Sodium in PDB 8bfe: A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)

The structure of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld), PDB code: 8bfe was solved by P.Kumar, N.G.Paterson, D.N.Woolfson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.54 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.891, 133.886, 72.634, 90, 104.47, 90
R / Rfree (%)	22.2 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) (pdb code 8bfe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld), PDB code: 8bfe:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:68.7 occ:1.00 CA A:GLY1 3.3 67.6 1.0 N A:AIB4 3.4 54.2 1.0 C A:GLY1 3.5 64.8 1.0 C J:TYR29 3.5 56.7 1.0 O J:GLY30 3.5 73.5 1.0 O J:TYR29 3.6 60.2 1.0 CB2 A:AIB4 3.6 56.9 1.0 O A:GLY1 3.8 67.3 1.0 CA J:TYR29 3.8 49.3 1.0 O J:LYS28 3.8 48.4 1.0 N J:GLY30 3.9 62.6 1.0 N A:LEU3 4.0 51.2 1.0 N A:GLU2 4.0 61.3 1.0 CB A:LEU3 4.1 56.1 1.0 CA A:AIB4 4.1 54.5 1.0 C J:GLY30 4.2 69.0 1.0 O A:ACE0 4.4 78.6 1.0 CA A:LEU3 4.4 52.8 1.0 C A:LEU3 4.4 52.3 1.0 N J:TYR29 4.4 47.5 1.0 C J:LYS28 4.4 47.6 1.0 N A:GLY1 4.6 72.0 1.0 CA J:GLY30 4.7 65.6 1.0 C A:GLU2 4.8 52.2 1.0 CB1 A:AIB4 4.9 54.0 1.0 C A:ACE0 4.9 75.9 1.0

Sodium binding site 2 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:88.3 occ:1.00 NZ A:LYS7 3.8 70.0 1.0 CE A:LYS7 4.4 62.5 1.0 CD A:LYS7 4.8 59.2 1.0

Sodium binding site 3 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:68.0 occ:1.00 O A:LYS7 3.2 47.1 1.0 CB A:LEU10 3.9 43.0 1.0 N A:AIB11 4.0 43.1 1.0 C A:LYS7 4.0 49.1 1.0 CA A:LYS7 4.1 48.4 1.0 CB1 A:AIB11 4.2 47.4 1.0 CB A:LYS7 4.3 52.7 1.0 CB2 A:AIB11 4.4 46.5 1.0 CA A:AIB11 4.4 46.1 1.0 CD1 A:LEU10 4.6 49.2 1.0 C A:LEU10 4.6 40.6 1.0 CG A:LYS7 4.7 55.2 1.0 CA A:LEU10 4.8 40.9 1.0 CG A:LEU10 4.9 45.6 1.0

Sodium binding site 4 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:57.9 occ:1.00 O P:LYS14 3.0 35.3 1.0 O B:AIB19 3.3 32.6 1.0 OE1 B:GLU23 3.4 54.1 1.0 CB B:GLU23 3.6 43.5 1.0 C B:AIB19 3.7 34.2 1.0 CB P:LYS14 3.8 34.3 1.0 C P:LYS14 3.8 35.7 1.0 CB2 P:AIB18 3.9 36.0 1.0 CB2 B:AIB19 4.0 36.1 1.0 CA P:LYS14 4.0 35.4 1.0 CB1 P:AIB18 4.0 37.8 1.0 CD B:GLU23 4.0 50.6 1.0 NA B:NA102 4.1 78.4 1.0 N P:AIB18 4.1 36.5 1.0 N B:LEU20 4.2 34.7 1.0 CA P:AIB18 4.3 37.4 1.0 CA B:AIB19 4.3 35.3 1.0 CG B:GLU23 4.3 47.5 1.0 CG P:LYS14 4.4 35.8 1.0 CA B:LEU20 4.4 36.4 1.0 CD2 P:LEU17 4.5 43.5 1.0 CD2 B:LEU20 4.6 42.1 1.0 CB1 B:AIB19 4.6 35.9 1.0 CD P:LYS14 4.7 38.6 1.0 CA B:GLU23 4.7 41.9 1.0 CB P:LEU17 4.8 39.8 1.0 N B:GLU23 4.8 41.0 1.0 N P:TRP15 4.9 36.2 1.0 OE2 B:GLU23 4.9 51.9 1.0

Sodium binding site 5 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:78.4 occ:1.00 OE1 B:GLU23 3.1 54.1 1.0 CD P:LYS14 3.7 38.6 1.0 CE P:LYS14 3.8 38.4 1.0 CD2 P:LEU17 3.9 43.5 1.0 CD2 B:LEU20 4.0 42.1 1.0 CG P:LYS14 4.0 35.8 1.0 NA B:NA101 4.1 57.9 1.0 CD B:GLU23 4.1 50.6 1.0 NZ P:LYS14 4.3 40.2 1.0 OE2 B:GLU23 4.4 51.9 1.0 CD1 I:LEU13 4.7 40.2 1.0 CB P:LYS14 4.9 34.3 1.0

Sodium binding site 6 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ F:Na101 b:96.8 occ:1.00 NE2 F:GLN8 3.3 80.9 1.0 OE1 F:GLN8 3.4 79.5 1.0 CD F:GLN8 3.7 75.0 1.0 CB1 F:AIB5 3.9 64.0 1.0

Sodium binding site 7 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ J:Na101 b:68.7 occ:1.00 OE1 J:GLU23 3.2 42.3 1.0 O J:HOH201 3.3 59.1 1.0 O J:AIB19 3.4 30.3 1.0 CB J:GLU23 3.5 31.4 1.0 C J:AIB19 3.7 30.7 1.0 CD J:GLU23 3.9 38.4 1.0 CB2 J:AIB19 3.9 28.0 1.0 N J:LEU20 4.1 29.7 1.0 CG J:GLU23 4.2 34.2 1.0 CA J:LEU20 4.2 32.1 1.0 CD2 J:LEU20 4.3 43.0 1.0 CA J:AIB19 4.3 29.1 1.0 CA J:GLU23 4.7 30.4 1.0 CB1 J:AIB19 4.8 30.6 1.0 N J:GLU23 4.8 28.3 1.0 OE2 J:GLU23 4.8 41.6 1.0

Sodium binding site 8 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ J:Na102 b:77.1 occ:1.00 CH3 J:ACE0 3.6 69.8 1.0 CD2 J:LEU3 3.7 80.5 1.0 O J:ACE0 4.3 61.4 1.0 C J:ACE0 4.5 68.0 1.0 O K:TYR29 4.5 79.7 1.0 CB J:LEU3 4.6 65.1 1.0 CG J:LEU3 4.7 73.7 1.0 C K:TYR29 5.0 75.7 1.0

Sodium binding site 9 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ K:Na101 b:84.0 occ:1.00 CB2 K:AIB5 4.1 46.9 1.0 CD2 K:LEU6 4.1 47.2 1.0 CG K:GLU2 4.3 71.4 1.0 CG K:LEU6 4.4 48.2 1.0 O K:GLU2 4.8 52.6 1.0 CA K:GLU2 5.0 62.8 1.0

Sodium binding site 10 out of 13 in the A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of A Dimeric De Novo Coiled-Coil Assembly: Pk-2 (Cc-Typen-Laubucld) within 5.0Å range: probe atom residue distance (Å) B Occ K:Na102 b:52.2 occ:1.00 N K:LEU3 3.3 52.7 1.0 C K:ACE0 3.3 65.5 1.0 N K:GLU2 3.4 63.0 1.0 O K:ACE0 3.5 63.7 1.0 CH3 K:ACE0 3.6 67.7 1.0 N K:GLY1 3.7 62.8 1.0 CB K:LEU3 3.7 56.4 1.0 CA K:GLU2 4.1 62.8 1.0 CB K:GLU2 4.1 68.7 1.0 C K:GLY1 4.1 58.4 1.0 CA K:LEU3 4.1 51.5 1.0 C K:GLU2 4.2 57.1 1.0 O K:HOH201 4.3 71.0 1.0 CA K:GLY1 4.4 59.7 1.0

P.Kumar, N.G.Paterson, J.Clayden, D.N.Woolfson. De Novo Design of Discrete, Stable 3 10 -Helix Peptide Assemblies. Nature V. 607 387 2022.
ISSN: ESSN 1476-4687
PubMed: 35732733
DOI: 10.1038/S41586-022-04868-X