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Chlorine in PDB 3smc: Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane

Enzymatic activity of Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane

All present enzymatic activity of Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane:
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane, PDB code: 3smc was solved by G.V.Crichlow, E.J.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 110.00 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 95.638, 95.638, 103.516, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 18.6

Other elements in 3smc:

The structure of Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane (pdb code 3smc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane, PDB code: 3smc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3smc

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Chlorine binding site 1 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:15.3
occ:1.00
 O C:HOH264 3.1 16.2 1.0
ND2 A:ASN105 3.2 16.0 1.0
N A:ASN102 3.2 15.0 1.0
CA A:MET101 3.8 13.9 1.0
O A:HOH390 3.8 24.6 1.0
CG A:ASN102 3.9 20.2 1.0
CB A:ASN102 3.9 17.3 1.0
CE A:MET101 3.9 15.7 1.0
CB A:ASN105 3.9 14.0 1.0
C A:MET101 4.0 14.5 1.0
ND2 A:ASN102 4.0 24.6 1.0
CG A:ASN105 4.0 14.5 1.0
O C:HOH401 4.0 25.1 1.0
CA A:ASN102 4.1 14.9 1.0
O A:ASP100 4.2 12.4 1.0
SD A:MET101 4.3 15.6 1.0
OD1 A:ASN102 4.4 23.4 1.0
CB A:MET101 4.5 13.9 1.0
NA A:NA802 4.5 52.1 1.0
O C:HOH353 4.6 21.2 1.0
O C:HOH432 4.7 27.9 1.0
O A:ASN102 4.7 12.8 1.0
N A:MET101 4.9 12.7 1.0
O C:TYR98 4.9 11.5 1.0
C A:ASN102 4.9 14.8 1.0
O A:HOH588 4.9 41.5 1.0
C A:ASP100 5.0 12.8 1.0

Chlorine binding site 2 out of 7 in 3smc

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Chlorine binding site 2 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:19.0
occ:1.00
 O A:HOH431 3.0 27.1 1.0
NE2 A:GLN24 3.3 9.3 1.0
CG A:GLN24 3.9 9.8 1.0
CA C:GLY51 4.0 16.6 1.0
O A:SER20 4.0 9.9 1.0
CG2 A:THR23 4.1 9.9 1.0
CD A:GLN24 4.1 8.9 1.0
CB A:SER20 4.1 10.1 1.0
CA A:SER20 4.1 10.5 1.0
CB A:THR23 4.2 9.1 1.0
OG A:SER20 4.2 11.5 1.0
C A:SER20 4.5 9.3 1.0
O C:GLY51 4.6 18.7 1.0
C C:GLY51 4.7 17.7 1.0
OG1 A:THR23 4.8 8.0 1.0
N A:GLN24 5.0 8.9 1.0

Chlorine binding site 3 out of 7 in 3smc

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Chlorine binding site 3 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:27.6
occ:1.00
 NE2 A:GLN71 3.4 17.1 1.0
CG A:GLN71 3.4 16.7 1.0
N A:GLN71 3.4 14.2 1.0
N A:ALA70 3.5 15.4 1.0
O A:HOH547 3.5 36.5 1.0
CA A:GLY68 3.6 16.1 1.0
C A:GLY68 3.6 15.7 1.0
N A:GLY69 3.7 15.8 1.0
CB A:ALA70 3.9 17.3 1.0
CD A:GLN71 3.9 18.0 1.0
CB A:GLN71 4.0 14.4 1.0
CA A:ALA70 4.1 15.0 1.0
O A:HOH590 4.1 37.5 1.0
O A:GLY68 4.2 17.2 1.0
C A:ALA70 4.3 14.1 1.0
C A:GLY69 4.3 15.6 1.0
N A:GLY68 4.3 13.9 1.0
CA A:GLN71 4.3 13.8 1.0
CA A:GLY69 4.4 16.0 1.0
C A:ILE67 5.0 14.1 1.0

Chlorine binding site 4 out of 7 in 3smc

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Chlorine binding site 4 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:14.8
occ:1.00
 O A:HOH221 3.1 12.3 1.0
ND2 B:ASN105 3.2 14.3 1.0
N B:ASN102 3.2 12.9 1.0
O B:HOH499 3.3 34.2 1.0
ND2 B:ASN102 3.6 24.2 1.0
CG B:ASN102 3.8 21.3 1.0
CA B:MET101 3.8 12.1 1.0
CB B:ASN105 3.9 11.1 1.0
CB B:ASN102 3.9 16.2 1.0
C B:MET101 4.0 12.8 1.0
CG B:ASN105 4.0 12.8 1.0
O B:HOH453 4.0 28.6 1.0
CE B:MET101 4.0 11.2 1.0
O A:HOH387 4.1 23.0 1.0
CA B:ASN102 4.1 13.7 1.0
O B:ASP100 4.1 10.6 1.0
SD B:MET101 4.3 12.7 1.0
NA B:NA803 4.4 48.8 1.0
OD1 B:ASN102 4.4 22.8 1.0
CB B:MET101 4.5 12.4 1.0
O B:HOH614 4.5 40.5 1.0
O B:ASN102 4.7 12.4 1.0
O A:HOH238 4.8 14.2 1.0
N B:MET101 4.8 11.9 1.0
C B:ASP100 4.9 10.7 1.0
O A:HOH549 4.9 36.6 1.0
O A:TYR98 4.9 10.3 1.0
C B:ASN102 5.0 13.4 1.0

Chlorine binding site 5 out of 7 in 3smc

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Chlorine binding site 5 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl706

b:23.6
occ:1.00
 NE2 B:GLN71 3.3 16.4 1.0
CG B:GLN71 3.4 14.9 1.0
N B:GLN71 3.5 12.4 1.0
CA B:GLY68 3.5 14.8 1.0
N B:ALA70 3.5 14.1 1.0
C B:GLY68 3.6 14.8 1.0
N B:GLY69 3.8 14.9 1.0
CB B:ALA70 3.8 15.7 1.0
CD B:GLN71 3.9 16.4 1.0
CB B:GLN71 4.0 14.0 1.0
CA B:ALA70 4.1 14.5 1.0
O B:GLY68 4.1 13.3 1.0
N B:GLY68 4.2 13.1 1.0
C B:ALA70 4.3 13.8 1.0
CA B:GLN71 4.4 13.1 1.0
C B:GLY69 4.4 14.6 1.0
O B:HOH582 4.5 37.4 1.0
CA B:GLY69 4.6 15.3 1.0
C B:ILE67 4.8 13.9 1.0
O B:ILE67 4.9 14.8 1.0

Chlorine binding site 6 out of 7 in 3smc

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Chlorine binding site 6 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl703

b:14.6
occ:1.00
 O B:HOH268 3.1 15.3 1.0
N C:ASN102 3.2 13.9 1.0
ND2 C:ASN105 3.2 13.0 1.0
O C:HOH539 3.4 38.1 1.0
O C:HOH409 3.8 25.8 1.0
CA C:MET101 3.8 13.3 1.0
CG C:ASN102 3.9 20.3 1.0
CB C:ASN102 3.9 17.0 1.0
CB C:ASN105 3.9 10.8 1.0
ND2 C:ASN102 3.9 23.4 1.0
C C:MET101 4.0 13.0 1.0
CE C:MET101 4.0 14.1 1.0
O C:HOH363 4.0 22.7 1.0
CG C:ASN105 4.1 12.7 1.0
CA C:ASN102 4.1 14.5 1.0
O C:ASP100 4.2 11.7 1.0
SD C:MET101 4.3 15.8 1.0
NA C:NA801 4.3 45.7 1.0
OD1 C:ASN102 4.4 23.0 1.0
O C:HOH458 4.5 29.4 1.0
CB C:MET101 4.5 13.4 1.0
O C:ASN102 4.7 13.3 1.0
O B:HOH262 4.7 16.2 1.0
N C:MET101 4.9 13.0 1.0
O C:HOH595 5.0 41.1 1.0
C C:ASN102 5.0 14.4 1.0
C C:ASP100 5.0 12.3 1.0
O B:TYR98 5.0 8.8 1.0

Chlorine binding site 7 out of 7 in 3smc

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Chlorine binding site 7 out of 7 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


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) with Covalently Bound L- Sulforaphane within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl705

b:34.4
occ:1.00
 O C:HOH613 3.0 46.0 1.0
NE2 C:GLN71 3.3 23.9 1.0
CG C:GLN71 3.4 23.0 1.0
N C:GLN71 3.6 18.8 1.0
N C:ALA70 3.6 19.9 1.0
CA C:GLY68 3.6 19.8 1.0
C C:GLY68 3.6 20.3 1.0
N C:GLY69 3.7 21.0 1.0
CD C:GLN71 3.8 23.6 1.0
CB C:ALA70 4.1 21.4 1.0
CB C:GLN71 4.1 19.8 1.0
CA C:ALA70 4.2 19.3 1.0
O C:GLY68 4.2 20.7 1.0
C C:GLY69 4.4 20.0 1.0
O C:HOH523 4.4 35.1 1.0
C C:ALA70 4.4 18.9 1.0
N C:GLY68 4.4 20.4 1.0
CA C:GLN71 4.5 18.3 1.0
CA C:GLY69 4.5 20.6 1.0

Reference:

G.V.Crichlow, C.Fan, C.Keeler, M.Hodsdon, E.J.Lolis. Structural Interactions Dictate the Kinetics of Macrophage Migration Inhibitory Factor Inhibition By Different Cancer-Preventive Isothiocyanates. Biochemistry V. 51 7506 2012.
ISSN: ISSN 0006-2960
PubMed: 22931430
DOI: 10.1021/BI3005494
Page generated: Fri Jul 11 10:22:35 2025

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