Sodium in PDB 3r46: Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24

The structure of Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24, PDB code: 3r46 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)	30.00 / 1.75
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	55.176, 55.176, 146.591, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.4

The structure of Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24 (pdb code 3r46). 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 Cc-Hex-D24, PDB code: 3r46:
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 Cc-Hex-D24


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 Cc-Hex-D24 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na186 b:25.4 occ:1.00 NZ B:LYS25 4.5 26.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24


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 Cc-Hex-D24 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na188 b:25.7 occ:1.00 O C:HOH37 2.6 33.0 1.0 O C:HOH38 2.9 32.9 1.0 O C:TRP22 2.9 16.4 1.0 NZ C:LYS25 3.1 25.8 1.0 CE2 C:TRP22 3.2 23.0 1.0 CD2 C:TRP22 3.5 24.2 1.0 NE1 C:TRP22 3.5 24.5 1.0 N C:ALA26 3.5 16.5 1.0 CB C:ALA26 3.5 17.8 1.0 CZ2 C:TRP22 3.6 25.3 1.0 O C:HOH138 3.7 45.7 1.0 CG C:LYS25 3.7 18.3 1.0 CA C:ALA26 3.8 16.8 1.0 CD C:LYS25 3.8 20.5 1.0 CD1 C:TRP22 3.9 23.2 1.0 CG C:TRP22 3.9 19.3 1.0 C C:TRP22 3.9 15.9 1.0 CB C:LYS25 4.0 14.9 1.0 CE3 C:TRP22 4.0 22.5 1.0 CH2 C:TRP22 4.0 26.3 1.0 CE C:LYS25 4.1 23.1 1.0 CZ3 C:TRP22 4.2 26.8 1.0 C C:LYS25 4.2 15.6 1.0 CA C:TRP22 4.5 15.7 1.0 CA C:LYS25 4.7 15.9 1.0 CB C:TRP22 4.8 16.3 1.0 N C:GLU23 5.0 15.3 1.0 O C:LYS25 5.0 16.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24


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 Cc-Hex-D24 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na185 b:25.7 occ:1.00 OE2 E:GLU23 2.6 19.0 1.0 CD E:GLU23 3.4 17.6 1.0 CZ3 E:TRP22 3.4 20.6 1.0 OE1 E:GLU23 3.5 16.7 1.0 CD F:LYS25 3.8 14.8 1.0 CG F:LYS25 3.9 15.3 1.0 CE3 E:TRP22 4.0 20.4 1.0 CH2 E:TRP22 4.2 21.5 1.0 CE F:LYS25 4.3 18.8 1.0 CB F:LYS25 4.6 14.3 1.0 CG E:GLU23 4.9 14.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of A Parallel 6-Helix Coiled Coil Cc-Hex-D24


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 Cc-Hex-D24 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na187 b:28.0 occ:1.00 O E:HOH105 2.5 44.5 1.0 O G:HOH56 2.7 25.1 1.0 O E:LYS18 2.8 16.6 1.0 O G:HOH55 2.9 31.0 1.0 CG E:LYS18 3.5 24.8 1.0 N E:TRP22 3.7 16.7 1.0 CB E:ALA21 3.7 15.5 1.0 C E:LYS18 3.7 17.4 1.0 CB E:TRP22 3.8 17.7 1.0 CA E:TRP22 4.0 16.2 1.0 CA E:LYS18 4.1 17.4 1.0 C E:ALA21 4.2 16.9 1.0 NZ E:LYS18 4.3 40.0 1.0 CB E:LYS18 4.3 18.6 1.0 OE1 G:GLU16 4.5 23.2 1.0 CA E:ALA21 4.5 16.4 1.0 O G:HOH57 4.6 40.6 1.0 O2 E:GOL35 4.6 57.5 1.0 CG E:TRP22 4.8 17.5 1.0 C2 E:GOL35 4.8 58.4 1.0 CD1 E:TRP22 4.8 20.6 1.0 CD E:LYS18 4.8 28.9 1.0 N E:ALA19 4.9 17.0 1.0 O E:ALA21 4.9 15.6 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