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Sodium in PDB 5v7n: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid

Enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid:
1.1.1.81;

Protein crystallography data

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid, PDB code: 5v7n was solved by I.G.Shabalin, K.B.Handing, C.D.Miks, J.Kutner, D.Matelska, J.Bonanno, S.C.Almo, W.Minor, New York Structural Genomics Research Consortium(Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.11 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 175.902, 175.902, 135.336, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 16.7

Other elements in 5v7n:

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid (pdb code 5v7n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid, PDB code: 5v7n:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5v7n

Go back to Sodium Binding Sites List in 5v7n
Sodium binding site 1 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:31.2
occ:1.00
 O A:HOH626 2.4 44.7 1.0
O A:ALA191 2.4 27.4 1.0
O A:VAL194 2.4 30.2 1.0
O A:LEU219 2.4 26.2 1.0
O A:ALA218 2.4 30.8 1.0
O A:GLU192 2.5 34.0 1.0
C A:LEU219 3.1 32.7 1.0
C A:GLU192 3.2 38.3 1.0
CA A:LEU219 3.4 30.2 1.0
C A:ALA218 3.5 41.2 1.0
C A:ALA191 3.5 35.6 1.0
C A:VAL194 3.6 24.3 1.0
CA A:GLU192 3.6 32.7 1.0
N A:LEU219 3.9 32.5 1.0
N A:VAL194 3.9 30.8 1.0
N A:GLU192 4.0 29.9 1.0
N A:ALA193 4.1 30.9 1.0
N A:GLY220 4.2 34.8 1.0
CA A:VAL194 4.4 26.9 1.0
C A:ALA193 4.5 39.0 1.0
N A:ASP195 4.6 25.6 1.0
O A:HOH663 4.6 29.2 1.0
CA A:GLY220 4.7 34.0 1.0
CA A:ASP195 4.7 24.2 1.0
CD1 A:LEU219 4.7 31.1 1.0
CB A:LEU219 4.8 25.5 1.0
CA A:ALA191 4.8 34.5 1.0
O A:HOH740 4.8 43.3 1.0
CA A:ALA193 4.8 40.7 1.0
CA A:ALA218 4.8 35.9 1.0

Sodium binding site 2 out of 4 in 5v7n

Go back to Sodium Binding Sites List in 5v7n
Sodium binding site 2 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:29.4
occ:1.00
 O B:ALA191 2.4 28.3 1.0
O B:VAL194 2.4 28.9 1.0
O B:HOH724 2.4 43.2 1.0
O B:ALA218 2.4 28.7 1.0
O B:LEU219 2.4 36.5 1.0
O B:GLU192 2.5 35.4 1.0
C B:LEU219 3.1 36.2 1.0
C B:GLU192 3.2 30.9 1.0
CA B:LEU219 3.4 35.8 1.0
C B:ALA191 3.5 32.9 1.0
C B:ALA218 3.5 31.2 1.0
CA B:GLU192 3.6 31.1 1.0
C B:VAL194 3.6 27.9 1.0
N B:LEU219 3.9 30.1 1.0
N B:VAL194 3.9 27.8 1.0
N B:GLU192 3.9 30.1 1.0
N B:ALA193 4.1 31.9 1.0
N B:GLY220 4.2 35.2 1.0
CA B:VAL194 4.4 25.2 1.0
O B:HOH622 4.4 32.4 1.0
C B:ALA193 4.5 36.2 1.0
O B:HOH780 4.5 49.4 1.0
N B:ASP195 4.6 29.8 1.0
O B:HOH700 4.6 50.6 1.0
CA B:GLY220 4.7 27.3 1.0
CA B:ASP195 4.7 24.2 1.0
CD1 B:LEU219 4.7 31.4 1.0
CA B:ALA191 4.7 32.8 1.0
CB B:LEU219 4.7 25.0 1.0
CA B:ALA193 4.8 29.9 1.0
CA B:ALA218 4.8 29.8 1.0
O B:HOH841 4.9 51.0 1.0

Sodium binding site 3 out of 4 in 5v7n

Go back to Sodium Binding Sites List in 5v7n
Sodium binding site 3 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na403

b:46.6
occ:1.00
 O C:HOH643 2.4 57.7 1.0
O C:ALA191 2.4 39.5 1.0
O C:VAL194 2.4 37.6 1.0
O C:ALA218 2.4 39.9 1.0
O C:LEU219 2.4 42.3 1.0
O C:GLU192 2.4 39.9 1.0
C C:LEU219 3.1 41.5 1.0
C C:GLU192 3.1 47.2 1.0
CA C:LEU219 3.4 47.6 1.0
C C:ALA218 3.5 49.2 1.0
C C:ALA191 3.5 35.9 1.0
CA C:GLU192 3.6 37.9 1.0
C C:VAL194 3.6 33.4 1.0
N C:LEU219 3.9 35.6 1.0
N C:VAL194 3.9 36.4 1.0
N C:GLU192 4.0 44.6 1.0
N C:ALA193 4.1 33.9 1.0
N C:GLY220 4.1 42.8 1.0
CA C:VAL194 4.4 36.6 1.0
C C:ALA193 4.5 41.8 1.0
O C:HOH647 4.6 42.8 1.0
N C:ASP195 4.6 33.5 1.0
CA C:GLY220 4.6 41.8 1.0
CA C:ASP195 4.7 29.3 1.0
O C:HOH793 4.8 50.3 1.0
CD1 C:LEU219 4.8 64.0 1.0
CA C:ALA191 4.8 38.8 1.0
CB C:LEU219 4.8 44.3 1.0
CA C:ALA193 4.8 39.8 1.0
CA C:ALA218 4.8 50.3 1.0
O C:HOH694 5.0 62.0 1.0
CB C:GLU192 5.0 38.7 1.0

Sodium binding site 4 out of 4 in 5v7n

Go back to Sodium Binding Sites List in 5v7n
Sodium binding site 4 out of 4 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and 2-Keto-D-Gluconic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:37.8
occ:1.00
 O D:HOH705 2.4 49.8 1.0
O D:VAL194 2.4 35.4 1.0
O D:ALA191 2.4 39.7 1.0
O D:ALA218 2.4 40.6 1.0
O D:LEU219 2.4 49.5 1.0
O D:GLU192 2.5 43.7 1.0
C D:LEU219 3.1 49.4 1.0
C D:GLU192 3.2 38.7 1.0
CA D:LEU219 3.4 41.4 1.0
C D:ALA218 3.5 55.0 1.0
C D:ALA191 3.5 49.1 1.0
CA D:GLU192 3.6 41.1 1.0
C D:VAL194 3.6 36.6 1.0
N D:LEU219 3.9 43.3 1.0
N D:VAL194 3.9 34.3 1.0
N D:GLU192 4.0 38.3 1.0
N D:ALA193 4.1 40.3 1.0
N D:GLY220 4.2 51.8 1.0
O D:HOH688 4.2 57.7 1.0
CA D:VAL194 4.4 37.4 1.0
C D:ALA193 4.5 43.1 1.0
O D:HOH643 4.6 41.0 1.0
N D:ASP195 4.6 33.1 1.0
CA D:GLY220 4.7 36.8 1.0
CA D:ASP195 4.7 32.1 1.0
O D:HOH715 4.8 42.1 1.0
CD1 D:LEU219 4.8 43.6 1.0
CA D:ALA191 4.8 42.7 1.0
CB D:LEU219 4.8 32.3 1.0
CA D:ALA193 4.8 40.5 1.0
CA D:ALA218 4.8 50.3 1.0

Reference:

J.Kutner, I.G.Shabalin, D.Matelska, K.B.Handing, O.Gasiorowska, P.Sroka, M.W.Gorna, K.Ginalski, K.Wozniak, W.Minor. Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division Into Two Distinct Subfamilies. Biochemistry V. 57 963 2018.
ISSN: ISSN 1520-4995
PubMed: 29309127
DOI: 10.1021/ACS.BIOCHEM.7B01137
Page generated: Tue Oct 8 00:45:24 2024

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