Sodium in PDB 6enk: The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B

The structure of The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B, PDB code: 6enk was solved by J.H.Naismith, S.A.Mcmahon, G.L.Challis, N.Kadi, M.Oke, H.Liu, L.G.Carter, K.A.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.99 / 1.96
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.163, 58.055, 101.194, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 20.4

The structure of The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Sodium atom in the The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B (pdb code 6enk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B, PDB code: 6enk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.0 occ:1.00 O A:HOH764 2.1 29.8 1.0 O A:GLU343 2.7 21.1 1.0 O A:HOH502 2.9 24.9 1.0 OD1 A:ASN344 2.9 28.1 1.0 C A:GLU343 3.4 20.6 1.0 O A:HOH600 3.9 44.0 1.0 CA A:ASN344 3.9 21.6 1.0 N A:ASN344 4.0 20.6 1.0 CG A:ASN344 4.0 23.9 1.0 CA A:GLU343 4.4 19.4 1.0 CB A:GLU343 4.5 19.5 1.0 CB A:ASN344 4.6 23.0 1.0 NZ A:LYS220 4.9 24.6 1.0

Sodium binding site 2 out of 3 in the The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:19.9 occ:1.00 O A:HOH658 2.2 19.4 1.0 O A:HOH733 2.4 19.2 1.0 O A:ASP113 2.4 21.1 1.0 O A:HOH653 2.5 19.9 1.0 C A:ASP113 3.6 21.9 1.0 O A:LYS114 4.1 20.2 1.0 O A:HOH684 4.1 36.5 1.0 OD1 A:ASP113 4.2 23.1 1.0 CG A:ASP113 4.3 24.8 1.0 OD2 A:ASP113 4.3 25.0 1.0 CA A:LYS114 4.4 23.7 1.0 C A:LYS114 4.4 22.8 1.0 N A:LYS114 4.4 22.7 1.0 O A:VAL115 4.6 18.8 1.0 CA A:ASP113 4.6 22.5 1.0 O A:HOH748 4.7 29.3 1.0

Sodium binding site 3 out of 3 in the The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The X-Ray Crystal Structure of Dese Bound to Desferrioxamine B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.1 occ:1.00 O A:HOH803 2.3 33.6 1.0 O A:HOH551 2.4 22.5 1.0 O A:HOH582 2.5 22.0 1.0 O A:GLU188 4.1 16.9 1.0 O A:HOH708 4.2 25.1 1.0 O A:HOH553 4.3 31.6 1.0 CG A:GLU188 4.4 21.4 1.0 OE2 A:GLU188 4.6 26.3 1.0 O A:ALA192 4.7 21.4 1.0 CA A:GLY191 4.9 21.4 1.0

J.L.Ronan, N.Kadi, S.A.Mcmahon, J.H.Naismith, L.M.Alkhalaf, G.L.Challis. Desferrioxamine Biosynthesis: Diverse Hydroxamate Assembly By Substrate-Tolerant Acyl Transferase Desc. Philos. Trans. R. Soc. V. 373 2018LOND., B, Biol. Sci..
ISSN: ESSN 1471-2970
PubMed: 29685972
DOI: 10.1098/RSTB.2017.0068