Sodium in PDB 8rbh: Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide

The structure of Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide, PDB code: 8rbh was solved by A.E.Ramdass, Z.Chen, E.V.Dalietou, C.E.Manning, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.83 / 1.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.001, 78.39, 73.784, 90, 99.24, 90
R / Rfree (%)	21 / 25.8

The binding sites of Sodium atom in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide (pdb code 8rbh). 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 the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide, PDB code: 8rbh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide


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 the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:35.4 occ:1.00 NZ A:LYS318 2.6 42.2 1.0 OD2 A:ASP297 2.9 31.8 1.0 O A:HOH814 3.2 46.5 1.0 O B:HOH766 3.3 28.9 1.0 OG B:SER425 3.7 29.3 1.0 CG A:ASP297 3.8 23.4 1.0 CE A:LYS318 3.8 27.0 1.0 OD1 A:ASP297 4.0 22.3 1.0 CD1 B:ILE495 4.2 42.0 1.0 O A:HOH849 4.3 47.9 1.0 O A:HOH801 4.3 26.6 1.0 CD2 B:LEU470 4.4 24.1 1.0 O A:HOH793 4.4 39.7 1.0 CA B:ASP473 4.5 41.3 1.0 N B:ASP473 4.7 35.4 1.0 N B:SER425 4.7 25.4 1.0 CB B:ASP473 4.7 49.2 1.0 CD1 B:LEU470 4.9 24.7 1.0 CB B:SER425 4.9 22.8 1.0 CD A:LYS318 5.0 22.8 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide


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 the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:49.7 occ:1.00 OE2 B:GLU567 2.6 65.8 1.0 O B:GLU355 3.1 43.8 1.0 CD B:GLU567 3.8 60.3 1.0 NZ B:LYS301 3.9 53.3 1.0 CD B:LYS301 4.0 38.5 1.0 CD2 B:LEU565 4.0 41.2 1.0 C B:GLU355 4.1 42.2 1.0 CD2 B:TYR351 4.2 44.7 1.0 CG B:GLU567 4.4 69.0 1.0 CE B:LYS301 4.4 44.7 1.0 CA B:GLU355 4.5 42.1 1.0 O B:HOH794 4.6 38.5 1.0 CB B:TYR351 4.6 45.1 1.0 CG B:GLU355 4.6 39.0 1.0 CG B:TYR351 4.7 44.3 1.0 OE1 B:GLU567 4.8 61.6 1.0 CE2 B:TYR351 4.9 38.8 1.0 CD1 B:LEU312 5.0 34.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide


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 the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:55.5 occ:1.00 OG B:SER310 3.3 48.2 1.0 NZ B:LYS301 3.3 53.3 1.0 OE2 B:GLU355 3.7 49.1 1.0 CE B:LYS301 3.8 44.7 1.0 CB B:SER310 4.1 28.3 1.0 CD B:GLU355 4.5 38.3 1.0 CG B:GLU355 4.6 39.0 1.0 CD2 B:LEU312 4.6 30.9 1.0 OD1 B:ASP356 4.9 36.1 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide


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 the Kelch Domain of Human KLHL12 in Complex with PEF1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:48.2 occ:1.00 NH1 B:ARG398 3.3 48.3 1.0 O B:PRO448 3.5 23.0 1.0 OH B:TYR446 3.5 24.9 1.0 CB B:PRO448 4.1 23.4 1.0 CA B:PRO448 4.1 22.1 1.0 C B:PRO448 4.3 27.9 1.0 OH B:TYR382 4.4 36.0 1.0 CZ B:ARG398 4.4 37.2 1.0 CZ B:TYR446 4.5 24.4 1.0 CE2 B:TYR446 4.6 18.4 1.0 NH2 B:ARG398 4.8 42.3 1.0 CE A:MET553 4.9 49.9 1.0 CD2 B:LEU409 4.9 30.3 1.0

A.E.Ramdass, E.V.Dalietou, Z.Chen, M.Platt, K.Aitmakhanova, O.Fedorov, A.N.Bullock. Structural Basis For Co-Adaptor and Antagonist Binding to the KLHL12 E3 Ligase To Be Published.