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

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

All present enzymatic activity of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine 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-Alanine and Nad, PDB code: 2eit 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) 27.96 / 1.65
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 101.586, 101.586, 278.785, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 18.4

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

Sodium binding site 1 out of 2 in 2eit

Go back to Sodium Binding Sites List in 2eit
Sodium binding site 1 out of 2 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine 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-Alanine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1521

b:18.2
occ:1.00
O A:HOH2692 2.5 26.2 1.0
O A:LEU56 2.5 12.2 1.0
O A:GLU123 2.6 8.7 1.0
O A:ASP211 2.8 11.7 1.0
O A:HOH2612 2.9 34.1 1.0
OG A:SER55 3.0 13.2 1.0
CG A:GLU123 3.5 8.9 1.0
N A:LEU56 3.6 12.5 1.0
C A:LEU56 3.7 12.2 1.0
C A:GLU123 3.7 8.3 1.0
C A:ASP211 3.8 11.5 1.0
C A:SER55 4.2 12.7 1.0
CA A:LEU56 4.2 12.4 1.0
CA A:GLU123 4.2 7.9 1.0
CB A:SER55 4.2 13.2 1.0
CA A:ASP211 4.2 11.8 1.0
O A:HOH2762 4.3 23.4 1.0
CA A:SER55 4.3 13.0 1.0
CB A:ASP211 4.5 12.7 1.0
OE1 A:GLU123 4.5 9.4 1.0
CD A:PRO58 4.5 10.0 1.0
CB A:GLU123 4.5 7.9 1.0
CD A:GLU123 4.5 9.4 1.0
OD1 A:ASP211 4.6 18.0 1.0
N A:ASN57 4.8 11.2 1.0
N A:VAL124 4.8 8.0 1.0
CB A:LEU56 4.9 12.7 1.0
N A:ALA212 5.0 10.4 1.0
O A:VAL364 5.0 9.8 1.0

Sodium binding site 2 out of 2 in 2eit

Go back to Sodium Binding Sites List in 2eit
Sodium binding site 2 out of 2 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Alanine 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-Alanine and Nad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2521

b:19.4
occ:1.00
O B:HOH2601 2.1 30.9 1.0
O B:GLU123 2.5 10.9 1.0
O B:HOH2812 2.5 27.9 1.0
O B:LEU56 2.5 14.3 1.0
O B:ASP211 2.9 14.1 1.0
O B:HOH2779 3.3 26.8 1.0
OG B:SER55 3.4 16.4 1.0
CG B:GLU123 3.5 11.6 1.0
C B:GLU123 3.6 10.5 1.0
C B:LEU56 3.7 14.9 1.0
N B:LEU56 3.7 15.6 1.0
C B:ASP211 4.0 13.2 1.0
CA B:GLU123 4.1 10.5 1.0
O B:HOH2813 4.2 31.1 1.0
CD B:PRO58 4.2 12.7 1.0
CA B:LEU56 4.3 15.4 1.0
CA B:ASP211 4.4 14.1 1.0
CB B:GLU123 4.5 10.2 1.0
C B:SER55 4.5 16.3 1.0
CB B:SER55 4.6 16.8 1.0
CD B:GLU123 4.6 13.9 1.0
OE1 B:GLU123 4.6 11.9 1.0
CB B:ASP211 4.6 14.4 1.0
OD1 B:ASP211 4.7 19.7 1.0
CA B:SER55 4.7 16.7 1.0
N B:VAL124 4.7 10.1 1.0
O B:VAL364 4.8 11.2 1.0
N B:ASN57 4.8 14.1 1.0
CB B:LEU56 4.9 16.0 1.0
CG2 B:VAL65 4.9 18.1 1.0
CG1 B:VAL124 5.0 11.3 1.0
CG B:PRO58 5.0 10.7 1.0
N B:PRO58 5.0 12.2 1.0
CA B:VAL124 5.0 10.0 1.0

Reference:

E.Inagaki, N.Ohshima, K.Sakamoto, 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: Tue Dec 15 05:48:16 2020

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