Sodium in PDB 2xn4: Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven)

The structure of Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven), PDB code: 2xn4 was solved by P.Canning, V.Hozjan, C.D.O.Cooper, V.Ayinampudi, M.Vollmar, A.C.W.Pike, F.Von Delft, J.Weigelt, 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)	19.82 / 1.99
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	45.994, 46.005, 71.762, 86.68, 82.75, 68.48
R / Rfree (%)	16.9 / 22.2

The binding sites of Sodium atom in the Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven) (pdb code 2xn4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven), PDB code: 2xn4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven)


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 KLHL2 (Mayven) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na900 b:3.1 occ:1.00 NH1 A:ARG345 3.1 7.9 1.0 NE A:ARG366 3.2 3.7 1.0 OG A:SER391 3.3 2.9 1.0 NH2 A:ARG366 3.4 4.0 1.0 CB A:SER391 3.6 3.0 1.0 CZ A:ARG366 3.7 3.9 1.0 CD2 A:PHE408 3.7 5.2 1.0 CG2 A:THR392 3.8 2.7 1.0 CD A:ARG345 3.8 4.1 1.0 CZ A:ARG345 4.2 9.6 1.0 CG A:ARG366 4.2 3.5 1.0 CD A:ARG366 4.3 4.0 1.0 NE A:ARG345 4.5 4.0 1.0 CE2 A:PHE408 4.5 5.7 1.0 O A:HOH2252 4.5 29.3 1.0 CB A:PHE408 4.6 3.2 1.0 C A:SER391 4.6 2.7 1.0 CG A:PHE408 4.7 3.5 1.0 CA A:SER391 4.7 2.9 1.0 O A:SER391 4.8 2.8 1.0 CB A:PHE361 4.8 3.2 1.0 O A:PHE408 4.8 3.3 1.0 CD1 A:PHE361 4.9 3.7 1.0 CG A:PHE361 4.9 3.5 1.0 N A:THR392 5.0 2.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Kelch Domain of Human KLHL2 (Mayven)


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 KLHL2 (Mayven) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na900 b:2.0 occ:1.00 NE B:ARG366 3.1 3.9 1.0 NH1 B:ARG345 3.1 9.0 1.0 NH2 B:ARG366 3.2 4.5 1.0 OG B:SER391 3.2 2.9 1.0 CZ B:ARG366 3.6 4.2 1.0 CB B:SER391 3.6 3.0 1.0 CD B:ARG345 3.7 4.6 1.0 CD2 B:PHE408 3.7 6.0 1.0 CG2 B:THR392 3.7 2.9 1.0 CZ B:ARG345 4.2 11.7 1.0 CG B:ARG366 4.2 3.6 1.0 CD B:ARG366 4.2 5.4 1.0 NE B:ARG345 4.4 5.2 1.0 CE2 B:PHE408 4.5 7.7 1.0 CB B:PHE408 4.6 3.3 1.0 CG B:PHE408 4.6 3.6 1.0 C B:SER391 4.7 2.7 1.0 CB B:PHE361 4.8 3.4 1.0 CA B:SER391 4.8 2.8 1.0 O B:SER391 4.8 2.8 1.0 CD1 B:PHE361 4.8 3.9 1.0 CG B:PHE361 4.8 3.8 1.0 CG B:ARG345 4.9 3.0 1.0 NH1 B:ARG366 4.9 5.2 1.0 N B:THR392 5.0 2.6 1.0 CB B:ARG345 5.0 2.8 1.0 CB B:THR392 5.0 2.7 1.0

P.Canning, C.D.O.Cooper, T.Krojer, J.W.Murray, A.C.W.Pike, A.Chaikuad, T.Keates, C.Thangaratnarajah, V.Hojzan, B.D.Marsden, O.Gileadi, S.Knapp, F.Von Delft, A.N.Bullock. Structural Basis For CUL3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases. J.Biol.Chem. V. 288 7803 2013.
ISSN: ISSN 0021-9258
PubMed: 23349464
DOI: 10.1074/JBC.M112.437996