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Sodium in PDB 2ejl: Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Serine

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

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

Protein crystallography data

The structure of Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Serine, PDB code: 2ejl 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) 25.00 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 102.040, 102.040, 279.352, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 20.5

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-Serine (pdb code 2ejl). 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-Serine, PDB code: 2ejl:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2ejl

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Sodium binding site 1 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Serine


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-Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1540

b:18.1
occ:1.00
O A:HOH2577 2.3 21.2 1.0
O A:LEU56 2.6 11.7 1.0
O A:GLU123 2.7 6.7 1.0
O A:ASP211 2.7 11.9 1.0
OG A:SER55 3.1 13.8 1.0
CG A:GLU123 3.5 8.2 1.0
N A:LEU56 3.7 11.5 1.0
C A:ASP211 3.7 11.5 1.0
C A:LEU56 3.7 10.9 1.0
O A:HOH2789 3.8 26.3 1.0
C A:GLU123 3.8 6.5 1.0
CA A:ASP211 4.1 11.5 1.0
C A:SER55 4.2 11.7 1.0
CA A:GLU123 4.3 7.1 1.0
CA A:LEU56 4.3 11.2 1.0
CB A:SER55 4.3 12.6 1.0
O A:HOH2856 4.3 21.4 1.0
CA A:SER55 4.4 12.2 1.0
OE1 A:GLU123 4.4 8.8 1.0
CB A:ASP211 4.4 12.4 1.0
CD A:GLU123 4.5 9.1 1.0
CD A:PRO58 4.5 8.1 1.0
CB A:GLU123 4.5 6.6 1.0
OD1 A:ASP211 4.6 16.8 1.0
N A:ALA212 4.9 9.9 1.0
N A:ASN57 4.9 9.5 1.0
N A:VAL124 4.9 6.4 1.0
CB A:LEU56 5.0 11.9 1.0

Sodium binding site 2 out of 3 in 2ejl

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Sodium binding site 2 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Serine


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-Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2540

b:13.3
occ:0.70
NA B:NA2540 0.0 13.3 0.7
NA B:NA2540 1.2 21.8 0.3
O B:HOH2984 2.4 18.3 0.7
O B:LEU56 2.5 12.1 1.0
O B:GLU123 2.5 9.4 1.0
O B:HOH2985 2.9 12.3 0.3
O B:ASP211 2.9 12.2 1.0
O B:HOH2954 3.1 30.2 1.0
OG B:SER55 3.3 15.4 1.0
CG B:GLU123 3.5 10.2 1.0
C B:GLU123 3.6 9.7 1.0
C B:LEU56 3.6 13.3 1.0
N B:LEU56 3.7 13.9 1.0
C B:ASP211 3.9 11.7 1.0
CA B:GLU123 4.1 9.4 1.0
CA B:LEU56 4.2 13.8 1.0
CA B:ASP211 4.2 12.0 1.0
O B:HOH2986 4.2 21.6 0.7
CD B:PRO58 4.3 10.0 1.0
CB B:ASP211 4.4 12.1 1.0
CB B:GLU123 4.4 9.9 1.0
C B:SER55 4.5 14.0 1.0
OE1 B:GLU123 4.5 12.1 1.0
CD B:GLU123 4.5 11.6 1.0
CB B:SER55 4.5 14.5 1.0
OD1 B:ASP211 4.6 18.7 1.0
CA B:SER55 4.7 14.4 1.0
N B:VAL124 4.7 9.3 1.0
O B:HOH2987 4.8 12.9 0.3
N B:ASN57 4.8 11.8 1.0
CB B:LEU56 4.8 14.8 1.0
CG1 B:VAL124 4.9 10.1 1.0
O B:VAL364 5.0 9.2 1.0
CG2 B:VAL65 5.0 15.3 1.0

Sodium binding site 3 out of 3 in 2ejl

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Sodium binding site 3 out of 3 in the Crystal Analysis of DELTA1-Pyrroline-5-Carboxylate Dehydrogenase From Thermus Thermophilus with Bound L-Serine


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-Serine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2540

b:21.8
occ:0.30
NA B:NA2540 0.0 21.8 0.3
NA B:NA2540 1.2 13.3 0.7
O B:HOH2954 2.2 30.2 1.0
OG B:SER55 2.8 15.4 1.0
O B:ASP211 2.9 12.2 1.0
O B:HOH2984 2.9 18.3 0.7
O B:HOH2985 2.9 12.3 0.3
O B:LEU56 3.0 12.1 1.0
N B:LEU56 3.2 13.9 1.0
C B:ASP211 3.6 11.7 1.0
O B:GLU123 3.7 9.4 1.0
CA B:ASP211 3.7 12.0 1.0
CA B:SER55 3.8 14.4 1.0
CB B:SER55 3.8 14.5 1.0
C B:SER55 3.9 14.0 1.0
C B:LEU56 3.9 13.3 1.0
CG B:GLU123 4.0 10.2 1.0
CA B:LEU56 4.0 13.8 1.0
O B:HOH2986 4.2 21.6 0.7
OD1 B:ASP211 4.2 18.7 1.0
CB B:ASP211 4.2 12.1 1.0
O B:HOH2987 4.4 12.9 0.3
OE1 B:GLU123 4.4 12.1 1.0
CB B:LEU56 4.6 14.8 1.0
CD B:GLU123 4.7 11.6 1.0
O B:GLU210 4.7 12.0 1.0
C B:GLU123 4.7 9.7 1.0
N B:ALA212 4.7 11.0 1.0
CG B:ASP211 4.7 15.6 1.0
N B:ASP211 5.0 11.7 1.0
O B:SER55 5.0 13.2 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 05:48:23 2020

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