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Sodium in PDB 3smb: Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif)

Enzymatic activity of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif)

All present enzymatic activity of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif):
5.3.2.1; 5.3.3.12;

Protein crystallography data

The structure of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif), PDB code: 3smb 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) 100.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.492, 67.670, 87.771, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 19.7

Other elements in 3smb:

The structure of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif) also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif) (pdb code 3smb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif), PDB code: 3smb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3smb

Go back to Sodium Binding Sites List in 3smb
Sodium binding site 1 out of 3 in the Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:48.0
occ:1.00
 O A:HOH238 2.3 18.7 1.0
O A:HOH345 2.4 25.2 1.0
O A:HOH504 2.5 33.9 1.0
O A:ASP100 2.5 16.0 1.0
O A:HOH573 2.5 39.0 1.0
O B:HOH429 2.9 29.9 1.0
C A:ASP100 3.5 13.6 1.0
N A:ASP100 3.8 13.8 1.0
CA A:ASP100 4.1 14.3 1.0
CB A:ASP100 4.1 14.8 1.0
O A:HOH404 4.2 28.6 1.0
O B:HOH596 4.4 42.6 1.0
O A:HOH624 4.5 48.4 1.0
O B:HOH288 4.5 21.7 1.0
O A:HOH262 4.5 20.3 1.0
O A:HOH216 4.5 16.7 1.0
N A:MET101 4.6 13.4 1.0
O C:HOH249 4.6 19.6 1.0
CL A:CL701 4.6 17.3 1.0
O C:HOH401 4.7 28.6 1.0
C A:TYR99 4.8 13.7 1.0
CA A:MET101 4.9 14.5 1.0

Sodium binding site 2 out of 3 in 3smb

Go back to Sodium Binding Sites List in 3smb
Sodium binding site 2 out of 3 in the Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na803

b:61.2
occ:1.00
 O B:HOH362 2.0 26.1 1.0
O B:HOH250 2.4 19.6 1.0
O B:ASP100 2.6 17.0 1.0
O C:HOH473 2.7 32.3 1.0
O C:HOH454 2.8 31.2 1.0
C B:ASP100 3.6 14.0 1.0
N B:ASP100 3.9 13.9 1.0
O C:HOH249 4.1 19.6 1.0
O B:HOH582 4.1 40.7 1.0
CA B:ASP100 4.2 15.3 1.0
O C:HOH613 4.3 44.1 1.0
CB B:ASP100 4.3 17.1 1.0
O C:HOH315 4.4 24.1 1.0
O B:HOH230 4.5 18.0 1.0
CL B:CL703 4.5 17.2 1.0
O B:HOH429 4.6 29.9 1.0
O C:HOH263 4.6 20.3 1.0
N B:MET101 4.6 14.4 1.0
C B:TYR99 4.8 15.1 1.0
CA B:MET101 4.9 14.8 1.0

Sodium binding site 3 out of 3 in 3smb

Go back to Sodium Binding Sites List in 3smb
Sodium binding site 3 out of 3 in the Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Phenethylisothiocyanate Covalently Bound to Macrophage Migration Inhibitory Factor (Mif) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na802

b:46.0
occ:1.00
 O C:HOH385 2.0 27.4 1.0
O C:HOH280 2.3 21.1 1.0
O C:ASP100 2.7 17.0 1.0
O C:HOH401 2.9 28.6 1.0
C C:ASP100 3.7 15.9 1.0
O C:HOH543 3.9 36.4 1.0
N C:ASP100 3.9 15.2 1.0
O C:HOH315 4.1 24.1 1.0
CA C:ASP100 4.3 15.3 1.0
CB C:ASP100 4.4 17.1 1.0
O A:HOH262 4.4 20.3 1.0
O C:HOH209 4.5 15.9 1.0
CL C:CL702 4.5 18.5 1.0
O C:HOH473 4.5 32.3 1.0
O A:HOH327 4.6 24.4 1.0
O C:HOH613 4.6 44.1 1.0
N C:MET101 4.7 14.4 1.0
C C:TYR99 4.9 14.1 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: Mon Oct 7 12:58:59 2024

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