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Fluorine in PDB 4k9g: 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound

Enzymatic activity of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound

All present enzymatic activity of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound, PDB code: 4k9g was solved by G.V.Crichlow, Y.Al-Abed, E.J.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.76 / 1.55
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.458, 95.458, 104.552, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 22

Other elements in 4k9g:

The structure of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound (pdb code 4k9g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound, PDB code: 4k9g:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4k9g

Go back to Fluorine Binding Sites List in 4k9g
Fluorine binding site 1 out of 4 in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:33.4
occ:0.88
 F2 A:1Q2201 0.0 33.4 0.9
F2 A:1Q1202 1.0 37.3 0.1
C2 A:1Q2201 1.3 26.3 0.9
C2 A:1Q1202 2.0 38.4 0.1
O1 A:1Q1202 2.3 39.4 0.1
C3 A:1Q2201 2.4 26.2 0.9
C1 A:1Q2201 2.4 25.7 0.9
C1 A:1Q1202 2.4 38.6 0.1
O1 A:1Q2201 2.7 30.0 0.9
C3 A:1Q1202 3.2 38.5 0.1
N A:SER63 3.3 19.6 1.0
CB A:HIS62 3.4 18.6 1.0
C A:HIS62 3.4 19.2 1.0
SD A:MET101 3.5 28.6 1.0
C4 A:1Q2201 3.6 30.0 0.9
CG A:MET101 3.6 23.7 1.0
C6 A:1Q2201 3.6 27.7 0.9
CA A:SER63 3.7 20.3 1.0
O A:HIS62 3.7 19.4 1.0
CB A:MET101 3.8 23.2 1.0
C A:SER63 3.8 20.6 1.0
CG2 A:VAL106 3.8 18.6 1.0
C6 A:1Q1202 3.8 38.7 0.1
OD1 B:ASN97 3.9 27.8 1.0
CA A:HIS62 4.0 18.3 1.0
O A:SER63 4.1 20.9 1.0
C5 A:1Q2201 4.1 29.0 0.9
N A:ILE64 4.2 21.3 1.0
C4 A:1Q1202 4.4 39.0 0.1
CG1 A:ILE64 4.5 21.9 1.0
CG A:HIS62 4.5 19.6 1.0
C5 A:1Q1202 4.6 38.9 0.1
CG1 A:VAL106 4.7 18.8 1.0
C7 A:1Q2201 4.8 34.1 0.9
CB A:VAL106 4.9 18.5 1.0
CG B:ASN97 4.9 21.0 1.0
CE A:MET101 4.9 24.2 1.0
N8 A:1Q2201 4.9 33.3 0.9
CD2 A:HIS62 5.0 18.9 1.0
CA A:MET101 5.0 22.7 1.0

Fluorine binding site 2 out of 4 in 4k9g

Go back to Fluorine Binding Sites List in 4k9g
Fluorine binding site 2 out of 4 in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:37.3
occ:0.12
 F2 A:1Q1202 0.0 37.3 0.1
F2 A:1Q2201 1.0 33.4 0.9
C2 A:1Q2201 1.3 26.3 0.9
C2 A:1Q1202 1.3 38.4 0.1
C3 A:1Q2201 1.6 26.2 0.9
C3 A:1Q1202 2.4 38.5 0.1
C1 A:1Q1202 2.4 38.6 0.1
C1 A:1Q2201 2.6 25.7 0.9
O1 A:1Q1202 2.8 39.4 0.1
C4 A:1Q2201 2.9 30.0 0.9
C A:SER63 3.2 20.6 1.0
CA A:SER63 3.2 20.3 1.0
N A:ILE64 3.3 21.3 1.0
N A:SER63 3.3 19.6 1.0
O1 A:1Q2201 3.4 30.0 0.9
C A:HIS62 3.6 19.2 1.0
C4 A:1Q1202 3.6 39.0 0.1
C6 A:1Q2201 3.6 27.7 0.9
C6 A:1Q1202 3.6 38.7 0.1
CG1 A:ILE64 3.6 21.9 1.0
O A:SER63 3.7 20.9 1.0
C5 A:1Q2201 3.7 29.0 0.9
O A:HIS62 3.8 19.4 1.0
CG2 A:VAL106 3.8 18.6 1.0
C7 A:1Q2201 3.9 34.1 0.9
N8 A:1Q2201 4.0 33.3 0.9
CB A:MET101 4.0 23.2 1.0
C5 A:1Q1202 4.1 38.9 0.1
CB A:HIS62 4.2 18.6 1.0
CG A:MET101 4.2 23.7 1.0
CA A:ILE64 4.2 22.1 1.0
SD A:MET101 4.3 28.6 1.0
CD1 A:ILE64 4.5 23.7 1.0
CB A:ILE64 4.5 22.1 1.0
CA A:HIS62 4.5 18.3 1.0
CG1 A:VAL106 4.6 18.8 1.0
CB A:SER63 4.7 21.4 1.0
C7 A:1Q1202 4.7 38.9 0.1
OD1 B:ASN97 4.8 27.8 1.0
CB A:VAL106 4.8 18.5 1.0

Fluorine binding site 3 out of 4 in 4k9g

Go back to Fluorine Binding Sites List in 4k9g
Fluorine binding site 3 out of 4 in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:34.6
occ:1.00
 F2 B:1Q2201 0.0 34.6 1.0
C2 B:1Q2201 1.3 31.0 1.0
C1 B:1Q2201 2.3 30.6 1.0
C3 B:1Q2201 2.4 31.4 1.0
O1 B:1Q2201 2.7 35.2 1.0
CB B:HIS62 3.2 17.7 1.0
SD B:MET101 3.3 36.2 1.0
OD1 C:ASN97 3.4 32.7 1.0
C6 B:1Q2201 3.6 31.4 1.0
C4 B:1Q2201 3.6 32.8 1.0
C B:HIS62 3.7 19.4 1.0
CG2 B:VAL106 3.8 20.4 1.0
CG B:MET101 3.8 27.5 1.0
N B:SER63 3.8 19.3 1.0
O B:HIS62 3.8 19.3 1.0
CB B:MET101 3.9 25.0 1.0
CA B:HIS62 4.0 17.8 1.0
C5 B:1Q2201 4.1 31.9 1.0
CA B:SER63 4.2 19.4 1.0
CG B:HIS62 4.3 19.6 1.0
CG C:ASN97 4.3 25.5 1.0
C B:SER63 4.4 20.6 1.0
CE B:MET101 4.6 30.5 1.0
ND2 C:ASN97 4.6 22.5 1.0
CG1 B:VAL106 4.6 21.0 1.0
O B:SER63 4.7 21.7 1.0
CD2 B:HIS62 4.7 20.6 1.0
N B:ILE64 4.7 21.3 1.0
C7 B:1Q2201 4.8 35.2 1.0
CB B:VAL106 4.8 20.8 1.0
CG1 B:ILE64 4.9 23.4 1.0

Fluorine binding site 4 out of 4 in 4k9g

Go back to Fluorine Binding Sites List in 4k9g
Fluorine binding site 4 out of 4 in the 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 1.55 A Crystal Structure of Macrophage Migration Inhibitory Factor Bound to Iso-66 and A Related Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:39.2
occ:1.00
 F2 C:1Q2201 0.0 39.2 1.0
C2 C:1Q2201 1.3 38.8 1.0
C3 C:1Q2201 2.4 39.2 1.0
C1 C:1Q2201 2.4 37.8 1.0
O1 C:1Q2201 2.7 39.0 1.0
SD C:MET101 3.3 28.3 0.6
CB C:HIS62 3.3 22.9 1.0
CG C:MET101 3.4 27.2 1.0
OD1 A:ASN97 3.5 30.3 1.0
C C:HIS62 3.6 23.7 1.0
N C:SER63 3.6 24.0 1.0
CG2 C:VAL106 3.6 21.5 1.0
C4 C:1Q2201 3.6 40.7 1.0
C6 C:1Q2201 3.6 38.6 1.0
CB C:MET101 3.8 26.4 1.0
O C:HIS62 3.9 24.4 1.0
CA C:HIS62 4.0 22.9 1.0
CA C:SER63 4.0 26.1 1.0
C5 C:1Q2201 4.1 39.0 1.0
C C:SER63 4.1 26.9 1.0
CG1 C:VAL106 4.4 22.4 1.0
CG C:HIS62 4.4 23.6 1.0
O C:SER63 4.4 27.1 1.0
CG A:ASN97 4.5 23.6 1.0
CE C:MET101 4.5 26.4 0.6
N C:ILE64 4.5 27.9 1.0
SD C:MET101 4.6 27.2 0.4
CE C:MET101 4.6 23.3 0.4
CB C:VAL106 4.6 21.4 1.0
CG1 C:ILE64 4.7 27.8 1.0
CD2 C:HIS62 4.7 24.0 1.0
C7 C:1Q2201 4.8 43.8 1.0
ND2 A:ASN97 4.9 24.8 1.0

Reference:

K.Ioannou, K.F.Cheng, G.V.Crichlow, A.I.Birmpilis, E.J.Lolis, O.E.Tsitsilonis, Y.Al-Abed. Iso-66, A Novel Inhibitor of Macrophage Migration, Shows Efficacy in Melanoma and Colon Cancer Models. Int J Oncol. V. 45 1457 2014.
ISSN: ISSN 1019-6439
PubMed: 25050663
DOI: 10.3892/IJO.2014.2551
Page generated: Sun Dec 13 12:06:00 2020

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