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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

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