Sodium in PDB 6h3z: Crystal Structure of A C-Terminal MIF4G Domain in NOT1

The structure of Crystal Structure of A C-Terminal MIF4G Domain in NOT1, PDB code: 6h3z was solved by T.Raisch, F.Sandmeir, O.Weichenrieder, E.Valkov, E.Izaurralde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.49 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.930, 79.770, 98.420, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24.4

The binding sites of Sodium atom in the Crystal Structure of A C-Terminal MIF4G Domain in NOT1 (pdb code 6h3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A C-Terminal MIF4G Domain in NOT1, PDB code: 6h3z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A C-Terminal MIF4G Domain in NOT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A C-Terminal MIF4G Domain in NOT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1701 b:92.9 occ:1.00 O A:ALA1481 2.5 0.6 1.0 O A:ALA1478 3.0 0.3 1.0 O A:GLU1483 3.0 0.0 1.0 O A:THR1479 3.6 0.8 1.0 C A:ALA1481 3.7 1.0 1.0 CD2 A:LEU1536 3.8 0.8 1.0 CB A:LEU1536 4.0 98.6 1.0 C A:GLU1483 4.1 0.2 1.0 C A:ALA1478 4.2 0.5 1.0 O A:THR1482 4.3 0.0 1.0 C A:THR1479 4.3 0.7 1.0 C A:THR1482 4.4 0.5 1.0 CA A:ALA1481 4.6 0.0 1.0 CG A:LEU1536 4.6 0.1 1.0 N A:THR1482 4.6 0.4 1.0 CA A:GLU1484 4.7 0.5 1.0 CA A:THR1479 4.7 0.1 1.0 N A:ALA1481 4.7 0.7 1.0 CB A:ALA1481 4.7 0.5 1.0 N A:GLU1483 4.7 0.2 1.0 N A:GLU1484 4.8 0.2 1.0 CA A:THR1482 4.8 0.4 1.0 N A:THR1479 4.9 0.8 1.0 C A:SER1480 5.0 0.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A C-Terminal MIF4G Domain in NOT1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A C-Terminal MIF4G Domain in NOT1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1701 b:90.1 occ:1.00 O B:ALA1481 2.8 0.2 1.0 O B:ALA1478 2.9 90.6 1.0 O B:GLU1483 3.0 0.3 1.0 O B:THR1479 3.8 91.6 1.0 CB B:LEU1536 3.9 84.2 1.0 C B:ALA1481 3.9 0.0 1.0 CD2 B:LEU1536 4.0 90.5 1.0 C B:GLU1483 4.1 0.6 1.0 C B:ALA1478 4.1 88.6 1.0 C B:THR1479 4.4 91.3 1.0 O B:THR1482 4.5 0.8 1.0 CA B:GLU1484 4.5 97.9 1.0 CG B:LEU1536 4.6 88.6 1.0 C B:THR1482 4.6 0.6 1.0 CA B:THR1479 4.7 84.8 1.0 N B:GLU1484 4.8 99.0 1.0 CA B:ALA1481 4.8 96.9 1.0 CB B:ALA1481 4.9 95.8 1.0 N B:THR1479 4.9 83.9 1.0 N B:GLU1483 4.9 99.0 1.0 N B:THR1482 4.9 0.2 1.0 N B:ALA1481 4.9 95.9 1.0

T.Raisch, F.Sandmeir, O.Weichenrieder, E.Valkov, E.Izaurralde. Structural and Biochemical Analysis of A NOT1 MIF4G-Like Domain of the CCR4-Not Complex. J. Struct. Biol. V. 204 388 2018.
ISSN: ESSN 1095-8657
PubMed: 30367941
DOI: 10.1016/J.JSB.2018.10.009