Sodium in PDB 8oio: Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide

The structure of Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide, PDB code: 8oio was solved by E.V.Dalietou, Z.Chen, A.E.Ramdass, C.Manning, W.Richardson, K.Aitmakhanova, M.Platt, A.Pike, O.Fedorov, P.Brennan, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.52 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.469, 73.086, 103.734, 90, 98.81, 90
R / Rfree (%)	20 / 24.9

The structure of Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide (pdb code 8oio). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide, PDB code: 8oio:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 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 PLEKHA4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:39.6 occ:1.00 O B:HOH768 2.1 43.2 1.0 O B:TRP547 2.2 25.9 1.0 OG D:SER361 2.4 26.0 1.0 O B:HOH776 2.4 41.9 1.0 O D:HOH662 2.5 34.2 1.0 OG B:SER546 2.8 46.8 1.0 C B:TRP547 3.3 30.8 1.0 CB D:SER361 3.4 26.1 1.0 N D:SER361 3.9 25.0 1.0 N B:TRP547 4.1 28.3 1.0 N B:GLU548 4.1 28.0 1.0 CB B:SER546 4.1 43.1 1.0 CA B:GLU548 4.1 28.6 1.0 O B:HOH765 4.2 42.4 1.0 CB B:GLU548 4.3 27.8 1.0 CA D:SER361 4.3 25.7 1.0 CA B:TRP547 4.3 26.1 1.0 O D:HOH716 4.5 50.1 1.0 C B:SER546 4.6 28.3 1.0 CG2 B:THR507 4.9 29.4 1.0 CA B:SER546 4.9 37.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 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 PLEKHA4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:41.8 occ:1.00 O B:HOH753 2.4 41.5 1.0 O B:HOH734 2.5 40.9 1.0 OG B:SER361 2.8 26.5 0.9 OG B:SER361 3.6 32.1 0.1 CB B:SER361 3.7 32.7 0.1 CB B:SER361 3.7 32.7 0.9 N B:SER361 4.1 29.8 1.0 CA B:SER361 4.5 30.4 0.1 CA B:SER361 4.5 30.3 0.9

Sodium binding site 3 out of 3 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 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 PLEKHA4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na604 b:52.3 occ:1.00 OD1 B:ASN531 2.6 61.4 1.0 OG B:SER532 2.9 49.4 1.0 OD2 B:ASP529 2.9 31.4 1.0 CG B:ASN531 3.7 56.8 1.0 CB B:SER532 3.8 36.9 1.0 CG B:ASP529 3.8 36.0 1.0 OD1 B:ASP529 3.9 30.7 1.0 N B:SER532 4.2 33.7 1.0 CB B:ASN531 4.2 37.5 1.0 O B:HOH707 4.2 35.4 1.0 CA B:SER532 4.6 36.9 1.0 C B:ASN531 4.8 32.8 1.0 ND2 B:ASN531 4.9 57.7 1.0

E.V.Dalietou, Z.Chen, A.E.Ramdass, C.Manning, W.Richardson, K.Aitmakhanova, M.Platt, A.Pike, O.Fedorov, P.Brennan, A.N.Bullock. Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with PLEKHA4 Peptide To Be Published.