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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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

Go back to Chlorine Binding Sites List in 3smc
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: Sun Jul 21 04:37:40 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy