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

Protein crystallography data

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

Other elements in 8wf5:

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

Fluorine Binding Sites:

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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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 8wf5

Go back to Fluorine Binding Sites List in 8wf5
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

Reference:

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
Page generated: Sat Aug 3 01:36:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy