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Sodium in PDB 8h5a: Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)

Protein crystallography data

The structure of Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound), PDB code: 8h5a 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) 35.00 / 2.80
Space group H 3 1
Cell size a, b, c (Å), α, β, γ (°) 215.745, 215.745, 264.158, 90, 90, 120
R / Rfree (%) 18.4 / 23.2

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound) (pdb code 8h5a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound), PDB code: 8h5a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 8h5a

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Sodium binding site 1 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:59.6
occ:1.00
 OG1 A:THR109 2.2 63.6 1.0
OD2 B:ASP230 2.4 50.1 1.0
CB A:THR109 3.0 58.1 1.0
CG B:ASP230 3.3 49.4 1.0
OG1 A:THR131 3.3 38.5 1.0
OD1 B:ASP230 3.4 73.2 1.0
N A:THR109 3.5 66.0 1.0
CA A:THR109 3.8 55.8 1.0
O A:VAL107 3.9 56.7 1.0
CG2 A:THR131 4.2 40.0 1.0
CG2 A:THR109 4.2 47.8 1.0
OG1 A:THR103 4.3 61.9 1.0
CB A:THR131 4.4 39.6 1.0
CG2 B:THR227 4.5 65.1 1.0
C A:PRO108 4.6 67.6 1.0
CB B:ASP230 4.7 44.0 1.0
CA A:PRO108 4.9 60.0 1.0
CD A:PRO110 5.0 40.1 1.0

Sodium binding site 2 out of 16 in 8h5a

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Sodium binding site 2 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:44.9
occ:1.00
 OG1 B:THR131 2.3 55.0 1.0
OD2 A:ASP230 2.7 69.3 1.0
OG1 B:THR109 2.7 70.3 1.0
CG2 B:THR131 3.2 58.1 1.0
CB B:THR131 3.3 65.3 1.0
OD1 A:ASP230 3.3 71.3 1.0
CG A:ASP230 3.4 66.1 1.0
CB B:THR109 3.8 54.9 1.0
OG1 B:THR103 4.2 91.0 1.0
OG1 A:THR227 4.4 75.1 1.0
CA B:THR131 4.4 63.9 1.0
CG2 A:THR227 4.5 66.7 1.0
N B:THR109 4.5 60.0 1.0
O B:VAL107 4.5 72.1 1.0
O B:THR103 4.6 71.8 1.0
CA B:THR109 4.7 55.2 1.0
CG2 B:THR109 4.8 54.2 1.0
CB A:ASP230 4.8 59.8 1.0
N B:THR131 5.0 67.3 1.0

Sodium binding site 3 out of 16 in 8h5a

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Sodium binding site 3 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:48.4
occ:1.00
 OG1 C:THR109 2.3 63.4 1.0
OD2 D:ASP230 2.6 72.4 1.0
OG1 C:THR131 3.0 45.6 1.0
OD1 D:ASP230 3.2 66.4 1.0
CB C:THR109 3.3 65.9 1.0
CG D:ASP230 3.3 56.5 1.0
CG2 C:THR131 3.9 53.4 1.0
N C:THR109 3.9 63.1 1.0
CB C:THR131 4.0 52.1 1.0
CA C:THR109 4.2 54.2 1.0
O C:VAL107 4.2 45.0 1.0
OG1 C:THR103 4.3 56.7 1.0
CG2 C:THR109 4.4 60.8 1.0
CB D:ASP230 4.7 53.4 1.0
OG1 D:THR227 4.9 34.4 1.0
C C:PRO108 5.0 61.6 1.0

Sodium binding site 4 out of 16 in 8h5a

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Sodium binding site 4 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na305

b:45.2
occ:1.00
 OG1 D:THR109 2.1 66.3 1.0
OG1 D:THR131 3.0 74.3 1.0
CB D:THR109 3.2 53.0 1.0
OD2 C:ASP230 3.5 48.3 1.0
OG1 D:THR103 3.5 68.0 1.0
O D:VAL107 3.6 76.1 1.0
N D:THR109 3.6 57.7 1.0
CG2 D:THR131 3.7 60.4 1.0
CA D:THR109 3.9 58.9 1.0
CB D:THR131 3.9 62.5 1.0
OD1 C:ASP230 4.1 55.9 1.0
CG C:ASP230 4.2 56.7 1.0
O D:THR103 4.3 67.0 1.0
CG2 D:THR109 4.4 46.2 1.0
C D:PRO108 4.6 59.0 1.0
O D:GLU104 4.6 63.3 1.0
CB D:THR103 4.7 60.3 1.0
C D:VAL107 4.8 65.3 1.0
CA D:THR131 4.8 59.6 1.0
O D:ALA105 4.9 89.6 1.0
CA D:PRO108 4.9 66.2 1.0

Sodium binding site 5 out of 16 in 8h5a

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Sodium binding site 5 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na304

b:43.1
occ:1.00
 O E:VAL107 3.0 51.3 1.0
CG2 E:THR131 3.0 45.4 1.0
OG1 E:THR109 3.2 45.5 1.0
O E:GLU104 3.3 59.3 1.0
OG1 E:THR131 3.3 55.6 1.0
O E:THR103 3.4 67.0 1.0
OG1 E:THR103 3.5 69.0 1.0
CB E:THR131 3.7 42.9 1.0
CA E:ALA105 3.7 51.6 1.0
O E:ALA105 3.8 71.0 1.0
C E:GLU104 3.9 50.4 1.0
C E:ALA105 4.0 51.6 1.0
C E:VAL107 4.1 42.4 1.0
N E:ALA105 4.1 51.2 1.0
C E:THR103 4.2 48.9 1.0
N E:THR109 4.3 49.4 1.0
CB E:THR103 4.4 51.4 1.0
CB E:THR109 4.5 55.8 1.0
CA E:THR131 4.5 45.3 1.0
OD2 F:ASP230 4.5 100.2 1.0
N E:VAL107 4.7 43.5 1.0
CA E:THR109 4.8 50.3 1.0
CA E:THR103 4.9 47.8 1.0
CB E:ALA105 4.9 49.3 1.0
N E:GLU104 4.9 37.7 1.0
CA E:VAL107 5.0 44.4 1.0
CA E:GLU104 5.0 37.8 1.0

Sodium binding site 6 out of 16 in 8h5a

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Sodium binding site 6 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:59.0
occ:1.00
 OG1 F:THR109 2.3 39.8 1.0
OG1 F:THR131 2.6 62.2 1.0
OG1 F:THR103 3.1 62.5 1.0
CG2 F:THR131 3.2 45.9 1.0
CB F:THR131 3.4 50.4 1.0
O F:VAL107 3.5 76.5 1.0
O F:THR103 3.5 65.6 1.0
OD2 E:ASP230 3.6 54.9 1.0
CB F:THR109 3.6 51.4 1.0
N F:THR109 4.0 67.8 1.0
O F:GLU104 4.1 62.6 1.0
CA F:THR131 4.2 54.8 1.0
CB F:THR103 4.2 58.5 1.0
CA F:THR109 4.2 57.6 1.0
C F:THR103 4.4 57.2 1.0
CG E:ASP230 4.5 58.5 1.0
OD1 E:ASP230 4.6 45.6 1.0
CG2 F:THR109 4.7 52.2 1.0
C F:GLU104 4.7 58.1 1.0
C F:VAL107 4.7 65.1 1.0
CA F:ALA105 4.7 54.4 1.0
O F:ALA105 4.8 65.1 1.0
N F:THR131 4.9 53.1 1.0
C F:PRO108 4.9 62.2 1.0
CA F:THR103 5.0 60.7 1.0

Sodium binding site 7 out of 16 in 8h5a

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Sodium binding site 7 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na304

b:55.6
occ:1.00
 OG1 G:THR131 2.5 41.3 1.0
CG2 G:THR131 2.9 41.3 1.0
OG1 G:THR109 2.9 52.0 1.0
OD2 H:ASP230 3.0 53.9 1.0
CB G:THR131 3.2 40.2 1.0
CG H:ASP230 4.0 61.0 1.0
CB G:THR109 4.1 44.3 1.0
OG1 G:THR103 4.2 61.2 1.0
O G:VAL107 4.2 55.0 1.0
OD1 H:ASP230 4.3 67.5 1.0
O G:THR103 4.4 74.0 1.0
CA G:THR131 4.4 47.5 1.0
CG2 H:THR227 4.5 59.9 1.0
N G:THR109 4.6 53.4 1.0
O G:ALA105 4.7 57.6 1.0
CA G:ALA105 4.7 51.0 1.0
O G:GLU104 4.8 61.1 1.0
CA G:THR109 4.9 43.0 1.0

Sodium binding site 8 out of 16 in 8h5a

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Sodium binding site 8 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na304

b:41.3
occ:1.00
 OG1 H:THR131 2.6 44.5 1.0
OD2 G:ASP230 2.8 63.4 1.0
OG1 H:THR109 2.9 63.0 1.0
CG2 H:THR131 3.2 34.8 1.0
CB H:THR131 3.4 47.7 1.0
CG G:ASP230 3.5 73.0 1.0
OD1 G:ASP230 3.5 60.8 1.0
CB H:THR109 4.0 65.8 1.0
OG1 H:THR103 4.3 99.0 1.0
O H:VAL107 4.4 96.6 1.0
CG2 G:THR227 4.5 61.5 1.0
N H:THR109 4.5 55.3 1.0
OG1 G:THR227 4.6 60.5 1.0
CA H:THR131 4.6 51.9 1.0
O H:HOH405 4.7 42.9 1.0
O H:THR103 4.7 59.0 1.0
CA H:THR109 4.9 66.9 1.0
O H:ALA105 4.9 79.0 1.0
CB G:ASP230 5.0 55.8 1.0

Sodium binding site 9 out of 16 in 8h5a

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Sodium binding site 9 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na304

b:48.3
occ:1.00
 OD2 I:ASP230 2.4 70.3 1.0
OG1 J:THR109 2.6 62.2 1.0
OG1 J:THR131 2.8 77.4 1.0
CG I:ASP230 3.2 55.5 1.0
OD1 I:ASP230 3.2 49.7 1.0
CB J:THR109 3.5 61.7 1.0
CG2 J:THR131 3.9 52.4 1.0
CB J:THR131 3.9 64.5 1.0
N J:THR109 4.2 67.4 1.0
CA J:THR109 4.4 64.2 1.0
OG1 I:THR227 4.4 63.9 1.0
CG2 I:THR227 4.5 64.3 1.0
OG1 J:THR103 4.5 73.2 1.0
CG2 J:THR109 4.5 64.1 1.0
O J:VAL107 4.6 73.0 1.0
CB I:ASP230 4.6 59.5 1.0

Sodium binding site 10 out of 16 in 8h5a

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Sodium binding site 10 out of 16 in the Crystal Structure of Yhaj Effector Binding Domain (Ligand-Bound)


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 (Ligand-Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na305

b:55.5
occ:1.00
 O I:VAL107 2.6 60.4 1.0
OG1 I:THR109 2.9 60.4 1.0
OG1 I:THR103 3.1 50.2 1.0
O I:GLU104 3.1 57.9 1.0
O I:THR103 3.3 43.9 1.0
CG2 I:THR131 3.4 52.6 1.0
OG1 I:THR131 3.5 64.2 1.0
C I:VAL107 3.8 48.1 1.0
C I:GLU104 3.9 51.4 1.0
O I:ALA105 3.9 55.5 1.0
N I:THR109 4.0 72.8 1.0
CA I:ALA105 4.0 44.2 1.0
C I:THR103 4.0 41.4 1.0
CB I:THR131 4.0 56.5 1.0
CB I:THR103 4.0 42.2 1.0
CB I:THR109 4.2 62.5 1.0
C I:ALA105 4.2 50.8 1.0
N I:ALA105 4.3 44.1 1.0
CA I:THR109 4.4 58.9 1.0
OD2 J:ASP230 4.5 43.4 1.0
N I:VAL107 4.5 51.4 1.0
C I:PRO108 4.6 69.2 1.0
CA I:THR103 4.7 43.9 1.0
CA I:VAL107 4.7 47.5 1.0
CA I:THR131 4.7 55.3 1.0
N I:PRO108 4.8 52.8 1.0
CA I:PRO108 4.8 54.6 1.0
N I:GLU104 4.8 40.5 1.0
CA I:GLU104 4.9 38.8 1.0
CB I:VAL107 5.0 43.3 1.0

Reference:

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
Page generated: Wed Oct 9 12:13:04 2024

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