Sodium in PDB 6ttk: Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 Peptide

The structure of Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 Peptide, PDB code: 6ttk was solved by Z.Chen, E.Williams, A.C.W.Pike, C.Strain-Damerell, D.Wang, R.Chalk, N.Burgess-Brown, T.Krojer, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.98 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	80.225, 73.145, 101.845, 90.00, 94.50, 90.00
R / Rfree (%)	22.5 / 25.1

The structure of Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 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 DVL1 Peptide (pdb code 6ttk). 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 DVL1 Peptide, PDB code: 6ttk:
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 DVL1 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 DVL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:30.0 occ:1.00 O A:THR502 2.9 22.4 1.0 CA A:VAL503 3.7 14.8 1.0 C A:THR502 3.9 22.0 1.0 OD2 A:ASP545 4.0 20.2 1.0 N A:VAL503 4.2 19.5 1.0 N A:THR504 4.3 16.4 1.0 C A:VAL503 4.4 16.2 1.0 OD1 A:ASP545 4.5 20.9 1.0 CB A:VAL503 4.6 16.9 1.0 CG1 A:VAL503 4.6 14.4 1.0 CG A:ASP545 4.7 16.7 1.0 OG1 A:THR504 4.8 14.5 1.0 CG2 A:VAL503 4.8 15.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 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 DVL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:39.3 occ:1.00 O B:HOH859 2.9 28.9 1.0 CE1 B:PHE289 3.7 31.4 1.0 NH1 B:ARG320 3.8 26.2 1.0 CD B:ARG320 4.0 24.8 1.0 CE2 B:TYR337 4.0 31.5 1.0 CD1 B:PHE289 4.3 30.0 1.0 CD B:PRO295 4.4 31.1 1.0 CG B:PRO295 4.5 30.7 1.0 O B:HOH863 4.5 28.0 1.0 CZ B:PHE289 4.5 29.9 1.0 CZ B:ARG320 4.7 25.6 1.0 CA B:GLY339 4.7 35.1 1.0 O B:GLN293 4.7 33.4 1.0 CD2 B:TYR337 4.7 25.6 1.0 NE B:ARG320 4.8 25.3 1.0 OH B:TYR337 4.9 40.6 1.0 CZ B:TYR337 5.0 35.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 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 DVL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:36.1 occ:1.00 O B:HOH847 2.0 27.1 1.0 N B:LEU327 3.6 33.1 1.0 C B:SER326 3.7 32.4 1.0 OG B:SER326 3.8 30.1 1.0 O B:SER326 3.8 27.2 1.0 CA B:LEU327 3.8 33.2 1.0 CB B:SER326 3.8 29.6 1.0 N B:HIS328 4.2 44.7 1.0 C B:LEU327 4.3 37.7 1.0 CA B:SER326 4.4 26.9 1.0 N B:ASP329 4.4 47.1 1.0 O B:VAL564 4.6 28.0 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 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 DVL1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na601 b:30.0 occ:1.00 ND2 C:ASN472 3.4 13.0 1.0 OH C:TYR476 3.7 14.7 1.0 CB C:ASN472 3.7 11.4 1.0 CG C:ASN472 4.1 14.7 1.0 O A:HOH801 4.1 30.0 1.0 CB C:PRO542 4.3 14.5 1.0 CG C:PRO542 4.4 12.3 1.0 ND1 C:HIS474 4.4 14.8 1.0 O C:LEU471 4.6 10.6 1.0 CE1 C:HIS474 4.6 15.5 1.0 O A:PRO542 4.7 24.6 1.0 CZ C:TYR476 4.8 9.1 1.0 O C:ASN472 4.8 12.8 1.0 CE1 C:TYR476 4.9 9.2 1.0 CG C:HIS474 4.9 13.0 1.0 CA C:ASN472 5.0 11.6 1.0

Z.Chen, E.Williams, A.C.W.Pike, C.Strain-Damerell, D.Wang, R.Chalk, N.Burgess-Brown, T.Krojer, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.N.Bullock. Crystal Structure of the Kelch Domain of Human KLHL12 in Complex with DVL1 Peptide To Be Published.