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

Protein crystallography data

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

Other elements in 5xl0:

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

Fluorine Binding Sites:

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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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 5xl0

Go back to Fluorine Binding Sites List in 5xl0
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

Reference:

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
Page generated: Sun Dec 13 12:42:43 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy