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Sodium 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:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium where determined in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane, PDB code: 3smc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3smc

Go back to Sodium Binding Sites List in 3smc
Sodium binding site 1 out of 4 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na802

b:52.1
occ:1.00
 O A:HOH390 2.1 24.6 1.0
O A:HOH576 2.3 37.5 1.0
O A:HOH238 2.5 14.2 1.0
O A:ASP100 2.6 12.4 1.0
O A:HOH549 3.0 36.6 1.0
C A:ASP100 3.6 12.8 1.0
N A:ASP100 3.9 11.4 1.0
O A:HOH588 4.1 41.5 1.0
CA A:ASP100 4.2 11.8 1.0
CB A:ASP100 4.3 13.5 1.0
O B:HOH499 4.3 34.2 1.0
O C:HOH401 4.3 25.1 1.0
O C:HOH432 4.4 27.9 1.0
CL A:CL702 4.5 15.3 1.0
O A:HOH387 4.6 23.0 1.0
O B:HOH281 4.6 16.7 1.0
N A:MET101 4.7 12.7 1.0
O A:HOH221 4.7 12.3 1.0
C A:TYR99 4.9 9.9 1.0

Sodium binding site 2 out of 4 in 3smc

Go back to Sodium Binding Sites List in 3smc
Sodium binding site 2 out of 4 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na804

b:37.1
occ:1.00
 O A:HOH288 2.5 16.8 1.0
O C:HOH313 2.5 18.8 1.0
O C:HOH372 2.5 22.4 1.0
O B:HOH349 2.5 20.3 1.0
O A:HOH345 2.6 21.7 1.0
O B:HOH280 2.6 15.9 1.0
O B:HOH285 3.9 16.9 1.0
O C:HOH301 4.1 17.6 1.0
O A:HOH256 4.1 15.6 1.0
O C:HOH335 4.4 20.3 1.0
O C:HOH261 4.4 15.6 1.0
O A:HOH375 4.4 23.1 1.0
O B:HOH382 4.5 23.5 1.0
NE2 C:GLN45 4.6 11.1 1.0
NE2 A:GLN45 4.6 8.2 1.0
NE2 B:GLN45 4.7 8.8 1.0

Sodium binding site 3 out of 4 in 3smc

Go back to Sodium Binding Sites List in 3smc
Sodium binding site 3 out of 4 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
B:Na803

b:48.8
occ:1.00
 O B:HOH262 2.5 16.2 1.0
O B:HOH453 2.5 28.6 1.0
O B:HOH504 2.5 33.7 1.0
O B:ASP100 2.7 10.6 1.0
O C:HOH458 3.1 29.4 1.0
O B:HOH614 3.7 40.5 1.0
C B:ASP100 3.7 10.7 1.0
N B:ASP100 4.0 10.5 1.0
O A:HOH387 4.1 23.0 1.0
O A:HOH549 4.3 36.6 1.0
O C:HOH539 4.3 38.1 1.0
CA B:ASP100 4.3 11.2 1.0
CL B:CL701 4.4 14.8 1.0
CB B:ASP100 4.4 12.9 1.0
O C:HOH267 4.5 15.7 1.0
O C:HOH363 4.7 22.7 1.0
O B:HOH268 4.7 15.3 1.0
N B:MET101 4.7 11.9 1.0
O B:HOH499 4.8 34.2 1.0
C B:TYR99 4.9 9.6 1.0
CA B:MET101 5.0 12.1 1.0

Sodium binding site 4 out of 4 in 3smc

Go back to Sodium Binding Sites List in 3smc
Sodium binding site 4 out of 4 in the Macrophage Migration Inhibitory Factor (Mif) with Covalently Bound L- Sulforaphane


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
C:Na801

b:45.7
occ:1.00
 O C:HOH409 2.5 25.8 1.0
O C:HOH353 2.5 21.2 1.0
O C:ASP100 2.6 11.7 1.0
O C:HOH432 3.0 27.9 1.0
C C:ASP100 3.6 12.3 1.0
N C:ASP100 3.9 11.8 1.0
O C:HOH595 4.1 41.1 1.0
CA C:ASP100 4.2 12.8 1.0
CB C:ASP100 4.3 14.8 1.0
O C:HOH458 4.3 29.4 1.0
CL C:CL703 4.3 14.6 1.0
O C:HOH363 4.4 22.7 1.0
O A:HOH299 4.5 17.8 1.0
N C:MET101 4.6 13.0 1.0
O C:HOH264 4.7 16.2 1.0
O C:HOH401 4.7 25.1 1.0
O C:HOH539 4.8 38.1 1.0
C C:TYR99 4.9 11.7 1.0
CA C:MET101 4.9 13.3 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 12:59:00 2024

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