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Potassium in PDB 4d79: Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution

Protein crystallography data

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution, PDB code: 4d79 was solved by M.Lopez-Estepa, A.Arda, M.Savko, A.Round, W.Shepard, M.Bruix, M.Coll, F.J.Fernandez, J.Jimenez-Barbero, M.C.Vega, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.128 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.690, 97.160, 83.190, 90.00, 111.61, 90.00
R / Rfree (%) 14.16 / 18.33

Other elements in 4d79:

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution (pdb code 4d79). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution, PDB code: 4d79:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4d79

Go back to Potassium Binding Sites List in 4d79
Potassium binding site 1 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:18.6
occ:0.58
 O A:GLN174 2.4 31.4 1.0
OE1 A:GLN158 2.4 34.3 1.0
O A:SER206 2.5 22.0 1.0
O A:GLU208 2.5 24.8 1.0
O A:HOH2087 3.4 29.2 1.0
CD A:GLN158 3.5 27.6 1.0
C A:SER206 3.5 25.1 1.0
C A:GLN174 3.5 37.5 1.0
C A:GLU208 3.7 29.1 1.0
CD1 A:LEU210 3.7 49.2 1.0
CB A:GLN174 3.9 32.8 1.0
N A:GLU208 3.9 21.6 1.0
CB A:SER206 4.1 20.6 1.0
CA A:SER206 4.2 19.6 1.0
C A:THR207 4.2 21.8 1.0
CA A:GLU208 4.3 25.0 1.0
NE2 A:GLN158 4.3 47.9 1.0
CA A:GLN174 4.3 37.8 1.0
OG A:SER206 4.3 25.7 1.0
CG A:GLN158 4.4 29.0 1.0
N A:SER206 4.4 17.8 1.0
N A:ASP175 4.4 32.5 1.0
O A:ILE173 4.4 27.2 1.0
N A:THR207 4.4 21.4 1.0
CA A:ASP175 4.5 26.1 1.0
CA A:THR207 4.6 27.1 1.0
CB A:ASP175 4.6 32.3 1.0
O A:HOH2104 4.7 42.9 1.0
N A:ALA209 4.7 28.9 1.0
CB A:GLU208 4.8 25.1 1.0
O A:THR207 4.8 25.3 1.0
CA A:ALA209 5.0 31.9 1.0

Potassium binding site 2 out of 4 in 4d79

Go back to Potassium Binding Sites List in 4d79
Potassium binding site 2 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:18.5
occ:0.61
 OE1 B:GLN158 2.4 37.8 1.0
O B:SER206 2.4 25.9 1.0
O B:GLN174 2.6 25.1 1.0
O B:GLU208 2.6 23.7 1.0
O B:HOH2088 3.0 31.1 1.0
CB B:GLN174 3.2 20.6 1.0
C B:SER206 3.4 29.5 1.0
CD B:GLN158 3.5 33.3 1.0
C B:GLN174 3.5 23.6 1.0
O B:ILE173 3.7 23.6 1.0
C B:GLU208 3.8 23.2 1.0
CD1 B:LEU210 3.9 63.6 1.0
CA B:GLN174 3.9 21.2 1.0
N B:GLU208 4.0 20.7 1.0
CB B:SER206 4.0 19.5 1.0
CA B:SER206 4.0 18.7 1.0
N B:SER206 4.2 19.2 1.0
C B:THR207 4.3 24.9 1.0
CG B:GLN158 4.3 28.4 1.0
OG B:SER206 4.3 24.5 1.0
NE2 B:GLN158 4.4 59.9 1.0
N B:THR207 4.4 20.5 1.0
CA B:GLU208 4.4 20.8 1.0
CG B:GLN174 4.6 19.9 1.0
N B:ASP175 4.6 22.9 1.0
C B:ILE173 4.6 20.2 1.0
CA B:THR207 4.6 20.7 1.0
N B:GLN174 4.8 21.2 1.0
CB B:GLU208 4.8 23.5 1.0
O B:THR207 4.9 26.5 1.0
N B:ALA209 4.9 21.2 1.0
CB B:ASP175 4.9 27.2 1.0
CA B:ASP175 5.0 22.3 1.0

Potassium binding site 3 out of 4 in 4d79

Go back to Potassium Binding Sites List in 4d79
Potassium binding site 3 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:20.3
occ:0.58
 OE1 C:GLN158 2.5 35.4 1.0
O C:GLN174 2.5 39.2 1.0
O C:SER206 2.5 26.2 1.0
O C:GLU208 2.6 26.6 1.0
O C:HOH2101 3.2 32.7 1.0
CD C:GLN158 3.4 34.0 1.0
C C:SER206 3.5 26.9 1.0
C C:GLN174 3.6 37.9 1.0
C C:GLU208 3.7 29.8 1.0
CD1 C:LEU210 3.8 49.0 1.0
CB C:GLN174 3.9 40.7 1.0
N C:GLU208 3.9 24.1 1.0
CB C:SER206 4.0 21.2 1.0
NE2 C:GLN158 4.2 42.1 1.0
CA C:SER206 4.2 27.6 1.0
C C:THR207 4.3 27.2 1.0
CG C:GLN158 4.3 29.0 1.0
CA C:GLU208 4.3 35.2 1.0
N C:SER206 4.4 23.2 1.0
OG C:SER206 4.4 28.0 1.0
CA C:GLN174 4.4 40.0 1.0
O C:ILE173 4.4 37.2 1.0
N C:THR207 4.5 24.5 1.0
N C:ASP175 4.5 35.6 1.0
CA C:ASP175 4.6 49.6 1.0
CA C:THR207 4.6 26.1 1.0
CB C:ASP175 4.7 36.2 1.0
O C:THR207 4.8 28.4 1.0
N C:ALA209 4.8 24.6 1.0
CB C:GLU208 4.8 22.4 1.0
O C:GLY154 5.0 25.1 1.0

Potassium binding site 4 out of 4 in 4d79

Go back to Potassium Binding Sites List in 4d79
Potassium binding site 4 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Atp at 1.768 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:24.5
occ:0.63
 OE1 D:GLN158 2.4 33.8 1.0
O D:SER206 2.5 27.7 1.0
O D:GLN174 2.5 34.2 1.0
O D:GLU208 2.6 27.4 1.0
CD D:GLN158 3.4 46.0 1.0
O D:HOH2071 3.4 29.4 1.0
C D:SER206 3.5 23.7 1.0
C D:GLN174 3.6 72.2 1.0
CD1 D:LEU210 3.7 43.2 1.0
C D:GLU208 3.7 27.7 1.0
CB D:GLN174 3.9 37.9 1.0
N D:GLU208 4.0 27.9 1.0
CB D:SER206 4.0 26.3 1.0
NE2 D:GLN158 4.1 41.2 1.0
CA D:SER206 4.2 23.1 1.0
OG D:SER206 4.2 25.8 1.0
CG D:GLN158 4.3 42.1 1.0
CA D:GLU208 4.3 27.0 1.0
C D:THR207 4.3 32.6 1.0
N D:SER206 4.4 24.1 1.0
CA D:GLN174 4.4 40.1 1.0
N D:ASP175 4.5 31.1 1.0
O D:ILE173 4.5 31.8 1.0
N D:THR207 4.5 26.2 1.0
CA D:ASP175 4.5 37.1 1.0
CB D:ASP175 4.7 31.6 1.0
CA D:THR207 4.7 27.4 1.0
CB D:GLU208 4.7 25.9 1.0
N D:ALA209 4.8 28.6 1.0
O D:THR207 4.9 28.7 1.0
O D:GLY154 5.0 26.1 1.0
CG D:ASP175 5.0 75.4 1.0
OD2 D:ASP175 5.0 68.3 1.0

Reference:

M.Lopez-Estepa, A.Arda, M.Savko, A.Round, W.E.Shepard, M.Bruix, M.Coll, F.J.Fernandez, J.Jimenez-Barbero, M.C.Vega. The Crystal Structure and Small-Angle X-Ray Analysis of Csdl/Tcda Reveal A New Trna Binding Motif in the Moeb/E1 Superfamily. Plos One V. 10 18606 2015.
ISSN: ISSN 1932-6203
PubMed: 25897750
DOI: 10.1371/JOURNAL.PONE.0118606
Page generated: Mon Aug 12 10:28:57 2024

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