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Sodium in PDB 5v6q: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate

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

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate:
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 Malonate, PDB code: 5v6q was solved by I.G.Shabalin, K.B.Handing, A.P.Miezaniec, O.A.Gasiorowska, 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) 40.29 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 176.484, 176.484, 135.857, 90.00, 90.00, 120.00
R / Rfree (%) 14.4 / 15.7

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 Malonate (pdb code 5v6q). 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 Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate, PDB code: 5v6q:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5v6q

Go back to Sodium Binding Sites List in 5v6q
Sodium binding site 1 out of 3 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:45.3
occ:1.00
 O A:HOH668 2.4 47.4 1.0
O A:VAL194 2.4 38.4 1.0
O A:LEU219 2.7 41.4 1.0
O A:GLU192 2.9 45.3 1.0
O A:ALA191 2.9 41.3 1.0
O A:ALA218 3.1 46.6 1.0
C A:GLU192 3.5 45.9 1.0
C A:VAL194 3.5 38.4 1.0
C A:LEU219 3.5 42.3 1.0
CA A:LEU219 3.9 42.8 1.0
CA A:GLU192 3.9 46.3 1.0
N A:VAL194 4.0 41.2 1.0
C A:ALA191 4.0 42.1 1.0
C A:ALA218 4.2 46.2 1.0
CA A:VAL194 4.3 39.5 1.0
N A:ALA193 4.4 45.7 1.0
C A:ALA193 4.4 43.5 1.0
N A:ASP195 4.4 36.9 1.0
N A:GLU192 4.5 44.3 1.0
N A:GLY220 4.5 42.4 1.0
N A:LEU219 4.5 44.8 1.0
CA A:ASP195 4.6 35.6 1.0
CA A:ALA193 4.9 45.1 1.0
CA A:GLY220 4.9 41.9 1.0

Sodium binding site 2 out of 3 in 5v6q

Go back to Sodium Binding Sites List in 5v6q
Sodium binding site 2 out of 3 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:62.0
occ:1.00
 O B:VAL194 2.7 33.6 1.0
O B:LEU219 2.8 36.9 1.0
O B:GLU192 2.9 38.7 1.0
O B:ALA218 3.1 36.6 1.0
O B:ALA191 3.2 36.6 1.0
O B:HOH611 3.3 48.3 1.0
C B:LEU219 3.5 37.5 1.0
C B:GLU192 3.6 39.5 1.0
C B:VAL194 3.8 32.8 1.0
CA B:LEU219 4.0 37.3 1.0
CA B:GLU192 4.0 40.3 1.0
C B:ALA218 4.2 37.5 1.0
O B:HOH615 4.2 38.0 1.0
N B:VAL194 4.3 35.4 1.0
C B:ALA191 4.3 37.6 1.0
N B:GLY220 4.5 37.8 1.0
N B:ALA193 4.5 38.9 1.0
N B:LEU219 4.6 37.0 1.0
C B:ALA193 4.6 37.3 1.0
N B:GLU192 4.6 39.0 1.0
CA B:VAL194 4.7 33.7 1.0
CA B:GLY220 4.7 38.2 1.0
N B:ASP195 4.7 31.8 1.0
CA B:ASP195 4.9 31.0 1.0

Sodium binding site 3 out of 3 in 5v6q

Go back to Sodium Binding Sites List in 5v6q
Sodium binding site 3 out of 3 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadp and Malonate


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 Malonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:39.9
occ:1.00
 O D:VAL194 2.3 34.9 1.0
O D:ALA191 2.7 34.5 1.0
O D:GLU192 2.7 39.1 1.0
O D:LEU219 2.8 39.3 1.0
O D:ALA218 3.0 40.0 1.0
C D:GLU192 3.3 38.7 1.0
C D:VAL194 3.5 33.4 1.0
C D:LEU219 3.5 39.2 1.0
C D:ALA191 3.8 35.2 1.0
CA D:GLU192 3.8 39.6 1.0
N D:VAL194 3.8 34.7 1.0
CA D:LEU219 3.8 38.9 1.0
C D:ALA218 4.1 39.7 1.0
O D:HOH502 4.1 44.7 1.0
N D:ALA193 4.2 37.5 1.0
N D:GLU192 4.2 37.5 1.0
CA D:VAL194 4.3 33.3 1.0
C D:ALA193 4.3 36.4 1.0
N D:LEU219 4.4 38.8 1.0
N D:ASP195 4.5 32.3 1.0
N D:GLY220 4.5 39.6 1.0
O D:HOH587 4.6 42.9 1.0
CA D:ASP195 4.7 32.0 1.0
CA D:ALA193 4.7 38.1 1.0
CA D:GLY220 4.9 39.5 1.0
O D:ALA193 5.0 36.4 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 Dec 15 11:44:27 2020

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