Iron 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:

Fluorine

(F)

6 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe201 b:5.2 occ:0.50 FE A:89R201 0.0 5.2 0.5 FE A:89R201 0.3 4.8 0.5 N1 A:89R201 1.8 5.8 0.5 N2 A:89R201 1.9 5.3 0.5 N2 A:89R201 2.0 5.4 0.5 N3 A:89R201 2.0 5.0 0.5 N A:89R201 2.0 5.8 0.5 N1 A:89R201 2.0 5.2 0.5 NE2 A:HIS93 2.2 6.7 1.0 O A:HOH322 2.2 7.4 1.0 N A:89R201 2.2 5.4 0.5 N3 A:89R201 2.3 5.5 0.5 C15 A:89R201 2.8 6.3 0.5 C16 A:89R201 2.8 6.2 0.5 C12 A:89R201 2.9 6.3 0.5 C19 A:89R201 3.0 6.0 0.5 C19 A:89R201 3.0 6.3 0.5 C20 A:89R201 3.0 5.7 0.5 C16 A:89R201 3.0 5.3 0.5 C23 A:89R201 3.1 5.6 0.5 C4 A:89R201 3.1 5.8 0.5 C7 A:89R201 3.1 4.8 0.5 C15 A:89R201 3.1 5.2 0.5 C12 A:89R201 3.1 5.4 0.5 C7 A:89R201 3.1 6.3 0.5 CD2 A:HIS93 3.1 5.8 1.0 C2 A:89R201 3.1 5.6 0.5 CE1 A:HIS93 3.1 7.5 1.0 C20 A:89R201 3.3 5.9 0.5 C4 A:89R201 3.3 5.7 0.5 C1 A:89R201 3.3 6.2 0.5 C23 A:89R201 3.4 5.3 0.5 C3 A:89R201 3.4 6.4 0.5 C A:89R201 3.4 6.7 0.5 C2 A:89R201 3.4 6.3 0.5 C1 A:89R201 3.4 5.3 0.5 C3 A:89R201 3.5 5.1 0.5 C A:89R201 3.7 6.3 0.5 C14 A:89R201 4.0 6.9 0.5 C13 A:89R201 4.1 6.5 0.5 C17 A:89R201 4.1 6.6 0.5 C18 A:89R201 4.2 6.8 0.5 ND1 A:HIS93 4.3 7.1 1.0 CG A:HIS93 4.3 5.8 1.0 C21 A:89R201 4.3 6.7 0.5 C18 A:89R201 4.3 6.8 0.5 C17 A:89R201 4.3 6.3 0.5 C22 A:89R201 4.3 6.5 0.5 C5 A:89R201 4.3 5.5 0.5 C14 A:89R201 4.3 6.5 0.5 C6 A:89R201 4.3 5.4 0.5 C13 A:89R201 4.3 6.3 0.5 C6 A:89R201 4.4 6.5 0.5 NE2 A:HIS64 4.4 7.2 1.0 C5 A:89R201 4.5 7.1 0.5 C21 A:89R201 4.6 5.6 0.5 C22 A:89R201 4.6 6.6 0.5 CG2 A:VAL68 4.8 7.0 1.0 CZ A:PHE43 4.9 8.7 1.0 CE1 A:HIS64 4.9 8.5 1.0

Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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:Fe201 b:4.8 occ:0.50 FE A:89R201 0.0 4.8 0.5 FE A:89R201 0.3 5.2 0.5 N A:89R201 1.7 5.8 0.5 N3 A:89R201 1.9 5.0 0.5 N A:89R201 2.0 5.4 0.5 N3 A:89R201 2.0 5.5 0.5 N2 A:89R201 2.0 5.3 0.5 N1 A:89R201 2.0 5.8 0.5 NE2 A:HIS93 2.2 6.7 1.0 O A:HOH322 2.2 7.4 1.0 N1 A:89R201 2.2 5.2 0.5 N2 A:89R201 2.3 5.4 0.5 C4 A:89R201 2.7 5.8 0.5 C23 A:89R201 2.8 5.6 0.5 C7 A:89R201 2.9 4.8 0.5 C20 A:89R201 3.0 5.7 0.5 CE1 A:HIS93 3.0 7.5 1.0 C4 A:89R201 3.0 5.7 0.5 C23 A:89R201 3.0 5.3 0.5 C19 A:89R201 3.0 6.0 0.5 C20 A:89R201 3.0 5.9 0.5 C7 A:89R201 3.1 6.3 0.5 C12 A:89R201 3.1 6.3 0.5 C16 A:89R201 3.1 6.2 0.5 C15 A:89R201 3.1 6.3 0.5 C A:89R201 3.1 6.7 0.5 C12 A:89R201 3.1 5.4 0.5 CD2 A:HIS93 3.2 5.8 1.0 C19 A:89R201 3.3 6.3 0.5 C15 A:89R201 3.3 5.2 0.5 C1 A:89R201 3.4 5.3 0.5 C16 A:89R201 3.4 5.3 0.5 C A:89R201 3.4 6.3 0.5 C3 A:89R201 3.4 5.1 0.5 C1 A:89R201 3.4 6.2 0.5 C2 A:89R201 3.5 5.6 0.5 C3 A:89R201 3.5 6.4 0.5 C2 A:89R201 3.8 6.3 0.5 C5 A:89R201 4.0 5.5 0.5 C6 A:89R201 4.0 5.4 0.5 C22 A:89R201 4.1 6.5 0.5 ND1 A:HIS93 4.2 7.1 1.0 C21 A:89R201 4.2 6.7 0.5 NE2 A:HIS64 4.3 7.2 1.0 C5 A:89R201 4.3 7.1 0.5 C22 A:89R201 4.3 6.6 0.5 C21 A:89R201 4.3 5.6 0.5 C6 A:89R201 4.3 6.5 0.5 C18 A:89R201 4.3 6.8 0.5 CG A:HIS93 4.3 5.8 1.0 C17 A:89R201 4.3 6.6 0.5 C13 A:89R201 4.3 6.5 0.5 C14 A:89R201 4.3 6.9 0.5 C13 A:89R201 4.4 6.3 0.5 C14 A:89R201 4.5 6.5 0.5 C18 A:89R201 4.6 6.8 0.5 C17 A:89R201 4.6 6.3 0.5 CE1 A:HIS64 4.7 8.5 1.0 CG2 A:VAL68 4.8 7.0 1.0 CD2 A:HIS97 5.0 7.8 1.0 CZ A:PHE43 5.0 8.7 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