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Chlorine in PDB 3ijj: Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)

Enzymatic activity of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)

All present enzymatic activity of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer):
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer), PDB code: 3ijj was solved by G.V.Crichlow, Y.Cho, E.J.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.61 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.236, 67.908, 87.329, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) (pdb code 3ijj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer), PDB code: 3ijj:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3ijj

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Chlorine binding site 1 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:23.8
occ:1.00
 O A:HOH648 2.9 45.9 1.0
NE2 A:GLN71 3.3 15.7 1.0
N A:GLN71 3.4 11.6 1.0
N A:ALA70 3.5 12.6 1.0
C A:GLY68 3.5 12.0 1.0
CA A:GLY68 3.6 13.7 1.0
CG A:GLN71 3.6 15.2 1.0
N A:GLY69 3.6 12.8 1.0
CB A:GLN71 3.9 11.5 1.0
CD A:GLN71 4.0 14.9 1.0
CB A:ALA70 4.0 13.9 1.0
O A:GLY68 4.0 12.3 1.0
CA A:ALA70 4.1 13.4 1.0
C A:ALA70 4.2 12.1 1.0
N A:GLY68 4.3 11.9 1.0
CA A:GLN71 4.3 11.3 1.0
C A:GLY69 4.3 12.5 1.0
O A:HOH427 4.4 26.1 1.0
CA A:GLY69 4.4 13.0 1.0
C A:ILE67 4.9 11.2 1.0
O A:ILE67 5.0 12.7 1.0

Chlorine binding site 2 out of 8 in 3ijj

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Chlorine binding site 2 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl805

b:13.3
occ:1.00
 O C:HOH215 3.0 12.8 1.0
N A:ASN102 3.2 9.0 1.0
O A:HOH480 3.2 29.5 1.0
ND2 A:ASN105 3.2 10.9 1.0
CG A:ASN102 3.8 17.7 1.0
CB A:ASN102 3.8 11.7 1.0
CA A:MET101 3.8 8.8 1.0
O A:HOH216 3.9 13.1 0.5
CB A:ASN105 3.9 9.0 1.0
C A:MET101 4.0 9.1 1.0
OD1 A:ASN102 4.1 18.2 1.0
CA A:ASN102 4.1 9.7 1.0
O A:HOH300 4.1 19.4 1.0
CG A:ASN105 4.1 10.3 1.0
ND2 A:ASN102 4.1 19.2 1.0
CE A:MET101 4.1 14.2 1.0
O A:ASP100 4.2 10.4 1.0
SD A:MET101 4.3 14.2 1.0
O A:HOH216 4.5 17.1 0.5
CB A:MET101 4.6 10.0 1.0
O C:HOH268 4.6 17.6 1.0
O A:ASN102 4.7 9.3 1.0
O A:HOH488 4.7 30.1 1.0
N A:MET101 4.9 8.5 1.0
C A:ASN102 4.9 9.2 1.0
O C:TYR98 4.9 9.4 1.0
C A:ASP100 5.0 9.2 1.0

Chlorine binding site 3 out of 8 in 3ijj

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Chlorine binding site 3 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl807

b:78.0
occ:1.00
 NE A:ARG73 3.0 21.5 1.0
O A:HOH265 3.2 17.4 1.0
NH2 A:ARG73 3.4 22.9 1.0
O B:HOH501 3.6 31.7 1.0
CZ A:ARG73 3.7 23.0 1.0
CB A:ALA70 3.9 13.9 1.0
CD A:ARG73 4.0 17.5 1.0
CA A:ALA70 4.0 13.4 1.0
O A:ALA70 4.7 12.2 1.0
CB A:ARG73 4.7 13.2 1.0
O A:HOH669 4.8 50.8 1.0
C A:ALA70 4.9 12.1 1.0
CG A:ARG73 4.9 14.1 1.0
NH1 A:ARG73 5.0 22.4 1.0

Chlorine binding site 4 out of 8 in 3ijj

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Chlorine binding site 4 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl802

b:30.7
occ:1.00
 O B:HOH598 2.9 40.8 1.0
NE2 B:GLN71 3.2 20.4 1.0
N B:GLN71 3.4 16.9 1.0
N B:ALA70 3.5 20.5 1.0
C B:GLY68 3.5 14.9 1.0
CA B:GLY68 3.6 16.9 1.0
N B:GLY69 3.6 18.1 1.0
CG B:GLN71 3.7 20.3 1.0
CB B:GLN71 3.9 14.8 1.0
CD B:GLN71 3.9 20.3 1.0
CB B:ALA70 4.0 19.5 1.0
O B:GLY68 4.0 15.9 1.0
CA B:ALA70 4.1 19.5 1.0
C B:ALA70 4.2 17.4 1.0
N B:GLY68 4.3 14.3 1.0
CA B:GLN71 4.3 15.8 1.0
C B:GLY69 4.3 20.3 1.0
CA B:GLY69 4.4 20.7 1.0
O B:HOH559 4.5 37.2 1.0
C B:ILE67 4.9 16.3 1.0
O B:ILE67 5.0 16.6 1.0

Chlorine binding site 5 out of 8 in 3ijj

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Chlorine binding site 5 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl804

b:12.9
occ:1.00
 O A:HOH204 3.1 11.0 1.0
O B:HOH617 3.2 42.9 1.0
N B:ASN102 3.2 9.9 1.0
ND2 B:ASN105 3.2 11.4 1.0
CB B:ASN102 3.8 11.7 1.0
CG B:ASN102 3.8 14.6 1.0
CA B:MET101 3.9 9.8 1.0
CB B:ASN105 3.9 9.3 1.0
O B:HOH347 3.9 21.9 1.0
C B:MET101 4.0 9.6 1.0
CE B:MET101 4.0 15.4 1.0
CG B:ASN105 4.1 9.6 1.0
CA B:ASN102 4.1 10.1 1.0
ND2 B:ASN102 4.1 18.5 1.0
O B:HOH316 4.1 20.1 1.0
OD1 B:ASN102 4.2 18.0 1.0
O B:ASP100 4.3 11.2 1.0
SD B:MET101 4.3 14.7 1.0
O B:HOH326 4.6 20.6 1.0
CB B:MET101 4.6 10.7 1.0
O B:ASN102 4.6 9.7 1.0
O A:HOH251 4.7 16.5 1.0
O B:HOH453 4.7 28.0 1.0
C B:ASN102 4.9 9.0 1.0
O B:HOH484 4.9 29.7 1.0
N B:MET101 4.9 9.8 1.0
O A:TYR98 5.0 8.5 1.0

Chlorine binding site 6 out of 8 in 3ijj

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Chlorine binding site 6 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl803

b:17.7
occ:1.00
 NE2 C:GLN71 3.3 15.1 1.0
N C:GLN71 3.3 11.8 1.0
N C:ALA70 3.4 13.4 1.0
C C:GLY68 3.5 11.6 1.0
CA C:GLY68 3.6 13.6 1.0
CG C:GLN71 3.6 13.6 1.0
N C:GLY69 3.6 13.0 1.0
O C:HOH519 3.7 32.9 1.0
CB C:GLN71 3.9 11.6 1.0
CB C:ALA70 3.9 13.8 1.0
CD C:GLN71 3.9 13.3 1.0
CA C:ALA70 4.0 13.8 1.0
O C:GLY68 4.0 11.7 1.0
C C:ALA70 4.1 13.4 1.0
CA C:GLN71 4.2 10.7 1.0
C C:GLY69 4.3 12.6 1.0
N C:GLY68 4.3 12.0 1.0
O C:HOH500 4.3 31.6 1.0
CA C:GLY69 4.4 14.1 1.0
O C:HOH582 4.8 39.6 1.0
C C:ILE67 4.9 12.2 1.0
O C:ILE67 5.0 13.6 1.0

Chlorine binding site 7 out of 8 in 3ijj

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Chlorine binding site 7 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl806

b:15.2
occ:1.00
 O B:HOH218 3.0 13.5 1.0
N C:ASN102 3.1 11.9 1.0
O C:HOH535 3.2 35.5 1.0
ND2 C:ASN105 3.2 13.8 1.0
CB C:ASN102 3.7 16.0 1.0
CG C:ASN102 3.8 21.8 1.0
CA C:MET101 3.8 10.1 1.0
O C:HOH258 3.9 16.9 0.5
ND2 C:ASN102 3.9 21.8 1.0
CB C:ASN105 4.0 11.8 1.0
C C:MET101 4.0 10.7 1.0
CA C:ASN102 4.0 13.0 1.0
O C:HOH315 4.0 20.0 1.0
CE C:MET101 4.1 16.5 1.0
CG C:ASN105 4.1 13.2 1.0
O C:ASP100 4.3 12.0 1.0
SD C:MET101 4.3 15.9 1.0
OD1 C:ASN102 4.3 23.5 1.0
O C:HOH258 4.5 17.9 0.5
CB C:MET101 4.5 10.8 1.0
O C:HOH565 4.6 38.0 1.0
O C:ASN102 4.6 12.7 1.0
O B:HOH264 4.7 17.4 1.0
O B:HOH495 4.8 31.2 1.0
C C:ASN102 4.8 12.9 1.0
N C:MET101 4.9 10.4 1.0
O B:TYR98 4.9 10.5 1.0

Chlorine binding site 8 out of 8 in 3ijj

Go back to Chlorine Binding Sites List in 3ijj
Chlorine binding site 8 out of 8 in the Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ternary Complex of Macrophage Migration Inhibitory Factor (Mif) Bound Both to 4-Hydroxyphenylpyruvate and to the Allosteric Inhibitor AV1013 (R-Stereoisomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl808

b:58.8
occ:1.00
 NE C:ARG73 2.9 24.7 1.0
O C:HOH277 3.2 17.9 1.0
NH2 C:ARG73 3.4 26.9 1.0
O A:HOH659 3.5 47.4 1.0
CZ C:ARG73 3.6 27.8 1.0
CB C:ALA70 3.9 13.8 1.0
CD C:ARG73 3.9 19.2 1.0
CA C:ALA70 4.0 13.8 1.0
CB C:ARG73 4.6 11.0 1.0
O C:ALA70 4.7 12.5 1.0
CG C:ARG73 4.8 13.4 1.0
C C:ALA70 4.9 13.4 1.0
NH1 C:ARG73 4.9 27.3 1.0
N C:ALA70 5.0 13.4 1.0

Reference:

Y.Cho, G.V.Crichlow, J.J.Vermeire, L.Leng, X.Du, M.E.Hodsdon, R.Bucala, M.Cappello, M.Gross, F.Gaeta, K.Johnson, E.J.Lolis. Allosteric Inhibition of Macrophage Migration Inhibitory Factor Revealed By Ibudilast. Proc.Natl.Acad.Sci.Usa V. 107 11313 2010.
ISSN: ISSN 0027-8424
PubMed: 20534506
DOI: 10.1073/PNAS.1002716107
Page generated: Sat Jul 20 21:36:34 2024

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