Sodium in PDB 4ajx: Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin

The structure of Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin, PDB code: 4ajx was solved by D.B.Steensgaard, G.Schluckebier, H.M.Strauss, M.Norrman, J.K.Thomsen, A.V.Friderichsen, S.Havelund, I.Jonassen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.497 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.310, 62.490, 57.270, 90.00, 111.80, 90.00
R / Rfree (%)	14.05 / 15.96

The structure of Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin (pdb code 4ajx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin, PDB code: 4ajx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1031 b:38.3 occ:1.00 O A:HOH2004 2.8 16.7 1.0 O B:HOH2037 2.9 42.0 1.0 O A:HOH2013 3.0 42.0 1.0 O08 A:16E1022 3.1 24.7 1.0 C06 A:16E1022 3.3 21.9 1.0 HB3 B:LYS29 3.3 28.8 1.0 HE2 B:LYS29 3.4 19.7 1.0 C07 A:16E1022 3.4 20.4 1.0 HD3 B:LYS29 3.6 23.3 1.0 NZ B:LYS29 3.6 16.1 1.0 CE B:LYS29 3.9 16.4 1.0 C05 A:16E1022 4.1 20.2 1.0 HB2 B:LYS29 4.1 28.8 1.0 CB B:LYS29 4.1 24.0 1.0 CD B:LYS29 4.2 19.4 1.0 O A:HOH2053 4.2 38.9 1.0 H2 A:GLY1 4.2 13.4 1.0 OE1 A:GLU4 4.4 19.2 1.0 OXT B:LYS29 4.5 29.5 1.0 CG B:LYS29 4.7 23.8 1.0 HE3 B:LYS29 4.8 19.7 1.0 O A:HOH2007 4.9 20.2 1.0

Sodium binding site 2 out of 2 in the Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By An Engineered Acylated Insulin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1032 b:25.1 occ:1.00 OE1 H:GLU13 2.4 20.3 0.4 HG H:LEU17 2.8 15.2 1.0 HD2 H:TYR16 2.8 12.6 1.0 HG B:SER9 2.9 14.8 0.2 OE2 L:GLU13 2.9 22.3 0.5 HB3 H:GLU13 2.9 19.4 0.6 OG B:SER9 3.0 12.3 0.2 HB3 H:GLU13 3.0 18.6 0.4 HB2 B:SER9 3.0 10.9 0.1 O B:HOH2016 3.1 22.3 1.0 O H:GLU13 3.1 11.9 1.0 HB3 B:SER9 3.1 10.9 0.1 OG B:SER9 3.2 18.1 0.7 HG B:SER9 3.3 21.8 0.7 HA H:GLU13 3.3 14.0 0.6 HB2 B:SER9 3.3 17.0 0.7 HB3 H:TYR16 3.4 13.1 1.0 CD H:GLU13 3.5 19.7 0.4 HD12 H:LEU17 3.5 17.3 1.0 HD22 H:LEU17 3.5 18.0 1.0 CB B:SER9 3.5 9.1 0.1 HB3 B:SER9 3.6 13.3 0.2 CG H:LEU17 3.6 12.7 1.0 CD2 H:TYR16 3.6 10.5 1.0 CB H:GLU13 3.7 15.5 0.4 CB H:GLU13 3.7 16.2 0.6 C H:GLU13 3.7 10.7 1.0 CA H:GLU13 3.7 11.7 0.4 CB B:SER9 3.8 14.2 0.7 CA H:GLU13 3.8 11.7 0.6 HA B:SER9 3.8 11.7 0.2 CB B:SER9 3.8 11.1 0.2 HA B:SER9 3.8 12.1 0.7 CD L:GLU13 3.8 21.6 0.5 HA B:SER9 3.9 10.9 0.1 CD1 H:LEU17 3.9 14.4 1.0 CD2 H:LEU17 3.9 15.0 1.0 CG H:GLU13 4.0 19.1 0.4 HD13 H:LEU17 4.0 17.3 1.0 HG2 H:GLU13 4.1 24.9 0.6 HD21 H:LEU17 4.1 18.0 1.0 OE1 L:GLU13 4.1 24.4 0.5 HG3 H:GLU13 4.2 22.9 0.4 CB H:TYR16 4.3 10.9 1.0 CA B:SER9 4.3 9.8 0.2 CA B:SER9 4.3 9.1 0.1 CA B:SER9 4.3 10.1 0.7 CG H:TYR16 4.4 10.3 1.0 CG H:GLU13 4.4 20.8 0.6 H H:LEU17 4.4 11.6 1.0 HE2 H:TYR16 4.4 12.8 1.0 O H:HOH2010 4.4 26.4 1.0 CE2 H:TYR16 4.5 10.7 1.0 HB2 H:GLU13 4.5 19.4 0.6 OE2 H:GLU13 4.5 17.9 0.4 HB2 H:GLU13 4.5 18.6 0.4 HB3 B:SER9 4.6 17.0 0.7 OE1 H:GLU13 4.6 26.1 0.6 HB2 B:SER9 4.6 13.3 0.2 OG B:SER9 4.7 8.5 0.1 HD1 L:HIS10 4.7 14.9 1.0 CD H:GLU13 4.8 24.0 0.6 HB2 H:TYR16 4.8 13.1 1.0 N H:LEU17 4.8 9.7 1.0 HD11 H:LEU17 4.8 17.3 1.0 O L:HOH2003 4.8 21.4 1.0 CB H:LEU17 4.8 11.6 1.0 HD23 H:LEU17 4.8 18.0 1.0 HG2 H:GLU13 4.9 22.9 0.4 HB2 H:LEU17 4.9 13.9 1.0 N H:ALA14 4.9 9.8 1.0 HG22 B:VAL12 5.0 2.0 0.1

D.B.Steensgaard, G.Schluckebier, H.M.Strauss, M.Norrman, J.K.Thomsen, A.V.Friderichsen, S.Havelund, I.Jonassen. Ligand Controlled Assembly of Hexamers, Dihexamers, and Linear Multihexamer Structures By the Engineered Acylated Insulin Degludec. Biochemistry V. 52 295 2013.
ISSN: ISSN 0006-2960
PubMed: 23256685
DOI: 10.1021/BI3008609