Sodium in PDB 6gy5: Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide

The structure of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide, PDB code: 6gy5 was solved by Z.Chen, V.Hozjan, C.Strain-Damerell, E.Williams, D.Wang, C.D.O.Cooper, C.E.Sanvitale, M.Fairhead, E.P.Carpenter, A.C.W.Pike, T.Krojer, V.Srikannathasan, F.Sorrell, C.Johansson, S.Mathea, N.Burgess-Brown, 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)	29.65 / 1.09
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.459, 47.361, 151.933, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.2

The structure of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide (pdb code 6gy5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 14 binding sites of Sodium where determined in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide, PDB code: 6gy5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 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 KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na711 b:17.3 occ:1.00 N A:SER333 3.2 10.6 1.0 O A:HOH824 3.2 40.6 1.0 O A:HOH904 3.2 22.5 1.0 O A:HOH878 3.5 21.5 1.0 OG A:SER333 3.5 14.2 1.0 N A:SER334 3.6 10.8 1.0 CG2 A:ILE332 3.7 12.5 1.0 CA A:ILE332 3.8 10.4 1.0 C A:ILE332 3.9 9.3 1.0 CA A:SER333 4.1 10.5 1.0 CB A:SER334 4.2 11.9 1.0 CB A:ILE332 4.3 10.1 1.0 C A:SER333 4.3 10.5 1.0 CB A:SER333 4.3 12.4 1.0 OG A:SER334 4.4 12.3 1.0 CA A:SER334 4.5 10.7 1.0 O A:HOH1183 4.5 32.7 1.0 O A:ALA331 4.7 12.4 1.0 CG1 A:ILE332 4.7 11.8 1.0 N A:ILE332 5.0 9.6 1.0

Sodium binding site 2 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 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 KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:16.9 occ:1.00 O A:HOH1097 2.6 38.8 1.0 N A:VAL598 3.2 10.7 1.0 CA A:GLY597 3.6 10.2 1.0 O A:HOH1163 3.6 47.4 1.0 O A:HOH841 3.7 34.5 1.0 N A:VAL362 3.7 10.6 1.0 O A:HOH922 3.8 30.2 1.0 O A:HOH843 3.8 43.2 1.0 OG A:SER361 3.9 16.0 1.0 CG2 A:VAL362 3.9 15.3 1.0 C A:GLY597 3.9 10.2 1.0 CB A:VAL362 4.0 11.8 1.0 CA A:SER361 4.1 9.7 1.0 O A:VAL598 4.1 14.0 1.0 C A:SER361 4.2 9.1 1.0 CA A:VAL598 4.2 11.8 1.0 CB A:VAL598 4.4 12.0 1.0 CA A:VAL362 4.5 9.8 1.0 O A:VAL596 4.5 10.1 1.0 CB A:SER361 4.6 11.6 1.0 C A:VAL598 4.7 13.5 1.0 CG2 A:VAL598 4.7 13.7 1.0 N A:GLY597 4.8 9.8 1.0 O A:HOH806 4.8 13.2 1.0

Sodium binding site 3 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 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 KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na713 b:18.3 occ:1.00 O A:HOH820 2.9 38.0 1.0 O A:HOH1028 3.1 15.7 1.0 ND2 A:ASN481 3.1 12.6 1.0 CE1 A:HIS488 3.7 17.2 1.0 CE1 A:PHE461 3.7 14.8 1.0 O A:HOH807 3.8 31.7 1.0 ND1 A:HIS488 3.8 19.5 1.0 OE1 A:GLU484 3.9 20.1 1.0 CZ A:PHE461 4.0 13.8 1.0 OE2 A:GLU484 4.1 22.2 1.0 CB A:ASN481 4.1 10.0 1.0 CG A:ASN481 4.1 11.5 1.0 CD A:GLU484 4.2 17.3 1.0 NE2 A:HIS488 4.5 22.7 1.0 O A:HOH1157 4.6 43.9 1.0 CG A:HIS488 4.7 18.6 1.0 CD1 A:PHE461 4.9 12.0 1.0

Sodium binding site 4 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 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 KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:22.1 occ:1.00 O A:HOH1067 2.8 31.6 1.0 OE1 A:GLU525 2.8 9.7 1.0 O A:HOH1164 2.9 50.5 1.0 CD A:PRO536 3.4 13.6 0.6 N A:PRO536 3.4 11.0 1.0 C A:SER535 3.5 9.5 1.0 N A:SER535 3.7 9.4 1.0 CA A:SER535 3.7 10.3 1.0 C A:TRP534 3.7 10.1 1.0 CD A:GLU525 3.7 8.5 1.0 O A:TRP534 3.7 12.5 1.0 CB A:GLU525 3.7 8.0 1.0 CG A:PRO536 3.8 16.7 0.6 CD A:PRO536 3.8 14.9 0.4 CB A:TRP534 3.9 9.2 1.0 O A:HOH885 3.9 15.8 1.0 N A:GLY494 4.0 9.0 1.0 O A:SER535 4.0 9.1 1.0 CA A:PRO536 4.1 10.2 0.4 CA A:PRO536 4.1 10.4 0.6 CA A:GLY494 4.2 10.0 1.0 CG A:GLU525 4.3 8.9 1.0 CA A:TRP534 4.4 8.7 1.0 OE2 A:GLU525 4.5 8.8 1.0 CB A:PRO536 4.5 14.1 0.4 CB A:PRO536 4.6 15.3 0.6 O A:HOH883 4.7 27.9 1.0 CG A:PRO536 4.8 13.3 0.4 O A:HOH954 5.0 15.7 1.0

Sodium binding site 5 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na715 b:23.5 occ:1.00 O A:HOH984 3.1 29.7 1.0 O A:HOH1177 3.2 41.6 1.0 O A:HOH1073 4.3 48.0 1.0 O A:HOH891 4.3 24.9 1.0 NH1 A:ARG496 4.6 17.7 1.0 O A:HOH1112 4.6 53.9 1.0 NH2 A:ARG496 4.8 17.1 1.0

Sodium binding site 6 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na716 b:14.4 occ:1.00 O A:HOH991 2.8 26.5 1.0 O A:HOH1143 2.9 37.1 1.0 O A:HOH814 3.0 19.5 1.0 N A:ARG496 3.2 7.7 1.0 O A:HOH1034 3.6 20.6 1.0 CG A:ARG496 3.8 9.8 1.0 CB A:ARG496 3.8 8.8 1.0 CG2 A:THR495 3.9 11.2 1.0 CA A:THR495 3.9 8.4 1.0 O A:HOH1135 4.0 40.1 1.0 C A:THR495 4.0 7.6 1.0 CA A:ARG496 4.1 7.8 1.0 CD A:ARG496 4.1 12.8 1.0 CB A:ASP516 4.1 9.3 1.0 OD2 A:ASP516 4.3 11.9 1.0 O A:HOH971 4.3 34.2 1.0 CB A:THR495 4.4 8.7 1.0 O A:ARG496 4.5 8.2 1.0 OD2 A:ASP517 4.6 17.3 0.7 NE A:ARG496 4.7 13.1 1.0 CG A:ASP516 4.7 9.1 1.0 NH1 A:ARG496 4.8 17.7 1.0 O A:GLY494 4.8 11.8 1.0 C A:ARG496 4.8 6.8 1.0 OG1 A:THR495 4.9 10.8 1.0 CZ A:ARG496 5.0 13.6 1.0

Sodium binding site 7 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na717 b:18.0 occ:1.00 O A:HOH1074 2.9 45.5 1.0 O A:HOH953 3.0 32.6 1.0 N A:TYR567 3.2 11.1 1.0 CG2 A:THR566 3.6 18.6 1.0 CD2 A:TYR567 3.7 13.1 1.0 CB A:TYR567 3.9 12.1 1.0 CA A:THR566 3.9 12.9 1.0 O A:TYR567 3.9 11.9 1.0 CA A:TYR567 4.0 11.0 1.0 C A:THR566 4.0 11.0 1.0 CD A:ARG590 4.1 14.5 1.0 CG A:TYR567 4.3 11.4 1.0 CB A:THR566 4.3 15.2 1.0 NH1 A:ARG590 4.4 18.1 1.0 NE A:ARG590 4.4 18.3 1.0 C A:TYR567 4.5 10.9 1.0 OG A:SER328 4.5 23.0 1.0 O A:HOH955 4.6 44.4 1.0 CZ A:ARG590 4.6 16.4 1.0 CE2 A:TYR567 4.8 14.6 1.0 O A:THR565 4.8 16.4 1.0 OG1 A:THR566 4.9 17.0 1.0

Sodium binding site 8 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na718 b:17.9 occ:1.00 NE2 A:GLN421 2.3 12.5 1.0 OG A:SER405 2.9 9.9 1.0 N U:LEU1339 3.1 8.7 1.0 N U:ASP1338 3.1 9.9 1.0 CD A:GLN421 3.5 16.3 1.0 CB A:SER405 3.5 9.0 1.0 CB U:PRO1337 3.7 19.0 1.0 CA U:ASP1338 3.7 9.1 1.0 CB U:ASP1338 3.7 10.0 1.0 C U:PRO1337 3.8 10.4 1.0 CB U:LEU1339 3.8 9.4 1.0 CE1 A:HIS499 3.8 9.3 1.0 C U:ASP1338 3.9 8.8 1.0 CA U:PRO1337 4.0 11.0 1.0 CA U:LEU1339 4.0 8.7 1.0 CG A:GLN421 4.1 10.3 1.0 CD1 A:LEU451 4.2 13.3 1.0 OE1 A:GLN421 4.4 20.3 1.0 CG2 A:THR404 4.4 10.8 1.0 NE2 A:HIS499 4.5 9.2 1.0 O U:PRO1337 4.7 11.1 1.0 CD2 A:LEU451 4.8 17.0 1.0 ND1 A:HIS499 4.8 8.6 1.0 O A:THR404 4.8 8.0 1.0 CA A:SER405 4.9 7.9 1.0 CG U:ASP1338 4.9 9.6 1.0 N A:SER405 5.0 7.7 1.0 CG A:LEU451 5.0 16.1 1.0

Sodium binding site 9 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na719 b:13.3 occ:1.00 O A:HOH851 3.1 16.5 1.0 O A:HOH1117 3.1 41.5 1.0 N A:ARG449 3.2 8.5 1.0 O A:HOH1090 3.5 31.6 1.0 CG2 A:THR448 3.9 10.8 1.0 CA A:THR448 3.9 8.1 1.0 CB A:ARG449 3.9 11.7 1.0 CG A:ARG449 3.9 12.7 1.0 C A:THR448 4.1 8.0 1.0 CA A:ARG449 4.2 8.9 1.0 CB A:ASP469 4.2 11.9 1.0 CD A:ARG449 4.3 19.5 1.0 CB A:THR448 4.4 9.0 1.0 O A:HOH1038 4.4 38.5 1.0 O A:ARG449 4.5 9.9 1.0 O A:SER447 4.7 12.2 1.0 O A:HOH804 4.8 45.5 1.0 OD2 A:ASP469 4.9 14.9 1.0 C A:ARG449 4.9 8.5 1.0 OG1 A:THR448 4.9 10.6 1.0 NE A:ARG449 5.0 23.2 1.0

Sodium binding site 10 out of 14 in the Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Kelch Domain of Human KLHL20 in Complex with DAPK1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na720 b:18.4 occ:1.00 O A:HOH893 3.0 26.2 1.0 O A:HOH1008 3.0 30.7 1.0 O A:HOH1123 3.1 19.7 1.0 O U:HOH1413 3.2 23.2 1.0 N A:TYR378 3.3 10.3 1.0 CD1 A:TYR378 3.6 10.6 1.0 CA A:SER377 3.7 12.2 1.0 CB A:SER377 3.9 13.1 1.0 C A:SER377 4.0 10.2 1.0 CB A:TYR378 4.1 10.9 1.0 O A:HOH818 4.1 43.7 1.0 O A:HOH1113 4.2 17.4 1.0 CA A:TYR378 4.2 10.3 1.0 CG A:TYR378 4.3 10.3 1.0 OG A:SER377 4.4 16.8 1.0 O A:TYR378 4.4 11.6 1.0 O A:HOH1182 4.5 53.9 1.0 CE1 A:TYR378 4.6 10.6 1.0 O A:SER376 4.6 17.5 1.0 O A:HOH1130 4.6 40.4 1.0 C A:TYR378 4.8 9.7 1.0 CD2 U:LEU1334 4.9 23.4 1.0 N A:SER377 4.9 12.5 1.0

Z.Chen, S.Picaud, P.Filippakopoulos, V.D'angiolella, A.N.Bullock. Structural Basis For Recruitment of DAPK1 to the KLHL20 E3 Ligase. Structure V. 27 1395 2019.
ISSN: ISSN 0969-2126
PubMed: 31279627
DOI: 10.1016/J.STR.2019.06.005