Atomistry » Sodium » PDB 2e54-2eka » 2eii
Atomistry »
  Sodium »
    PDB 2e54-2eka »
      2eii »

Sodium in PDB 2eii: Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.

Enzymatic activity of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.

All present enzymatic activity of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.:
1.5.1.12;

Protein crystallography data

The structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad., PDB code: 2eii was solved by E.Inagaki, K.Sakamoto, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.88
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 102.208, 102.208, 278.432, 90.00, 90.00, 120.00
R / Rfree (%) 13.4 / 16.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad. (pdb code 2eii). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad., PDB code: 2eii:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2eii

Go back to Sodium Binding Sites List in 2eii
Sodium binding site 1 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1540

b:22.2
occ:1.00
 O A:HOH2701 2.4 29.2 1.0
O A:HOH2813 2.5 33.9 1.0
O A:LEU56 2.6 13.6 1.0
O A:GLU123 2.7 9.8 1.0
O A:ASP211 2.8 13.3 1.0
OG A:SER55 3.0 14.1 1.0
CG A:GLU123 3.5 11.0 1.0
N A:LEU56 3.6 13.3 1.0
C A:LEU56 3.7 13.3 1.0
C A:GLU123 3.8 10.3 1.0
C A:ASP211 3.8 12.8 1.0
C A:SER55 4.1 13.2 1.0
CA A:LEU56 4.2 13.5 1.0
CA A:ASP211 4.2 13.2 1.0
O A:HOH2666 4.2 23.3 1.0
CB A:SER55 4.2 13.4 1.0
CA A:GLU123 4.2 9.8 1.0
CA A:SER55 4.3 13.3 1.0
CD A:PRO58 4.4 11.5 1.0
CB A:ASP211 4.4 13.6 1.0
OE1 A:GLU123 4.5 9.6 1.0
CB A:GLU123 4.5 10.0 1.0
CD A:GLU123 4.5 12.5 1.0
OD1 A:ASP211 4.6 20.5 1.0
N A:ASN57 4.8 12.7 1.0
N A:VAL124 4.9 9.9 1.0
CB A:LEU56 4.9 13.5 1.0
O A:SER55 4.9 13.8 1.0
O A:VAL364 5.0 12.1 1.0
N A:ALA212 5.0 12.0 1.0

Sodium binding site 2 out of 3 in 2eii

Go back to Sodium Binding Sites List in 2eii
Sodium binding site 2 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2540

b:11.2
occ:0.60
 NA B:NA2540 0.0 11.2 0.6
NA B:NA2540 1.3 15.2 0.4
O B:GLU123 2.3 11.6 1.0
O B:HOH2872 2.3 32.8 1.0
O B:LEU56 2.4 13.5 1.0
O B:HOH2857 3.1 34.0 1.0
O B:ASP211 3.2 14.7 1.0
C B:GLU123 3.4 11.9 1.0
OG B:SER55 3.4 16.6 1.0
CG B:GLU123 3.5 13.1 1.0
C B:LEU56 3.6 14.4 1.0
N B:LEU56 3.8 14.1 1.0
CA B:GLU123 4.0 12.0 1.0
CD B:PRO58 4.1 12.9 1.0
O B:HOH2807 4.2 34.4 1.0
C B:ASP211 4.2 13.3 1.0
CA B:LEU56 4.2 14.5 1.0
CB B:GLU123 4.4 12.5 1.0
C B:SER55 4.5 15.0 1.0
N B:VAL124 4.5 12.0 1.0
CA B:ASP211 4.6 13.5 1.0
CD B:GLU123 4.6 15.3 1.0
N B:ASN57 4.6 13.5 1.0
CB B:SER55 4.7 15.7 1.0
CB B:ASP211 4.7 13.7 1.0
OE1 B:GLU123 4.7 13.4 1.0
O B:VAL364 4.7 12.3 1.0
CA B:SER55 4.8 14.5 1.0
CA B:VAL124 4.8 11.8 1.0
OD1 B:ASP211 4.8 20.4 1.0
N B:PRO58 4.8 12.4 1.0
CG1 B:VAL124 4.9 12.0 1.0
CB B:LEU56 4.9 14.5 1.0
CG B:PRO58 4.9 11.8 1.0
CG2 B:VAL65 4.9 18.0 1.0
CA B:ASN57 5.0 12.9 1.0

Sodium binding site 3 out of 3 in 2eii

Go back to Sodium Binding Sites List in 2eii
Sodium binding site 3 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Valine and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2540

b:15.2
occ:0.40
 NA B:NA2540 0.0 15.2 0.4
NA B:NA2540 1.3 11.2 0.6
O B:HOH2857 2.4 34.0 1.0
OG B:SER55 2.7 16.6 1.0
O B:ASP211 2.7 14.7 1.0
O B:HOH2872 2.8 32.8 1.0
O B:LEU56 3.1 13.5 1.0
N B:LEU56 3.4 14.1 1.0
C B:ASP211 3.5 13.3 1.0
O B:GLU123 3.5 11.6 1.0
CA B:ASP211 3.7 13.5 1.0
CG B:GLU123 3.8 13.1 1.0
CB B:SER55 3.8 15.7 1.0
CA B:SER55 3.8 14.5 1.0
C B:SER55 4.0 15.0 1.0
C B:LEU56 4.1 14.4 1.0
CB B:ASP211 4.2 13.7 1.0
OE1 B:GLU123 4.2 13.4 1.0
OD1 B:ASP211 4.3 20.4 1.0
CA B:LEU56 4.3 14.5 1.0
O B:HOH2807 4.4 34.4 1.0
CD B:GLU123 4.5 15.3 1.0
C B:GLU123 4.5 11.9 1.0
N B:ALA212 4.6 12.6 1.0
CG B:ASP211 4.8 16.7 1.0
O B:GLU210 4.8 11.8 1.0
CB B:LEU56 4.9 14.5 1.0
CA B:GLU123 4.9 12.0 1.0
CB B:GLU123 5.0 12.5 1.0
N B:ASP211 5.0 12.4 1.0

Reference:

E.Inagaki, N.Ohshima, K.Sakamoto, H.Kato, S.Yokoyama, T.H.Tahirov. Crystal Structure Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase in Ternary Complex with Inhibitor and Nad. To Be Published.
Page generated: Mon Oct 7 02:19:44 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy