Sodium in PDB 6rog: Crystal Structure of the Kelch Domain of Human KEAP1

The structure of Crystal Structure of the Kelch Domain of Human KEAP1, PDB code: 6rog was solved by R.Sethi, T.Krojer, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.N.Bullock, F.Von Delft, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.24 / 2.16
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.300, 76.440, 213.630, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.6

The binding sites of Sodium atom in the Crystal Structure of the Kelch Domain of Human KEAP1 (pdb code 6rog). 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 KEAP1, PDB code: 6rog:
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 KEAP1


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 KEAP1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Na706 b:53.6 occ:1.00 O X:VAL512 2.3 37.3 1.0 O X:VAL465 2.3 40.5 1.0 O X:HOH983 2.4 52.5 1.0 O X:HOH813 2.5 57.4 1.0 O X:HOH944 2.6 36.9 1.0 C X:VAL512 3.4 42.1 1.0 C X:VAL465 3.6 40.9 1.0 O X:HOH942 4.1 37.7 1.0 CA X:CYS513 4.1 40.0 1.0 N X:CYS513 4.2 40.4 1.0 N X:VAL465 4.3 38.8 1.0 O X:HOH935 4.4 37.7 1.0 CA X:VAL465 4.4 39.2 1.0 CA X:VAL512 4.5 39.1 1.0 N X:ALA466 4.5 41.8 1.0 CB X:VAL512 4.6 40.7 1.0 O X:HOH955 4.6 59.1 1.0 CB X:CYS513 4.7 39.0 1.0 CA X:ALA466 4.7 43.3 1.0 O X:VAL418 4.7 36.1 1.0 CG1 X:VAL512 4.8 42.2 1.0 CG2 X:ILE559 4.8 43.8 1.0 N X:VAL512 4.9 37.0 1.0 CB X:VAL465 4.9 41.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Kelch Domain of Human KEAP1


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 KEAP1 within 5.0Å range: probe atom residue distance (Å) B Occ X:Na707 b:51.3 occ:1.00 O X:SER383 2.3 44.3 1.0 OD1 X:ASN382 2.5 44.5 1.0 O X:HOH980 2.5 49.4 1.0 OD1 X:ASN387 2.6 56.6 1.0 O X:HOH977 2.6 53.3 1.0 O X:GLY386 2.9 47.3 1.0 CG X:ASN387 3.3 53.5 1.0 C X:SER383 3.4 49.2 1.0 CG X:ASN382 3.5 46.9 1.0 N X:SER383 3.5 47.0 1.0 C X:GLY386 3.5 46.3 1.0 ND2 X:ASN387 3.8 48.8 1.0 C X:ASN382 3.8 45.1 1.0 O X:HOH916 3.9 50.9 1.0 CA X:ASN382 3.9 44.7 1.0 O X:HOH913 4.1 52.0 1.0 CA X:SER383 4.1 47.9 1.0 N X:ASN387 4.1 48.5 1.0 CB X:ASN382 4.2 43.9 1.0 O A:HOH986 4.2 57.4 1.0 CA X:GLY386 4.3 48.4 1.0 N X:GLY386 4.3 47.5 1.0 ND2 X:ASN382 4.4 42.6 1.0 CA X:ASN387 4.4 50.0 1.0 CB X:ASN387 4.5 50.5 1.0 N X:PRO384 4.5 48.7 1.0 O X:ASN382 4.7 44.5 1.0 CA X:PRO384 4.7 50.6 1.0 C X:PRO384 4.9 47.0 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Kelch Domain of Human KEAP1


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 KEAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:54.5 occ:1.00 OD1 A:ASN387 2.4 54.7 1.0 O A:HOH927 2.5 54.9 1.0 O A:HOH991 2.5 53.8 1.0 O A:SER383 2.5 36.7 1.0 OD1 A:ASN382 2.6 47.1 1.0 O A:GLY386 2.8 42.1 1.0 CG A:ASN387 3.3 49.6 1.0 C A:GLY386 3.4 45.5 1.0 CG A:ASN382 3.5 40.9 1.0 C A:SER383 3.6 40.7 1.0 O A:HOH989 3.6 56.5 1.0 N A:SER383 3.7 38.2 1.0 ND2 A:ASN387 3.8 53.9 1.0 C A:ASN382 4.0 38.4 1.0 CA A:ASN382 4.1 39.8 1.0 N A:ASN387 4.1 45.6 1.0 CA A:GLY386 4.1 45.9 1.0 N A:GLY386 4.1 50.9 1.0 O A:HOH908 4.3 43.3 1.0 CB A:ASN382 4.3 39.9 1.0 CA A:SER383 4.3 40.7 1.0 ND2 A:ASN382 4.4 37.7 1.0 CA A:ASN387 4.4 45.4 1.0 CB A:ASN387 4.5 46.6 1.0 N A:PRO384 4.6 42.1 1.0 O A:HOH967 4.7 55.0 1.0 O X:HOH974 4.8 53.6 1.0 CA A:PRO384 4.8 47.2 1.0 O A:ASN382 4.9 39.7 1.0 C A:PRO384 4.9 45.7 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Kelch Domain of Human KEAP1


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 KEAP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:59.8 occ:1.00 O A:VAL512 2.4 35.1 1.0 O A:VAL465 2.5 44.7 1.0 O A:HOH994 2.5 52.6 1.0 O A:HOH973 2.6 44.2 1.0 O A:HOH896 2.6 58.1 1.0 O A:HOH801 2.6 53.3 1.0 C A:VAL512 3.5 38.8 1.0 C A:VAL465 3.7 46.1 1.0 CA A:CYS513 4.2 40.3 1.0 O A:HOH988 4.2 51.4 1.0 O A:HOH970 4.2 52.4 1.0 N A:CYS513 4.3 40.3 1.0 O A:HOH961 4.4 41.6 1.0 N A:VAL465 4.4 40.2 1.0 O A:HOH964 4.5 41.2 1.0 CA A:VAL465 4.6 41.5 1.0 O A:HOH942 4.6 58.5 1.0 O1 A:FMT703 4.6 78.7 1.0 CA A:VAL512 4.6 37.6 1.0 N A:ALA466 4.6 42.9 1.0 CB A:CYS513 4.7 39.0 1.0 CG2 A:ILE559 4.7 40.3 1.0 O A:VAL418 4.7 38.9 1.0 CA A:ALA466 4.8 43.4 1.0 CB A:VAL512 4.8 38.4 1.0 N A:VAL512 4.9 37.5 1.0 O A:HOH947 5.0 52.8 1.0

R.Sethi, T.Krojer, C.Bountra, C.H.Arrowsmith, A.M.Edwards, A.N.Bullock, F.Von Delft. Crystal Structure of the Kelch Domain of Human KEAP1 To Be Published.