Atomistry » Potassium » PDB 4cn5-4edj » 4d7a
Atomistry »
  Potassium »
    PDB 4cn5-4edj »
      4d7a »

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: Sat Aug 9 06:37:05 2025

Last articles

Na in 3HWF
Na in 3HWE
Na in 3HWT
Na in 3HWD
Na in 3HW8
Na in 3HVY
Na in 3HVU
Na in 3HHQ
Na in 3HVI
Na in 3HSS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy