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Chlorine in PDB 3ijg: Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013

Enzymatic activity of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013

All present enzymatic activity of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013, PDB code: 3ijg 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) 100.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.958, 68.035, 87.279, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 20.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 (pdb code 3ijg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013, PDB code: 3ijg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 3ijg

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Chlorine binding site 1 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:19.6
occ:1.00
 O C:HOH213 3.0 18.2 1.0
N A:ASN102 3.2 17.2 1.0
ND2 A:ASN105 3.2 18.8 1.0
CG A:ASN102 3.7 22.8 1.0
O A:HOH328 3.8 27.0 1.0
CA A:MET101 3.8 16.3 1.0
ND2 A:ASN102 3.8 26.3 1.0
CB A:ASN102 3.9 19.6 1.0
CB A:ASN105 3.9 16.9 1.0
C A:MET101 4.0 16.5 1.0
CG A:ASN105 4.0 18.3 1.0
O A:HOH261 4.1 23.0 1.0
CA A:ASN102 4.1 17.9 1.0
CE A:MET101 4.1 17.2 1.0
O A:ASP100 4.2 15.5 1.0
OD1 A:ASN102 4.2 23.7 1.0
SD A:MET101 4.3 20.4 1.0
CB A:MET101 4.5 17.6 1.0
O C:HOH279 4.6 24.0 1.0
O A:HOH445 4.7 34.6 1.0
O A:ASN102 4.7 18.1 1.0
O A:HOH469 4.9 36.4 1.0
N A:MET101 4.9 15.3 1.0
C A:ASP100 4.9 15.5 1.0
C A:ASN102 5.0 18.0 1.0
O C:TYR98 5.0 17.1 1.0

Chlorine binding site 2 out of 10 in 3ijg

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Chlorine binding site 2 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:30.4
occ:1.00
 NE2 A:GLN71 3.2 22.3 1.0
CG A:GLN71 3.4 21.7 1.0
O A:HOH557 3.4 44.6 1.0
N A:GLN71 3.4 17.5 1.0
N A:ALA70 3.5 19.4 1.0
CA A:GLY68 3.5 19.3 1.0
C A:GLY68 3.6 19.8 1.0
N A:GLY69 3.7 19.6 1.0
CD A:GLN71 3.8 21.4 1.0
CB A:GLN71 3.9 18.9 1.0
CB A:ALA70 4.0 21.9 1.0
O A:GLY68 4.1 19.0 1.0
CA A:ALA70 4.1 18.9 1.0
C A:ALA70 4.3 18.2 1.0
N A:GLY68 4.3 19.6 1.0
CA A:GLN71 4.3 17.9 1.0
C A:GLY69 4.4 19.7 1.0
CA A:GLY69 4.5 20.2 1.0
O A:HOH367 4.6 29.3 1.0
C A:ILE67 4.9 19.3 1.0
O A:ILE67 4.9 20.0 1.0

Chlorine binding site 3 out of 10 in 3ijg

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Chlorine binding site 3 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl607

b:34.8
occ:1.00
 N A:SER53 3.1 23.9 1.0
O A:HOH546 3.4 43.4 1.0
OG A:SER53 3.4 24.0 0.6
CA A:SER52 3.6 25.0 1.0
OE1 A:GLU54 3.7 39.3 1.0
CB A:SER52 3.7 26.9 1.0
C A:SER52 3.9 24.0 1.0
CA A:SER53 4.1 22.9 1.0
CB A:SER53 4.3 24.1 1.0
C A:SER53 4.6 23.7 1.0
N A:GLU54 4.6 22.9 1.0
CD A:GLU54 4.7 35.8 1.0
O A:GLY51 4.8 29.9 1.0
OG A:SER53 4.8 23.4 0.4
OG A:SER52 4.9 29.7 1.0
CG A:GLU54 4.9 32.0 1.0
N A:SER52 5.0 25.0 1.0

Chlorine binding site 4 out of 10 in 3ijg

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Chlorine binding site 4 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:26.0
occ:1.00
 O A:HOH388 3.0 30.3 1.0
N A:LEU19 3.2 16.0 1.0
N A:PHE18 3.5 18.0 1.0
CG A:LEU19 3.6 21.2 1.0
CB A:LEU19 3.8 17.4 1.0
CB A:PHE18 3.9 18.0 1.0
CA A:PHE18 4.0 18.2 1.0
C A:PHE18 4.1 17.9 1.0
CA A:LEU19 4.1 17.8 1.0
CD1 A:LEU19 4.1 20.9 1.0
N A:GLY17 4.2 20.4 1.0
O A:PRO15 4.2 20.8 1.0
C A:GLY17 4.3 19.2 1.0
CD1 C:LEU46 4.4 21.6 1.0
CA A:GLY17 4.6 19.1 1.0
CD2 C:LEU46 4.6 20.5 1.0
CG C:LEU46 4.8 18.5 1.0
CD2 A:LEU19 4.8 22.3 1.0
C A:ASP16 4.9 20.2 1.0
NH2 A:ARG11 4.9 36.0 1.0
CG1 A:VAL14 4.9 17.7 1.0

Chlorine binding site 5 out of 10 in 3ijg

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Chlorine binding site 5 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:48.4
occ:1.00
 NE A:ARG73 3.2 27.2 1.0
O A:HOH322 3.2 26.3 1.0
NH2 A:ARG73 3.7 29.6 1.0
CZ A:ARG73 3.9 29.5 1.0
CB A:ALA70 4.0 21.9 1.0
CA A:ALA70 4.2 18.9 1.0
CD A:ARG73 4.2 23.5 1.0
O A:ALA70 4.8 17.8 1.0
CB A:ARG73 4.9 18.6 1.0

Chlorine binding site 6 out of 10 in 3ijg

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Chlorine binding site 6 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:19.1
occ:1.00
 O A:HOH210 3.2 17.6 1.0
N B:ASN102 3.2 17.8 1.0
ND2 B:ASN105 3.2 18.8 1.0
CG B:ASN102 3.7 21.4 1.0
CB B:ASN102 3.8 20.2 1.0
ND2 B:ASN102 3.8 25.6 1.0
CA B:MET101 3.9 17.3 1.0
CB B:ASN105 3.9 15.6 1.0
C B:MET101 4.0 16.5 1.0
CG B:ASN105 4.1 17.6 1.0
CA B:ASN102 4.1 18.1 1.0
OD1 B:ASN102 4.1 23.4 1.0
O B:HOH233 4.1 20.0 0.5
CE B:MET101 4.1 18.4 1.0
O A:HOH362 4.1 28.8 1.0
O B:ASP100 4.3 18.9 1.0
SD B:MET101 4.3 20.5 1.0
O B:HOH233 4.5 25.2 0.5
CB B:MET101 4.5 16.8 1.0
O B:ASN102 4.6 16.6 1.0
O A:HOH401 4.6 31.1 1.0
O A:HOH267 4.8 23.3 1.0
C B:ASN102 4.9 18.0 1.0
N B:MET101 4.9 16.5 1.0
O A:TYR98 5.0 14.3 1.0

Chlorine binding site 7 out of 10 in 3ijg

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Chlorine binding site 7 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl605

b:32.3
occ:1.00
 NE2 B:GLN71 3.3 24.2 1.0
CG B:GLN71 3.4 23.4 1.0
N B:GLN71 3.4 21.0 1.0
N B:ALA70 3.5 23.2 1.0
CA B:GLY68 3.5 20.8 1.0
C B:GLY68 3.6 21.9 1.0
N B:GLY69 3.7 23.8 1.0
CB B:ALA70 3.8 23.1 1.0
CD B:GLN71 3.9 22.7 1.0
CB B:GLN71 3.9 20.9 1.0
CA B:ALA70 4.0 22.1 1.0
O B:GLY68 4.1 21.9 1.0
C B:ALA70 4.2 21.3 1.0
N B:GLY68 4.3 19.2 1.0
C B:GLY69 4.3 23.2 1.0
CA B:GLN71 4.3 20.3 1.0
CA B:GLY69 4.5 23.2 1.0
O B:HOH513 4.5 40.1 1.0
O B:HOH581 4.6 48.8 1.0
C B:ILE67 4.9 20.1 1.0
O B:ILE67 4.9 21.4 1.0

Chlorine binding site 8 out of 10 in 3ijg

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Chlorine binding site 8 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl608

b:60.6
occ:1.00
 NE B:ARG73 3.0 29.1 1.0
O B:HOH383 3.3 30.1 1.0
NH2 B:ARG73 3.5 31.6 1.0
CZ B:ARG73 3.7 30.6 1.0
CD B:ARG73 4.0 27.5 1.0
CA B:ALA70 4.0 22.1 1.0
CB B:ALA70 4.1 23.1 1.0
O B:ALA70 4.6 21.2 1.0
CB B:ARG73 4.7 22.5 1.0
C B:ALA70 4.8 21.3 1.0
CG B:ARG73 4.9 26.2 1.0
N B:ALA70 5.0 23.2 1.0
NH1 B:ARG73 5.0 30.9 1.0

Chlorine binding site 9 out of 10 in 3ijg

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Chlorine binding site 9 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl603

b:23.0
occ:1.00
 O B:HOH229 3.1 19.8 1.0
N C:ASN102 3.2 20.6 1.0
ND2 C:ASN105 3.2 21.5 1.0
CB C:ASN102 3.8 23.1 1.0
CG C:ASN102 3.8 26.8 1.0
O C:HOH219 3.8 18.7 0.5
CA C:MET101 3.8 18.4 1.0
ND2 C:ASN102 3.9 30.1 1.0
C C:MET101 4.0 18.6 1.0
CB C:ASN105 4.0 19.4 1.0
CE C:MET101 4.0 20.0 1.0
CA C:ASN102 4.1 20.2 1.0
O A:HOH332 4.1 27.2 1.0
CG C:ASN105 4.1 21.1 1.0
O C:ASP100 4.2 19.2 1.0
O C:HOH219 4.3 19.6 0.5
SD C:MET101 4.3 21.6 1.0
OD1 C:ASN102 4.3 28.7 1.0
CB C:MET101 4.6 19.4 1.0
O B:HOH201 4.7 10.9 0.5
O C:ASN102 4.7 19.1 1.0
O C:HOH524 4.7 41.0 1.0
N C:MET101 4.9 18.2 1.0
C C:ASN102 4.9 19.7 1.0
C C:ASP100 5.0 17.6 1.0
O B:TYR98 5.0 16.5 1.0

Chlorine binding site 10 out of 10 in 3ijg

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Chlorine binding site 10 out of 10 in the Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Macrophage Migration Inhibitory Factor (Mif) Bound to the (R)- Stereoisomer of AV1013 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl606

b:28.2
occ:1.00
 NE2 C:GLN71 3.3 20.6 1.0
N C:GLN71 3.4 18.1 1.0
CG C:GLN71 3.4 20.2 1.0
N C:ALA70 3.4 18.8 1.0
C C:GLY68 3.5 20.2 1.0
CA C:GLY68 3.5 19.9 1.0
O C:HOH489 3.6 38.2 1.0
N C:GLY69 3.6 20.2 1.0
CD C:GLN71 3.9 19.6 1.0
CB C:ALA70 3.9 19.5 1.0
CB C:GLN71 4.0 18.7 1.0
CA C:ALA70 4.0 19.3 1.0
O C:GLY68 4.0 19.6 1.0
C C:ALA70 4.2 18.4 1.0
O C:HOH473 4.2 36.7 1.0
C C:GLY69 4.2 20.1 1.0
N C:GLY68 4.2 20.1 1.0
CA C:GLN71 4.3 17.7 1.0
CA C:GLY69 4.4 19.5 1.0
C C:ILE67 4.9 20.3 1.0
O C:ILE67 5.0 20.8 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 Dec 12 09:48:09 2020

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