Fluorine in PDB 5j7p: Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785

Enzymatic activity of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785

All present enzymatic activity of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785, PDB code: 5j7p was solved by M.J.Robertson, W.L.Jorgensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.82 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.629, 95.629, 103.497, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 20.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 (pdb code 5j7p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785, PDB code: 5j7p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5j7p

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Fluorine binding site 1 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:34.3
occ:0.90
 F19 A:6H1201 0.0 34.3 0.9
C18 A:6H1201 1.3 31.3 0.9
F20 A:6H1201 2.1 33.5 0.9
F21 A:6H1201 2.1 32.8 0.9
C5 A:6H1201 2.3 27.1 0.9
OD1 C:ASN97 2.6 34.6 1.0
C4 A:6H1201 2.7 25.9 0.9
CG C:ASN97 3.1 27.7 1.0
ND2 C:ASN97 3.2 31.1 1.0
C6 A:6H1201 3.5 25.6 0.9
CG1 A:VAL106 3.6 16.3 1.0
CB C:TYR95 3.8 15.6 1.0
C3 A:6H1201 4.1 24.9 0.9
N C:ASN97 4.2 17.5 1.0
CG C:TYR95 4.3 16.3 1.0
CB C:ASN97 4.3 22.5 1.0
CG2 A:VAL106 4.3 16.8 1.0
C C:ILE96 4.3 16.8 1.0
O C:HOH329 4.3 32.5 1.0
CA C:ASN97 4.4 19.2 1.0
O C:ILE96 4.4 16.9 1.0
CB A:VAL106 4.5 16.2 1.0
N C:ILE96 4.6 15.7 1.0
SD A:MET2 4.6 24.2 1.0
C7 A:6H1201 4.6 24.8 0.9
CE A:MET2 4.7 24.7 1.0
CD2 C:TYR95 4.8 16.7 1.0
C C:TYR95 4.8 15.6 1.0
CD1 C:TYR95 4.8 17.1 1.0
CA C:TYR95 4.8 15.3 1.0
C2 A:6H1201 4.8 24.0 0.9
CA A:VAL106 5.0 16.2 1.0

Fluorine binding site 2 out of 9 in 5j7p

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Fluorine binding site 2 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:33.5
occ:0.90
 F20 A:6H1201 0.0 33.5 0.9
C18 A:6H1201 1.3 31.3 0.9
F19 A:6H1201 2.1 34.3 0.9
F21 A:6H1201 2.1 32.8 0.9
C5 A:6H1201 2.3 27.1 0.9
ND2 C:ASN97 2.6 31.1 1.0
OD1 C:ASN97 2.7 34.6 1.0
C4 A:6H1201 3.0 25.9 0.9
CG C:ASN97 3.0 27.7 1.0
CB A:HIS62 3.1 16.9 1.0
C6 A:6H1201 3.2 25.6 0.9
CE A:MET2 3.3 24.7 1.0
CG A:HIS62 3.5 18.4 1.0
SD A:MET2 3.8 24.2 1.0
CB A:MET2 3.9 18.8 1.0
CD2 A:HIS62 3.9 19.4 1.0
C3 A:6H1201 4.2 24.9 0.9
ND1 A:HIS62 4.3 19.8 1.0
C7 A:6H1201 4.4 24.8 0.9
O C:HOH329 4.5 32.5 1.0
CA A:HIS62 4.5 15.9 1.0
CB C:ASN97 4.5 22.5 1.0
CG A:MET2 4.5 21.0 1.0
CG A:MET101 4.5 19.7 1.0
O A:HIS62 4.7 15.7 1.0
C A:HIS62 4.7 15.9 1.0
C2 A:6H1201 4.8 24.0 0.9
NE2 A:HIS62 4.9 20.0 1.0

Fluorine binding site 3 out of 9 in 5j7p

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Fluorine binding site 3 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:32.8
occ:0.90
 F21 A:6H1201 0.0 32.8 0.9
C18 A:6H1201 1.3 31.3 0.9
OD1 C:ASN97 2.1 34.6 1.0
F19 A:6H1201 2.1 34.3 0.9
F20 A:6H1201 2.1 33.5 0.9
C5 A:6H1201 2.3 27.1 0.9
C6 A:6H1201 2.7 25.6 0.9
CG2 A:VAL106 3.1 16.8 1.0
CG C:ASN97 3.2 27.7 1.0
CG A:MET101 3.3 19.7 1.0
C4 A:6H1201 3.5 25.9 0.9
ND2 C:ASN97 3.6 31.1 1.0
CG1 A:VAL106 3.8 16.3 1.0
CE A:MET101 3.9 21.6 1.0
CB A:MET101 4.0 18.7 1.0
C7 A:6H1201 4.0 24.8 0.9
CB A:VAL106 4.0 16.2 1.0
CB A:HIS62 4.1 16.9 1.0
SD A:MET101 4.1 21.5 1.0
CB C:ASN97 4.4 22.5 1.0
C3 A:6H1201 4.6 24.9 0.9
CG A:HIS62 4.7 18.4 1.0
CD2 A:HIS62 4.7 19.4 1.0
CA C:ASN97 4.7 19.2 1.0
CA A:VAL106 4.8 16.2 1.0
C2 A:6H1201 4.8 24.0 0.9

Fluorine binding site 4 out of 9 in 5j7p

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Fluorine binding site 4 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:34.0
occ:0.90
 F19 B:6H1201 0.0 34.0 0.9
C18 B:6H1201 1.3 31.2 0.9
F20 B:6H1201 2.1 33.1 0.9
F21 B:6H1201 2.1 36.6 0.9
C5 B:6H1201 2.3 26.7 0.9
ND2 A:ASN97 2.5 27.6 0.9
C6 B:6H1201 2.7 24.9 0.9
CG A:ASN97 3.2 25.7 0.9
OD1 A:ASN97 3.4 30.3 0.9
C4 B:6H1201 3.5 25.9 0.9
CB A:TYR95 3.6 14.7 1.0
CG1 B:VAL106 3.8 15.3 1.0
C7 B:6H1201 4.0 22.9 0.9
CG A:TYR95 4.1 15.0 1.0
SD B:MET2 4.2 24.4 1.0
CB A:ASN97 4.3 15.8 0.1
N A:ASN97 4.3 16.7 0.9
N A:ASN97 4.3 15.9 0.1
C A:ILE96 4.4 16.2 1.0
CB A:ASN97 4.4 21.2 0.9
CE B:MET2 4.4 25.2 1.0
O A:ILE96 4.4 17.3 1.0
N A:ILE96 4.5 14.6 1.0
CA A:ASN97 4.5 15.8 0.1
CA A:ASN97 4.5 18.3 0.9
CG2 B:VAL106 4.6 15.2 1.0
CD2 A:TYR95 4.6 15.7 1.0
C A:TYR95 4.6 14.3 1.0
CD1 A:TYR95 4.6 15.3 1.0
CA A:TYR95 4.6 14.1 1.0
C3 B:6H1201 4.7 24.6 0.9
CB B:VAL106 4.7 14.7 1.0
CB B:MET2 4.7 18.5 1.0
C2 B:6H1201 4.8 23.2 0.9
CA A:ILE96 5.0 15.3 1.0

Fluorine binding site 5 out of 9 in 5j7p

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Fluorine binding site 5 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:33.1
occ:0.90
 F20 B:6H1201 0.0 33.1 0.9
C18 B:6H1201 1.3 31.2 0.9
F19 B:6H1201 2.1 34.0 0.9
F21 B:6H1201 2.1 36.6 0.9
C5 B:6H1201 2.3 26.7 0.9
ND2 A:ASN97 2.6 27.6 0.9
OD1 A:ASN97 2.7 30.3 0.9
CG A:ASN97 3.0 25.7 0.9
CB B:HIS62 3.0 17.5 1.0
C6 B:6H1201 3.1 24.9 0.9
C4 B:6H1201 3.2 25.9 0.9
CE B:MET2 3.3 25.2 1.0
CG B:HIS62 3.5 18.9 1.0
SD B:MET2 3.7 24.4 1.0
CB B:MET2 3.8 18.5 1.0
CD2 B:HIS62 4.0 19.8 1.0
ND1 B:HIS62 4.3 20.7 1.0
C7 B:6H1201 4.3 22.9 0.9
CB A:ASN97 4.4 15.8 0.1
CG B:MET2 4.4 21.9 1.0
CA B:HIS62 4.4 16.0 1.0
C3 B:6H1201 4.4 24.6 0.9
CG B:MET101 4.5 18.6 1.0
CB A:ASN97 4.5 21.2 0.9
C B:HIS62 4.6 15.9 1.0
O B:HIS62 4.6 15.5 1.0
C2 B:6H1201 4.9 23.2 0.9
NE2 B:HIS62 4.9 21.6 1.0

Fluorine binding site 6 out of 9 in 5j7p

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Fluorine binding site 6 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:36.6
occ:0.90
 F21 B:6H1201 0.0 36.6 0.9
C18 B:6H1201 1.3 31.2 0.9
ND2 A:ASN97 2.0 27.6 0.9
F20 B:6H1201 2.1 33.1 0.9
F19 B:6H1201 2.1 34.0 0.9
C5 B:6H1201 2.3 26.7 0.9
C4 B:6H1201 2.7 25.9 0.9
CG2 B:VAL106 3.1 15.2 1.0
CG A:ASN97 3.2 25.7 0.9
CG B:MET101 3.5 18.6 1.0
C6 B:6H1201 3.5 24.9 0.9
CG1 B:VAL106 3.6 15.3 1.0
OD1 A:ASN97 3.6 30.3 0.9
CB B:VAL106 3.9 14.7 1.0
CE B:MET101 4.0 20.4 1.0
C3 B:6H1201 4.1 24.6 0.9
CB B:MET101 4.2 18.0 1.0
SD B:MET101 4.3 20.5 1.0
CB B:HIS62 4.3 17.5 1.0
CB A:ASN97 4.3 15.8 0.1
CB A:ASN97 4.4 21.2 0.9
CA B:VAL106 4.5 14.2 1.0
CA A:ASN97 4.6 15.8 0.1
CA A:ASN97 4.6 18.3 0.9
C7 B:6H1201 4.6 22.9 0.9
C2 B:6H1201 4.9 23.2 0.9
CG B:HIS62 4.9 18.9 1.0
O B:ASN105 4.9 13.4 1.0
O A:ILE96 4.9 17.3 1.0
CD2 B:HIS62 5.0 19.8 1.0

Fluorine binding site 7 out of 9 in 5j7p

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Fluorine binding site 7 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:35.1
occ:1.00
 F19 C:6H1201 0.0 35.1 1.0
C18 C:6H1201 1.3 32.9 1.0
F20 C:6H1201 2.1 33.9 1.0
F21 C:6H1201 2.1 34.3 1.0
C5 C:6H1201 2.3 28.5 1.0
C4 C:6H1201 2.8 28.0 1.0
ND2 B:ASN97 3.1 26.8 0.7
CG B:ASN97 3.4 25.5 0.7
OD1 B:ASN97 3.4 31.7 0.7
C6 C:6H1201 3.6 28.5 1.0
CB B:TYR95 3.8 16.8 1.0
CG1 C:VAL106 3.8 16.4 1.0
O B:HOH303 4.1 32.8 1.0
C3 C:6H1201 4.1 27.6 1.0
CB B:ASN97 4.1 16.4 0.3
N B:ASN97 4.2 17.7 0.7
N B:ASN97 4.2 16.3 0.3
CG B:TYR95 4.3 16.9 1.0
C B:ILE96 4.3 17.1 1.0
CA B:ASN97 4.4 16.2 0.3
SD C:MET2 4.4 24.3 1.0
CE C:MET2 4.4 24.3 1.0
O B:ILE96 4.4 17.0 1.0
CA B:ASN97 4.4 19.0 0.7
CB B:ASN97 4.5 22.1 0.7
N B:ILE96 4.5 15.8 1.0
C B:TYR95 4.7 16.0 1.0
C7 C:6H1201 4.7 27.7 1.0
CG2 C:VAL106 4.7 16.7 1.0
CD2 B:TYR95 4.7 18.1 1.0
CB C:VAL106 4.8 16.2 1.0
CA B:TYR95 4.8 15.6 1.0
CD1 B:TYR95 4.8 17.6 1.0
CB C:MET2 4.9 20.4 1.0
C2 C:6H1201 4.9 27.4 1.0
CA B:ILE96 4.9 16.7 1.0

Fluorine binding site 8 out of 9 in 5j7p

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Fluorine binding site 8 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:33.9
occ:1.00
 F20 C:6H1201 0.0 33.9 1.0
C18 C:6H1201 1.3 32.9 1.0
F21 C:6H1201 2.1 34.3 1.0
F19 C:6H1201 2.1 35.1 1.0
C5 C:6H1201 2.3 28.5 1.0
ND2 B:ASN97 2.4 26.8 0.7
CB C:HIS62 3.1 18.9 1.0
C4 C:6H1201 3.1 28.0 1.0
CE C:MET2 3.1 24.3 1.0
C6 C:6H1201 3.2 28.5 1.0
CG B:ASN97 3.2 25.5 0.7
OD1 B:ASN97 3.4 31.7 0.7
CG C:HIS62 3.5 19.5 1.0
SD C:MET2 3.8 24.3 1.0
CD2 C:HIS62 3.9 20.7 1.0
CB C:MET2 4.0 20.4 1.0
ND1 C:HIS62 4.2 21.2 1.0
CB B:ASN97 4.3 16.4 0.3
C3 C:6H1201 4.4 27.6 1.0
O B:HOH303 4.4 32.8 1.0
C7 C:6H1201 4.4 27.7 1.0
ND2 B:ASN97 4.5 16.8 0.3
CA C:HIS62 4.5 18.2 1.0
CG C:MET2 4.6 22.5 1.0
CB B:ASN97 4.6 22.1 0.7
CG C:MET101 4.7 22.9 1.0
CG B:ASN97 4.7 16.6 0.3
NE2 C:HIS62 4.8 21.2 1.0
C C:HIS62 4.8 18.7 1.0
O C:HIS62 4.8 18.4 1.0
CE1 C:HIS62 4.9 21.3 1.0
C2 C:6H1201 4.9 27.4 1.0

Fluorine binding site 9 out of 9 in 5j7p

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Fluorine binding site 9 out of 9 in the Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Macrophage Migration Inhibitory Factor Bound to Covalent Inhibitor RDR03785 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:34.3
occ:1.00
 F21 C:6H1201 0.0 34.3 1.0
C18 C:6H1201 1.3 32.9 1.0
F20 C:6H1201 2.1 33.9 1.0
F19 C:6H1201 2.1 35.1 1.0
C5 C:6H1201 2.3 28.5 1.0
ND2 B:ASN97 2.7 26.8 0.7
C6 C:6H1201 2.8 28.5 1.0
CG2 C:VAL106 3.3 16.7 1.0
C4 C:6H1201 3.6 28.0 1.0
CG B:ASN97 3.6 25.5 0.7
CG1 C:VAL106 3.6 16.4 1.0
CG C:MET101 3.7 22.9 1.0
CE C:MET101 3.9 25.0 1.0
CB C:VAL106 4.0 16.2 1.0
CB B:ASN97 4.1 16.4 0.3
C7 C:6H1201 4.1 27.7 1.0
OD1 B:ASN97 4.2 31.7 0.7
CB C:HIS62 4.3 18.9 1.0
SD C:MET101 4.3 25.8 1.0
CB C:MET101 4.3 21.4 1.0
CB B:ASN97 4.4 22.1 0.7
CA B:ASN97 4.4 16.2 0.3
CG B:ASN97 4.4 16.6 0.3
CA B:ASN97 4.5 19.0 0.7
CA C:VAL106 4.5 15.8 1.0
ND2 B:ASN97 4.6 16.8 0.3
C3 C:6H1201 4.7 27.6 1.0
CG C:HIS62 4.7 19.5 1.0
CD2 C:HIS62 4.8 20.7 1.0
O C:ASN105 4.9 16.5 1.0
N B:ASN97 4.9 17.7 0.7
N B:ASN97 4.9 16.3 0.3
O B:ILE96 4.9 17.0 1.0
C2 C:6H1201 4.9 27.4 1.0

Reference:

J.A.Cisneros, M.J.Robertson, M.Valhondo, W.L.Jorgensen. Irregularities in Enzyme Assays: the Case of Macrophage Migration Inhibitory Factor. Bioorg.Med.Chem.Lett. V. 26 2764 2016.
ISSN: ESSN 1464-3405
PubMed: 27156768
DOI: 10.1016/J.BMCL.2016.04.074
Page generated: Sun Dec 13 12:25:12 2020

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