Sodium in PDB 9gf3: This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat.

The structure of This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat., PDB code: 9gf3 was solved by K.W.Kurgan, F.J.O.Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.41 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.267, 61.754, 154.441, 90, 90, 90
R / Rfree (%)	17.7 / 20

The binding sites of Sodium atom in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat. (pdb code 9gf3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat., PDB code: 9gf3:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:43.8 occ:1.00 O C:HOH201 2.3 52.0 1.0 O E:HOH208 2.4 41.5 1.0 O C:LYS26 3.0 18.2 1.0 OE1 E:GLU27 3.5 38.5 1.0 NZ C:LYS33 3.6 69.0 1.0 C C:LYS26 3.7 16.7 1.0 CB C:LYS26 3.8 17.5 1.0 CA C:LYS26 3.9 16.9 1.0 N C:GLN30 3.9 20.0 1.0 CB C:ALA29 4.0 17.1 1.0 OE1 C:GLN30 4.1 38.4 1.0 CB C:GLN30 4.1 24.9 1.0 CE C:LYS33 4.3 60.0 1.0 CA C:GLN30 4.3 22.8 1.0 CG C:LYS26 4.4 21.3 1.0 CD E:GLU27 4.4 28.5 1.0 C C:ALA29 4.5 19.0 1.0 CA C:ALA29 4.8 17.7 1.0 OE2 E:GLU27 4.9 33.0 1.0 N C:GLU27 4.9 15.9 1.0 CD C:GLN30 5.0 38.9 1.0

Sodium binding site 2 out of 4 in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat. within 5.0Å range: probe atom residue distance (Å) B Occ F:Na102 b:56.5 occ:1.00 OE1 H:GLU2 2.6 47.4 1.0 O F:HOH226 3.1 32.3 1.0 O F:HOH207 3.1 42.8 1.0 O I:HOH118 3.4 33.0 1.0 N F:ILE3 3.4 28.1 1.0 CG F:GLU2 3.5 41.6 1.0 CD H:GLU2 3.5 49.7 1.0 CG H:GLU2 3.6 41.1 1.0 N F:GLU2 3.6 31.1 1.0 CG1 F:ILE3 3.7 27.8 1.0 CD1 F:ILE3 3.8 33.5 1.0 CB F:ILE3 3.9 26.9 1.0 CD1 H:ILE3 4.2 30.4 1.0 CG1 H:ILE3 4.2 28.5 1.0 CA F:GLU2 4.3 32.7 1.0 CA F:ILE3 4.3 25.6 1.0 C F:GLY1 4.3 31.2 1.0 C F:GLU2 4.3 31.8 1.0 OE2 F:GLU2 4.3 50.8 1.0 CA F:GLY1 4.5 32.6 1.0 CB F:GLU2 4.5 37.4 1.0 CD F:GLU2 4.5 50.3 1.0 OE2 H:GLU2 4.7 52.4 1.0 O B:HOH207 4.8 42.9 1.0

Sodium binding site 3 out of 4 in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat. within 5.0Å range: probe atom residue distance (Å) B Occ G:Na103 b:47.9 occ:1.00 OE2 M:GLU2 2.6 37.8 1.0 O G:HOH218 3.0 30.4 1.0 O G:HOH213 3.2 48.0 1.0 N G:ILE3 3.3 26.7 1.0 CG G:GLU2 3.4 39.6 1.0 N G:GLU2 3.5 28.9 1.0 CG1 G:ILE3 3.6 28.4 1.0 CD M:GLU2 3.6 43.8 1.0 O H:HOH221 3.7 33.6 1.0 CG M:GLU2 3.7 36.1 1.0 CB G:ILE3 3.8 26.1 1.0 CD1 G:ILE3 3.8 28.7 1.0 C G:GLY1 4.1 30.6 1.0 CD1 M:ILE3 4.1 31.4 1.0 CA G:ILE3 4.1 27.1 1.0 CA G:GLU2 4.1 29.6 1.0 C G:GLU2 4.2 29.9 1.0 CA G:GLY1 4.3 32.0 1.0 CG1 M:ILE3 4.3 30.3 1.0 OE2 G:GLU2 4.4 45.7 1.0 CB G:GLU2 4.4 35.1 1.0 CD G:GLU2 4.5 47.9 1.0 OE1 M:GLU2 4.8 45.5 1.0 O F:HOH207 4.9 42.8 1.0

Sodium binding site 4 out of 4 in the This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of This Peptide Is A Variant of the De Novo Coiled-Coil Heptameric Peptic, Cc-Hept, Which Consists of 4 Heptad Repeats. This Peptide Is Denoted As Cc-Hept-HEN2 As Its Second Heptad Repeat Has Been Replaced with A Hendecad Repeat. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:43.4 occ:1.00 O B:HOH213 2.4 46.7 1.0 O F:HOH202 2.5 37.9 1.0 OE1 B:GLU27 3.0 34.9 1.0 O F:LYS26 3.0 19.7 1.0 O B:HOH201 3.5 47.2 1.0 C F:LYS26 3.7 16.3 1.0 CB F:LYS26 3.8 20.5 1.0 CA F:LYS26 3.8 18.2 1.0 CD B:GLU27 4.0 32.5 1.0 CB F:ALA29 4.0 18.4 1.0 N F:GLN30 4.1 18.2 1.0 CG F:LYS26 4.3 23.9 1.0 OE2 B:GLU27 4.3 37.7 1.0 OE1 F:GLN30 4.4 27.6 1.0 CB F:GLN30 4.4 18.5 1.0 CA F:GLN30 4.5 18.8 1.0 C F:ALA29 4.7 17.5 1.0 NZ F:LYS33 4.7 48.6 1.0 CA F:ALA29 4.8 17.8 1.0 CE F:LYS33 4.8 48.6 1.0 N F:GLU27 4.9 19.1 1.0 CD F:LYS26 5.0 30.1 1.0 CB B:GLU27 5.0 21.9 1.0

K.W.Kurgan, F.J.O.Martin, W.M.Dawson, T.Brunnock, A.J.Orr-Ewing, D.N.Woolfson. Exchange, Promiscuity, and Orthogonality in De Novo Designed Coiled-Coil Peptide Assemblies. Chem Sci 2024.
ISSN: ISSN 2041-6520
PubMed: 39720134
DOI: 10.1039/D4SC06329E