:89R201 1.2 5.2 0.5 C28 A:89R201 1.3 8.0 0.5 C33 A:89R201 1.4 8.7 0.5 F1 A:89R201 2.2 14.7 0.5 C17 A:89R201 2.2 6.3 0.5 F2 A:89R201 2.2 14.5 0.5 C14 A:89R201 2.4 6.9 0.5 C32 A:89R201 2.6 8.5 0.5 C18 A:89R201 2.7 6.8 0.5 C30 A:89R201 2.9 7.9 0.5 C13 A:89R201 2.9 6.5 0.5 C31 A:89R201 2.9 15.9 0.5 CB A:TYR103 3.2 8.7 1.0 O A:TYR103 3.5 6.7 1.0 C16 A:89R201 3.5 5.3 0.5 C15 A:89R201 3.8 6.3 0.5 C A:TYR103 3.8 5.7 1.0 CD2 A:TYR103 3.9 10.0 1.0 CG2 A:ILE99 3.9 9.5 1.0 CG A:TYR103 4.0 8.9 1.0 C19 A:89R201 4.0 6.3 0.5 CA A:TYR103 4.1 6.3 1.0 CG2 A:THR39 4.1 8.9 1.0 C2 A:89R201 4.2 6.3 0.5 C12 A:89R201 4.3 6.3 0.5 CD2 A:LEU32 4.4 9.8 1.0 CB A:THR39 4.4 6.7 1.0 N2 A:89R201 4.5 5.4 0.5 N A:LEU104 4.5 6.5 1.0 C2 A:89R201 4.5 5.6 0.5 N1 A:89R201 4.7 5.8 0.5 CB A:ILE107 4.9 6.0 1.0 CD1 A:LEU32 5.0 8.3 1.0 CG2 A:ILE107 5.0 8.4 1.0

Fluorine binding site 3 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:7.7 occ:0.50 F1 A:89R201 0.0 7.7 0.5 C29 A:89R201 0.6 9.5 0.5 C33 A:89R201 1.3 7.8 0.5 C28 A:89R201 1.7 10.4 0.5 F2 A:89R201 2.2 6.5 0.5 F A:89R201 2.2 6.6 0.5 C14 A:89R201 2.4 6.5 0.5 C17 A:89R201 2.7 6.6 0.5 C2 A:89R201 2.9 6.3 0.5 C15 A:89R201 2.9 5.2 0.5 C2 A:89R201 3.1 5.6 0.5 C16 A:89R201 3.2 6.2 0.5 CD2 A:LEU104 3.3 14.6 1.0 CG2 A:ILE107 3.4 8.4 1.0 C13 A:89R201 3.6 6.3 0.5 CE2 A:PHE138 3.8 11.2 1.0 C18 A:89R201 4.0 6.8 0.5 F2 A:89R201 4.0 14.5 0.5 CZ A:PHE138 4.0 9.7 1.0 C16 A:89R201 4.2 5.3 0.5 N1 A:89R201 4.2 5.2 0.5 F1 A:89R201 4.3 14.7 0.5 C15 A:89R201 4.4 6.3 0.5 CG A:LEU104 4.4 11.9 1.0 CB A:LEU104 4.5 7.5 1.0 C30 A:89R201 4.5 8.1 0.5 CA A:LEU104 4.5 6.9 1.0 C12 A:89R201 4.5 5.4 0.5 N2 A:89R201 4.6 5.3 0.5 C33 A:89R201 4.6 8.7 0.5 C28 A:89R201 4.6 8.0 0.5 C32 A:89R201 4.7 10.8 0.5 CB A:ILE107 4.8 6.0 1.0 CD1 A:ILE107 4.8 7.9 1.0 C19 A:89R201 4.9 6.0 0.5 C17 A:89R201 4.9 6.3 0.5 CD2 A:PHE138 4.9 9.9 1.0 C14 A:89R201 5.0 6.9 0.5 O A:LEU104 5.0 7.0 1.0

Fluorine binding site 4 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:14.7 occ:0.50 F1 A:89R201 0.0 14.7 0.5 C29 A:89R201 1.3 5.2 0.5 C33 A:89R201 1.4 8.7 0.5 C28 A:89R201 1.6 8.0 0.5 F A:89R201 2.2 17.4 0.5 F2 A:89R201 2.2 14.5 0.5 C17 A:89R201 2.2 6.3 0.5 C14 A:89R201 2.3 6.9 0.5 C16 A:89R201 2.8 5.3 0.5 C2 A:89R201 2.9 6.3 0.5 C15 A:89R201 3.0 6.3 0.5 C2 A:89R201 3.2 5.6 0.5 C18 A:89R201 3.3 6.8 0.5 CG2 A:ILE107 3.3 8.4 1.0 CB A:ILE107 3.4 6.0 1.0 C13 A:89R201 3.4 6.5 0.5 CD1 A:ILE107 3.5 7.9 1.0 O A:TYR103 3.9 6.7 1.0 CD2 A:LEU32 3.9 9.8 1.0 N2 A:89R201 4.0 5.4 0.5 CG1 A:ILE107 4.0 7.1 1.0 C32 A:89R201 4.0 8.5 0.5 C31 A:89R201 4.1 15.9 0.5 C15 A:89R201 4.2 5.2 0.5 C30 A:89R201 4.2 7.9 0.5 C19 A:89R201 4.2 6.3 0.5 N1 A:89R201 4.2 5.8 0.5 F1 A:89R201 4.3 7.7 0.5 C12 A:89R201 4.4 6.3 0.5 C16 A:89R201 4.4 6.2 0.5 C A:TYR103 4.5 5.7 1.0 F2 A:89R201 4.7 6.5 0.5 CA A:ILE107 4.7 5.7 1.0 CD2 A:LEU104 4.7 14.6 1.0 C29 A:89R201 4.8 9.5 0.5 N A:ILE107 4.8 6.0 1.0 C33 A:89R201 4.9 7.8 0.5 CD1 A:LEU32 4.9 8.3 1.0 CA A:LEU104 4.9 6.9 1.0 C14 A:89R201 4.9 6.5 0.5 N A:LEU104 5.0 6.5 1.0 CB A:TYR103 5.0 8.7 1.0

Fluorine binding site 5 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:6.5 occ:0.50 F2 A:89R201 0.0 6.5 0.5 C33 A:89R201 1.3 7.8 0.5 C28 A:89R201 1.5 10.4 0.5 F A:89R201 2.2 6.6 0.5 F1 A:89R201 2.2 7.7 0.5 C14 A:89R201 2.3 6.5 0.5 C29 A:89R201 2.3 9.5 0.5 C17 A:89R201 2.5 6.6 0.5 C13 A:89R201 3.1 6.3 0.5 C15 A:89R201 3.2 5.2 0.5 CG2 A:ILE107 3.4 8.4 1.0 C16 A:89R201 3.4 6.2 0.5 CD1 A:ILE107 3.5 7.9 1.0 C18 A:89R201 3.5 6.8 0.5 C2 A:89R201 3.6 5.6 0.5 C30 A:89R201 3.6 8.1 0.5 C2 A:89R201 3.7 6.3 0.5 CG1 A:VAL68 3.9 5.7 1.0 C32 A:89R201 4.0 10.8 0.5 CG1 A:ILE107 4.2 7.1 1.0 C12 A:89R201 4.2 5.4 0.5 N1 A:89R201 4.3 5.2 0.5 CB A:ILE107 4.4 6.0 1.0 CD1 A:ILE111 4.6 7.3 1.0 N2 A:89R201 4.6 5.3 0.5 C19 A:89R201 4.6 6.0 0.5 F1 A:89R201 4.7 14.7 0.5 C31 A:89R201 4.7 4.2 0.5 CD2 A:LEU72 4.9 8.6 1.0 C16 A:89R201 5.0 5.3 0.5 C15 A:89R201 5.0 6.3 0.5

Fluorine binding site 6 out of 6 in the Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Met-Aquo Form of Sperm Whale Myoglobin Reconstituted with 7-Pf, A Heme Possesseing CF3 Group As Side Chain within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:14.5 occ:0.50 F2 A:89R201 0.0 14.5 0.5 C28 A:89R201 1.0 8.0 0.5 C33 A:89R201 1.3 8.7 0.5 C17 A:89R201 2.1 6.3 0.5 F A:89R201 2.2 17.4 0.5 F1 A:89R201 2.2 14.7 0.5 C14 A:89R201 2.4 6.9 0.5 C29 A:89R201 2.4 5.2 0.5 C16 A:89R201 2.8 5.3 0.5 C2 A:89R201 2.9 6.3 0.5 CD2 A:LEU104 2.9 14.6 1.0 C15 A:89R201 3.1 6.3 0.5 C18 A:89R201 3.3 6.8 0.5 C2 A:89R201 3.3 5.6 0.5 O A:TYR103 3.4 6.7 1.0 C A:TYR103 3.5 5.7 1.0 N A:LEU104 3.5 6.5 1.0 C13 A:89R201 3.5 6.5 0.5 CG2 A:ILE99 3.5 9.5 1.0 CA A:LEU104 3.6 6.9 1.0 CB A:TYR103 3.8 8.7 1.0 CG A:LEU104 3.9 11.9 1.0 C32 A:89R201 4.0 8.5 0.5 F1 A:89R201 4.0 7.7 0.5 N2 A:89R201 4.0 5.4 0.5 CG2 A:ILE107 4.1 8.4 1.0 C30 A:89R201 4.2 7.9 0.5 C19 A:89R201 4.2 6.3 0.5 CA A:TYR103 4.3 6.3 1.0 C15 A:89R201 4.3 5.2 0.5 CB A:LEU104 4.3 7.5 1.0 N1 A:89R201 4.3 5.8 0.5 C29 A:89R201 4.5 9.5 0.5 C12 A:89R201 4.5 6.3 0.5 C16 A:89R201 4.6 6.2 0.5 CB A:ILE107 4.7 6.0 1.0 C31 A:89R201 4.7 15.9 0.5 CB A:ILE99 4.9 9.4 1.0 C A:LEU104 4.9 6.7 1.0

Y.Kanai, A.Harada, T.Shibata, R.Nishimura, K.Namiki, M.Watanabe, S.Nakamura, F.Yumoto, T.Senda, A.Suzuki, S.Neya, Y.Yamamoto. Characterization of Heme Orientational Disorder in A Myoglobin Reconstituted with A Trifluoromethyl-Group-Substituted Heme Cofactor Biochemistry V. 56 4500 2017.
ISSN: ISSN 1520-4995
PubMed: 28758387
DOI: 10.1021/ACS.BIOCHEM.7B00457