Sodium in PDB 8h58: Crystal Structure of Yhaj Effector Binding Domain

The structure of Crystal Structure of Yhaj Effector Binding Domain, PDB code: 8h58 was solved by M.Kim, S.E.Ryu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.91 / 2.64
Space group	H 3 1
Cell size a, b, c (Å), α, β, γ (°)	215.193, 215.193, 263.409, 90, 90, 120
R / Rfree (%)	17.7 / 23.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Yhaj Effector Binding Domain (pdb code 8h58). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Crystal Structure of Yhaj Effector Binding Domain, PDB code: 8h58:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:33.4 occ:1.00 OD2 A:ASP230 2.2 34.4 1.0 OD1 A:ASP230 2.4 37.7 1.0 CG A:ASP230 2.6 39.5 1.0 OG1 B:THR109 2.6 47.1 1.0 CB B:THR109 2.9 40.5 1.0 N B:THR109 3.6 47.0 1.0 OG1 B:THR131 3.7 55.1 1.0 CA B:THR109 3.9 38.9 1.0 CG2 B:THR109 4.0 30.2 1.0 CB A:ASP230 4.1 38.7 1.0 CG2 A:THR227 4.3 38.8 1.0 OG1 A:THR227 4.3 42.6 1.0 CD B:PRO110 4.4 45.5 1.0 O B:VAL107 4.8 63.7 1.0 C B:PRO108 4.8 50.8 1.0 C B:THR109 5.0 45.5 1.0 CA A:ASP230 5.0 44.1 1.0 CB B:THR131 5.0 45.2 1.0

Sodium binding site 2 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:37.8 occ:1.00 OG1 A:THR109 2.1 40.3 1.0 OD2 B:ASP230 2.3 46.8 1.0 OG1 A:THR131 2.4 39.7 1.0 CB A:THR109 3.1 43.4 1.0 CG B:ASP230 3.2 39.1 1.0 OD1 B:ASP230 3.4 46.2 1.0 CB A:THR131 3.6 39.8 1.0 CG2 A:THR131 3.9 31.6 1.0 OG1 A:THR103 3.9 42.3 1.0 N A:THR109 4.0 52.3 1.0 CG2 A:THR109 4.1 32.7 1.0 CA A:THR109 4.1 46.9 1.0 O A:VAL107 4.4 52.6 1.0 CB B:ASP230 4.6 35.7 1.0 CA A:THR131 4.6 42.2 1.0 CG2 B:THR227 4.7 46.4 1.0 OG1 B:THR227 4.8 56.3 1.0 O A:THR103 5.0 48.1 1.0

Sodium binding site 3 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:32.3 occ:1.00 OD2 D:ASP230 2.1 47.6 1.0 OG1 C:THR109 2.6 38.7 1.0 OG1 C:THR131 2.8 45.5 1.0 CG D:ASP230 2.8 50.9 1.0 OD1 D:ASP230 2.9 56.2 1.0 CB C:THR109 3.3 40.0 1.0 CB C:THR131 4.0 36.4 1.0 N C:THR109 4.1 44.1 1.0 CG2 C:THR131 4.2 31.4 1.0 OG1 D:THR227 4.2 37.9 1.0 CG2 D:THR227 4.2 39.9 1.0 CB D:ASP230 4.3 50.4 1.0 CA C:THR109 4.3 42.0 1.0 CG2 C:THR109 4.4 34.5 1.0 OG1 C:THR103 4.6 45.1 1.0 O C:VAL107 4.7 45.7 1.0 CB D:THR227 4.9 42.0 1.0

Sodium binding site 4 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:49.4 occ:1.00 OG1 D:THR131 1.9 40.4 1.0 OD2 C:ASP230 2.1 48.8 1.0 OG1 D:THR109 2.9 44.8 1.0 CB D:THR131 3.2 35.6 1.0 CG C:ASP230 3.2 53.1 1.0 CG2 D:THR131 3.6 39.6 1.0 OD1 C:ASP230 3.6 46.8 1.0 CG2 C:THR227 3.7 59.0 1.0 CB D:THR109 3.8 47.4 1.0 OG1 C:THR227 4.2 48.7 1.0 CA D:THR131 4.4 40.5 1.0 CB C:ASP230 4.5 46.5 1.0 OG1 D:THR103 4.5 63.8 1.0 CG2 D:THR109 4.6 33.8 1.0 CB C:THR227 4.6 52.6 1.0 N D:THR131 4.7 47.8 1.0 N D:THR109 5.0 52.7 1.0

Sodium binding site 5 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Na301 b:40.9 occ:1.00 OG1 F:THR109 2.7 47.5 1.0 OG1 F:THR131 2.9 39.3 1.0 O F:VAL107 3.3 52.6 1.0 OD2 E:ASP230 3.4 47.3 1.0 CG2 F:THR131 3.5 37.4 1.0 OG1 F:THR103 3.7 54.1 1.0 CB F:THR131 3.8 39.1 1.0 CB F:THR109 3.8 42.7 1.0 N F:THR109 3.9 44.2 1.0 O F:THR103 4.3 52.4 1.0 CG E:ASP230 4.3 39.4 1.0 O F:GLU104 4.3 44.4 1.0 CA F:THR109 4.4 45.0 1.0 OD1 E:ASP230 4.4 39.5 1.0 C F:VAL107 4.5 44.0 1.0 O F:ALA105 4.5 36.8 1.0 CB F:THR103 4.7 45.5 1.0 CA F:ALA105 4.7 38.2 1.0 CA F:THR131 4.7 43.6 1.0 C F:PRO108 4.7 40.3 1.0 CA F:PRO108 4.9 41.2 1.0 C F:ALA105 4.9 42.8 1.0 C F:GLU104 5.0 42.4 1.0

Sodium binding site 6 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Na301 b:41.0 occ:1.00 OG1 G:THR109 2.6 32.3 1.0 OG1 G:THR131 2.9 33.6 1.0 OG1 G:THR103 2.9 38.5 1.0 O G:VAL107 3.0 33.6 1.0 CG2 G:THR131 3.5 35.4 1.0 O G:THR103 3.6 53.9 1.0 CB G:THR131 3.7 39.4 1.0 CB G:THR109 3.7 34.1 1.0 N G:THR109 3.8 35.4 1.0 O G:GLU104 3.9 54.1 1.0 CB G:THR103 3.9 41.4 1.0 OD2 H:ASP230 4.1 33.7 1.0 C G:VAL107 4.2 35.7 1.0 CA G:THR109 4.2 36.0 1.0 C G:THR103 4.3 46.5 1.0 CA G:THR131 4.4 41.5 1.0 C G:GLU104 4.5 44.5 1.0 C G:PRO108 4.6 38.0 1.0 O G:ALA105 4.6 35.9 1.0 CA G:ALA105 4.7 35.3 1.0 CA G:THR103 4.7 39.9 1.0 CA G:PRO108 4.9 40.2 1.0 CG H:ASP230 4.9 37.4 1.0 OD1 H:ASP230 4.9 35.0 1.0 CG2 G:THR109 4.9 30.4 1.0 C G:ALA105 4.9 33.1 1.0 N G:ALA105 5.0 37.2 1.0 CG2 G:THR103 5.0 38.6 1.0 N G:PRO108 5.0 43.7 1.0

Sodium binding site 7 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:44.6 occ:1.00 OG1 H:THR109 2.4 50.5 1.0 OG1 H:THR131 2.7 34.5 1.0 OD2 G:ASP230 2.8 50.7 1.0 CB H:THR109 3.4 43.8 1.0 CG G:ASP230 3.7 50.0 1.0 CG2 H:THR131 3.7 36.1 1.0 OD1 G:ASP230 3.8 45.5 1.0 CB H:THR131 3.8 43.6 1.0 N H:THR109 3.8 38.2 1.0 O H:VAL107 3.8 63.3 1.0 OG1 H:THR103 3.9 55.5 1.0 CA H:THR109 4.2 40.8 1.0 CG2 H:THR109 4.6 36.3 1.0 O H:THR103 4.8 41.3 1.0 CA H:THR131 4.8 46.1 1.0 CG2 G:THR227 4.8 42.6 1.0 C H:PRO108 4.9 40.5 1.0 C H:VAL107 5.0 44.9 1.0

Sodium binding site 8 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Na301 b:26.7 occ:1.00 O I:VAL107 2.7 44.0 1.0 OG1 I:THR109 2.9 35.6 1.0 OG1 I:THR103 3.2 40.7 1.0 OG1 I:THR131 3.3 42.9 1.0 O I:GLU104 3.5 43.9 1.0 CG2 I:THR131 3.6 35.3 1.0 O I:THR103 3.7 50.6 1.0 N I:THR109 3.8 47.3 1.0 C I:VAL107 3.9 36.6 1.0 CB I:THR131 4.0 41.0 1.0 CB I:THR109 4.0 44.0 1.0 CB I:THR103 4.1 41.5 1.0 O I:ALA105 4.1 45.6 1.0 OD2 J:ASP230 4.3 50.8 1.0 C I:GLU104 4.3 41.9 1.0 CA I:ALA105 4.3 41.7 1.0 C I:THR103 4.3 41.0 1.0 CA I:THR109 4.4 47.9 1.0 C I:ALA105 4.4 43.4 1.0 C I:PRO108 4.6 43.2 1.0 CA I:PRO108 4.7 46.0 1.0 N I:ALA105 4.7 42.3 1.0 CA I:THR131 4.7 43.5 1.0 N I:PRO108 4.7 46.3 1.0 N I:VAL107 4.7 38.6 1.0 CA I:VAL107 4.8 35.0 1.0 CA I:THR103 4.8 34.9 1.0

Sodium binding site 9 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ J:Na301 b:37.8 occ:1.00 OG1 J:THR109 2.3 51.9 1.0 OG1 J:THR131 2.5 46.4 1.0 OG1 J:THR103 2.9 63.3 1.0 O J:VAL107 3.4 47.0 1.0 CG2 J:THR131 3.4 35.9 1.0 CB J:THR131 3.5 42.6 1.0 CB J:THR109 3.5 37.5 1.0 OD2 I:ASP230 3.7 39.8 1.0 O J:THR103 3.7 56.9 1.0 N J:THR109 3.8 39.0 1.0 CB J:THR103 4.0 52.4 1.0 CA J:THR109 4.1 37.0 1.0 CA J:THR131 4.2 47.4 1.0 O J:GLU104 4.3 46.5 1.0 C J:THR103 4.4 52.6 1.0 C J:VAL107 4.6 46.0 1.0 CG I:ASP230 4.6 47.8 1.0 CG2 J:THR109 4.7 36.1 1.0 C J:PRO108 4.8 44.0 1.0 CA J:THR103 4.8 49.2 1.0 N J:THR131 4.8 54.0 1.0 OD1 I:ASP230 4.8 56.0 1.0 C J:GLU104 4.9 52.8 1.0

Sodium binding site 10 out of 15 in the Crystal Structure of Yhaj Effector Binding Domain


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 Yhaj Effector Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:46.3 occ:1.00 OD2 K:ASP230 1.9 60.1 1.0 OG1 L:THR131 2.0 56.0 1.0 OG1 L:THR109 2.9 47.1 1.0 CG K:ASP230 2.9 58.5 1.0 CB L:THR131 3.2 36.3 1.0 OD1 K:ASP230 3.4 48.3 1.0 CG2 L:THR131 3.4 35.2 1.0 CB L:THR109 3.9 40.0 1.0 CG2 K:THR227 3.9 50.2 1.0 OG1 K:THR227 4.1 55.1 1.0 CB K:ASP230 4.3 49.7 1.0 CA L:THR131 4.4 42.3 1.0 OG1 L:THR103 4.4 49.9 1.0 CB K:THR227 4.6 50.6 1.0 CG2 L:THR109 4.7 43.3 1.0 N L:THR109 4.8 45.2 1.0 N L:THR131 4.8 41.1 1.0 CA L:THR109 4.9 43.1 1.0

M.Kim, R.Kang, T.J.Jeon, S.E.Ryu. Structural Basis of Transcription Factor Yhaj For Dnt Detection. Iscience V. 26 07984 2023.
ISSN: ESSN 2589-0042
PubMed: 37822509
DOI: 10.1016/J.ISCI.2023.107984