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Potassium in PDB 4d7a: Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution

Protein crystallography data

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 Angstroem Resolution, PDB code: 4d7a 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) 41.138 / 1.80
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 (%) 13.92 / 17.66

Other elements in 4d7a:

The structure of Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 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 Amp at 1.801 Angstroem Resolution (pdb code 4d7a). 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 Amp at 1.801 Angstroem Resolution, PDB code: 4d7a:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4d7a

Go back to Potassium Binding Sites List in 4d7a
Potassium binding site 1 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 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 Amp at 1.801 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K301

b:17.4
occ:0.48
 O A:SER206 2.6 17.5 1.0
O A:GLN174 2.7 28.8 1.0
OE1 A:GLN158 2.7 28.4 1.0
O A:GLU208 2.8 21.0 1.0
O A:HOH2111 3.3 43.4 1.0
O A:HOH2112 3.4 22.2 1.0
C A:SER206 3.6 18.4 1.0
CD A:GLN158 3.6 33.2 1.0
C A:GLN174 3.6 30.8 1.0
CB A:GLN174 3.9 33.4 1.0
C A:GLU208 3.9 24.5 1.0
N A:GLU208 4.0 17.7 1.0
CB A:SER206 4.1 17.9 1.0
CD2 A:LEU210 4.1 48.7 1.0
CA A:SER206 4.2 15.8 1.0
N A:SER206 4.3 16.4 1.0
NE2 A:GLN158 4.3 36.2 1.0
OG A:SER206 4.4 18.3 1.0
CA A:GLN174 4.4 29.6 1.0
C A:THR207 4.4 23.3 1.0
O A:ILE173 4.4 28.2 1.0
CA A:GLU208 4.5 18.0 1.0
N A:ASP175 4.5 27.7 1.0
CG A:GLN158 4.5 23.0 1.0
CA A:ASP175 4.5 28.5 1.0
N A:THR207 4.5 19.4 1.0
CB A:ASP175 4.6 27.1 1.0
CA A:THR207 4.8 20.6 1.0
O A:HOH2135 4.8 40.1 1.0
CG A:LEU210 4.8 55.1 1.0
CB A:GLU208 4.9 17.1 1.0
O A:THR207 5.0 22.1 1.0
N A:ALA209 5.0 25.4 1.0
O A:GLY154 5.0 20.9 1.0

Potassium binding site 2 out of 4 in 4d7a

Go back to Potassium Binding Sites List in 4d7a
Potassium binding site 2 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 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 Amp at 1.801 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K301

b:14.4
occ:0.39
 O B:GLN174 2.8 17.9 1.0
OE1 B:GLN158 2.8 36.6 1.0
O B:SER206 2.8 18.9 1.0
O B:GLU208 2.9 19.0 1.0
O B:HOH2136 2.9 35.0 1.0
CB B:GLN174 3.3 16.5 1.0
C B:SER206 3.6 13.7 1.0
CD B:GLN158 3.6 32.1 1.0
C B:GLN174 3.7 16.9 1.0
O B:ILE173 3.7 17.6 1.0
CB B:SER206 3.9 20.3 1.0
C B:GLU208 4.0 20.7 1.0
CA B:GLN174 4.0 16.1 1.0
N B:GLU208 4.1 16.2 1.0
CA B:SER206 4.1 14.0 1.0
N B:SER206 4.2 18.2 1.0
CD2 B:LEU210 4.3 31.4 1.0
OG B:SER206 4.3 20.2 1.0
CG B:GLN158 4.3 19.7 1.0
CA B:GLU208 4.5 17.8 1.0
NE2 B:GLN158 4.5 23.4 1.0
C B:THR207 4.5 21.0 1.0
CG B:GLN174 4.6 14.9 1.0
N B:THR207 4.6 15.9 1.0
C B:ILE173 4.6 15.9 1.0
N B:ASP175 4.7 21.7 1.0
CB B:GLU208 4.7 17.2 1.0
N B:GLN174 4.8 16.4 1.0
CG B:LEU210 4.9 25.0 1.0
CA B:THR207 4.9 16.2 1.0

Potassium binding site 3 out of 4 in 4d7a

Go back to Potassium Binding Sites List in 4d7a
Potassium binding site 3 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 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 Amp at 1.801 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K301

b:24.9
occ:0.54
 OE1 C:GLN158 2.7 45.8 1.0
O C:SER206 2.7 27.6 1.0
O C:GLN174 2.8 39.0 1.0
O C:GLU208 2.8 31.4 1.0
O C:HOH2137 3.4 31.6 1.0
CD C:GLN158 3.5 41.9 1.0
O C:HOH2138 3.5 42.1 1.0
C C:SER206 3.6 27.7 1.0
C C:GLN174 3.7 37.8 1.0
CB C:GLN174 3.8 35.7 1.0
C C:GLU208 3.9 24.8 1.0
N C:GLU208 4.0 27.8 1.0
NE2 C:GLN158 4.1 43.3 1.0
CB C:SER206 4.1 34.1 1.0
CD2 C:LEU210 4.2 56.7 1.0
CA C:SER206 4.3 29.7 1.0
O C:ILE173 4.4 38.5 1.0
CG C:GLN158 4.4 34.1 1.0
C C:THR207 4.4 25.9 1.0
OG C:SER206 4.4 30.7 1.0
N C:SER206 4.4 26.1 1.0
CA C:GLU208 4.4 30.6 1.0
CA C:GLN174 4.4 34.1 1.0
N C:THR207 4.6 27.4 1.0
N C:ASP175 4.6 36.2 1.0
CA C:ASP175 4.7 35.9 1.0
CB C:ASP175 4.7 41.5 1.0
CA C:THR207 4.8 27.4 1.0
CB C:GLU208 4.9 27.9 1.0
O C:THR207 4.9 25.7 1.0
CG C:LEU210 5.0 61.4 1.0
N C:ALA209 5.0 25.4 1.0

Potassium binding site 4 out of 4 in 4d7a

Go back to Potassium Binding Sites List in 4d7a
Potassium binding site 4 out of 4 in the Crystal Structure of E. Coli Trna N6-Threonylcarbamoyladenosine Dehydratase, Tcda, in Complex with Amp at 1.801 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 Amp at 1.801 Angstroem Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K301

b:22.4
occ:0.40
 OE1 D:GLN158 2.7 44.9 1.0
O D:GLN174 2.8 50.3 1.0
O D:SER206 2.8 26.3 1.0
O D:GLU208 2.8 31.6 1.0
O D:HOH2073 3.4 30.3 1.0
CD D:GLN158 3.5 39.5 1.0
C D:SER206 3.6 25.4 1.0
C D:GLN174 3.7 38.6 1.0
CB D:GLN174 3.8 39.3 1.0
C D:GLU208 3.9 31.5 1.0
N D:GLU208 4.0 26.7 1.0
CB D:SER206 4.1 31.0 1.0
CD2 D:LEU210 4.1 59.8 1.0
NE2 D:GLN158 4.2 39.0 1.0
CA D:SER206 4.2 25.6 1.0
CA D:GLN174 4.4 39.8 1.0
C D:THR207 4.4 34.3 1.0
CG D:GLN158 4.4 41.6 1.0
N D:SER206 4.4 27.2 1.0
O D:ILE173 4.4 37.5 1.0
CA D:GLU208 4.4 34.3 1.0
OG D:SER206 4.5 27.6 1.0
N D:THR207 4.5 26.2 1.0
N D:ASP175 4.5 42.0 1.0
CA D:ASP175 4.7 40.2 1.0
CA D:THR207 4.8 26.8 1.0
CB D:GLU208 4.8 30.7 1.0
CB D:ASP175 4.8 44.3 1.0
CG D:LEU210 4.9 58.0 1.0
O D:THR207 4.9 28.6 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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