Atomistry » Fluorine » PDB 5ifd-5j82 » 5j7p
Atomistry »
  Fluorine »
    PDB 5ifd-5j82 »
      5j7p »

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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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

Go back to Fluorine Binding Sites List in 5j7p
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: Thu Aug 1 10:26:59 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