Sodium in PDB 3r3k: Crystal Structure of A Parallel 6-Helix Coiled Coil

The structure of Crystal Structure of A Parallel 6-Helix Coiled Coil, PDB code: 3r3k was solved by N.R.Zaccai, B.H.C.Chi, D.N.Woolfson, R.L.Brady, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.21 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	31.660, 54.480, 128.270, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.2

The structure of Crystal Structure of A Parallel 6-Helix Coiled Coil also contains other interesting chemical elements:

Iodine	(I)	3 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of A Parallel 6-Helix Coiled Coil (pdb code 3r3k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Parallel 6-Helix Coiled Coil, PDB code: 3r3k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil


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 Parallel 6-Helix Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ B:Na34 b:30.8 occ:1.00 O B:LYS18 2.8 18.9 1.0 O A:HOH75 3.2 26.9 1.0 C B:LYS18 3.7 18.9 1.0 N B:PHI22 3.8 19.6 1.0 CB B:PHI22 3.8 21.8 1.0 O B:HOH77 3.8 33.6 1.0 CA B:LYS18 4.0 21.6 1.0 CA B:PHI22 4.1 19.5 1.0 CB B:LYS18 4.2 20.6 1.0 CB B:ALA21 4.2 15.6 1.0 O B:HOH71 4.3 30.5 1.0 C B:ALA21 4.4 20.7 1.0 N B:ALA19 4.8 17.8 1.0 OE1 A:GLU16 4.8 25.4 1.0 CG B:PHI22 4.8 22.9 1.0 CA B:ALA21 4.8 17.4 1.0 CD1 B:PHI22 4.8 21.9 1.0 CG B:LYS18 4.9 22.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil


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 Parallel 6-Helix Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ C:Na34 b:30.5 occ:1.00 O C:HOH69 2.4 40.1 1.0 O C:HOH80 2.9 29.4 1.0 O C:LYS11 3.1 18.0 1.0 C C:LYS11 3.8 18.6 1.0 CA C:LYS11 4.0 22.6 1.0 N C:LYS15 4.0 17.6 1.0 CB C:ALA14 4.0 16.3 1.0 NZ C:LYS11 4.1 39.1 1.0 CB C:LYS15 4.1 21.5 1.0 CB C:LYS11 4.2 25.5 1.0 CG C:LYS11 4.2 29.7 1.0 CA C:LYS15 4.4 19.6 1.0 O C:HOH82 4.5 28.3 1.0 C C:ALA14 4.5 18.1 1.0 CE C:LYS11 4.5 42.6 1.0 CA C:ALA14 4.8 19.1 1.0 N C:ALA12 5.0 19.4 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of A Parallel 6-Helix Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ C:Na35 b:42.2 occ:1.00 OE2 C:GLU23 2.5 28.1 1.0 CD C:GLU23 3.4 22.7 1.0 CG A:LYS25 3.6 25.5 1.0 OE1 C:GLU23 3.7 24.9 1.0 O C:HOH76 3.8 31.2 1.0 O C:HOH67 4.0 32.5 1.0 O C:HOH77 4.1 30.1 1.0 CD A:LYS25 4.2 28.9 1.0 CB A:LYS25 4.3 20.7 1.0 CG C:GLU23 4.8 18.8 1.0 O A:HOH77 4.9 29.1 1.0 NA C:NA38 4.9 39.2 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of A Parallel 6-Helix Coiled Coil within 5.0Å range: probe atom residue distance (Å) B Occ C:Na38 b:39.2 occ:1.00 CB C:PHI22 3.6 24.6 1.0 CL C:CL37 3.9 38.3 1.0 O C:PHI22 3.9 19.6 1.0 C C:PHI22 4.1 20.6 1.0 CG C:PHI22 4.2 31.3 1.0 CA C:PHI22 4.4 21.5 1.0 OE2 C:GLU23 4.4 28.1 1.0 CD1 C:PHI22 4.4 36.1 1.0 O C:HOH76 4.5 31.2 1.0 N C:GLU23 4.7 20.1 1.0 CD C:GLU23 4.9 22.7 1.0 NA C:NA35 4.9 42.2 1.0

N.R.Zaccai, B.Chi, A.R.Thomson, A.L.Boyle, G.J.Bartlett, M.Bruning, N.Linden, R.B.Sessions, P.J.Booth, R.L.Brady, D.N.Woolfson. A De Novo Peptide Hexamer with A Mutable Channel. Nat.Chem.Biol. V. 7 935 2011.
ISSN: ISSN 1552-4450
PubMed: 22037471
DOI: 10.1038/NCHEMBIO.692