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Sodium in PDB 3ker: D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp

Enzymatic activity of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp

All present enzymatic activity of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp:
4.1.1.84;

Protein crystallography data

The structure of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp, PDB code: 3ker was solved by S.Zierow, E.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.23 / 2.78
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 82.172, 82.172, 144.253, 90.00, 90.00, 120.00
R / Rfree (%) 22.2 / 23.8

Other elements in 3ker:

The structure of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp (pdb code 3ker). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp, PDB code: 3ker:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3ker

Go back to Sodium Binding Sites List in 3ker
Sodium binding site 1 out of 4 in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na121

b:46.4
occ:1.00
 OG1 A:THR46 3.0 31.7 1.0
CB A:THR46 3.9 30.0 1.0
CG C:PRO43 4.1 33.0 1.0
CD1 C:ILE14 4.3 43.9 1.0
CG2 C:ILE14 4.4 42.6 1.0
O C:HOH123 4.4 48.3 1.0
CG2 C:ILE41 4.4 27.2 1.0
CB C:ALA11 4.4 45.4 1.0
CD C:PRO43 4.4 33.8 1.0
CB C:ILE41 4.5 29.8 1.0
CG2 A:THR46 4.5 29.5 1.0
CA C:ALA11 4.6 47.5 1.0
CB C:ILE14 4.6 44.2 1.0
CB C:PRO43 4.6 33.1 1.0
O C:ALA11 4.8 51.5 1.0
CD1 C:ILE41 4.9 26.6 1.0
O C:ILE41 5.0 32.9 1.0

Sodium binding site 2 out of 4 in 3ker

Go back to Sodium Binding Sites List in 3ker
Sodium binding site 2 out of 4 in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na121

b:46.4
occ:1.00
 OG1 B:THR46 3.0 31.7 1.0
CG A:PRO43 3.7 33.0 1.0
CB B:THR46 3.9 30.0 1.0
CD1 A:ILE14 4.1 43.9 1.0
CD A:PRO43 4.1 33.8 1.0
CB A:ALA11 4.2 45.4 1.0
CB A:PRO43 4.2 33.1 1.0
CG2 A:ILE41 4.3 27.2 1.0
CA A:ALA11 4.3 47.5 1.0
CG2 A:ILE14 4.4 42.6 1.0
CB A:ILE41 4.4 29.8 1.0
CG2 B:THR46 4.5 29.5 1.0
O A:HOH123 4.5 48.3 1.0
CB A:ILE14 4.5 44.2 1.0
O A:ALA11 4.7 51.5 1.0
O A:ILE41 4.8 32.9 1.0
CG1 A:ILE14 4.9 43.1 1.0
C A:ALA11 5.0 49.5 1.0

Sodium binding site 3 out of 4 in 3ker

Go back to Sodium Binding Sites List in 3ker
Sodium binding site 3 out of 4 in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na121

b:46.4
occ:1.00
 OG1 C:THR46 3.0 31.7 1.0
CB C:THR46 3.9 30.0 1.0
CD1 B:ILE14 4.0 43.9 1.0
CG2 B:ILE14 4.0 42.6 1.0
CG B:PRO43 4.0 33.0 1.0
O B:HOH123 4.2 48.3 1.0
CB B:ILE14 4.2 44.2 1.0
CG2 B:ILE41 4.3 27.2 1.0
CB B:ALA11 4.3 45.4 1.0
CA B:ALA11 4.4 47.5 1.0
CB B:PRO43 4.5 33.1 1.0
CG2 C:THR46 4.5 29.5 1.0
CB B:ILE41 4.5 29.8 1.0
CD B:PRO43 4.5 33.8 1.0
O B:ALA11 4.6 51.5 1.0
CG1 B:ILE14 4.7 43.1 1.0
CD1 B:ILE41 4.8 26.6 1.0
C B:ALA11 4.9 49.5 1.0

Sodium binding site 4 out of 4 in 3ker

Go back to Sodium Binding Sites List in 3ker
Sodium binding site 4 out of 4 in the D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of D-Dopachrome Tautomerase (D-Dt)/ Macrophage Migration Inhibitory Factor 2 (MIF2) Complexed with Inhibitor 4-Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na121

b:46.4
occ:1.00
 OG1 D:THR46 3.0 31.7 1.0
CB D:THR46 3.9 30.0 1.0
CG2 D:THR46 4.5 29.5 1.0

Reference:

S.Zierow, E.Lolis. Solution Structure of D-Dt/MIF2 Complexed with 4-Ipp To Be Published.
Page generated: Mon Oct 7 11:12:37 2024

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