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Sodium in PDB 5v72: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate

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

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate:
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 Citrate, PDB code: 5v72 was solved by I.G.Shabalin, K.B.Handing, O.A.Gasiorowska, D.R.Cooper, D.Matelska, J.Bonanno, S.C.Almo, W.Minor, New York Structural Genomics Researchconsortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.188, 157.926, 64.719, 90.00, 110.74, 90.00
R / Rfree (%) 16.4 / 20.4

Other elements in 5v72:

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate also contains other interesting chemical elements:

Chlorine (Cl) 4 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 Citrate (pdb code 5v72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate, PDB code: 5v72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 5v72

Go back to Sodium Binding Sites List in 5v72
Sodium binding site 1 out of 5 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:33.2
occ:1.00
 O A:HOH668 2.1 33.4 1.0
O A:VAL194 2.3 32.1 1.0
O A:ALA191 2.4 38.7 1.0
O A:LEU219 2.6 40.8 1.0
O A:GLU192 2.7 45.8 1.0
O A:ALA218 2.8 36.1 1.0
C A:LEU219 3.2 35.9 1.0
C A:GLU192 3.2 41.3 1.0
C A:VAL194 3.4 28.4 1.0
C A:ALA191 3.5 36.6 1.0
CA A:LEU219 3.6 33.8 1.0
CA A:GLU192 3.6 44.1 1.0
C A:ALA218 3.8 34.9 1.0
N A:VAL194 3.9 30.9 1.0
N A:GLU192 4.0 40.0 1.0
N A:LEU219 4.1 32.6 1.0
N A:ALA193 4.2 38.7 1.0
O A:HOH583 4.2 36.4 1.0
CA A:VAL194 4.3 29.1 1.0
N A:GLY220 4.3 36.2 1.0
C A:ALA193 4.4 34.4 1.0
N A:ASP195 4.4 26.2 1.0
CA A:ASP195 4.6 27.1 1.0
CD1 A:LEU219 4.7 33.6 1.0
CA A:ALA193 4.8 36.8 1.0
CA A:ALA191 4.8 34.9 1.0
CA A:GLY220 4.8 38.2 1.0
CB A:LEU219 4.9 31.6 1.0

Sodium binding site 2 out of 5 in 5v72

Go back to Sodium Binding Sites List in 5v72
Sodium binding site 2 out of 5 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:18.1
occ:1.00
 O C:HOH667 2.2 25.3 1.0
O B:VAL194 2.3 28.6 1.0
O B:LEU219 2.4 26.5 1.0
O B:ALA191 2.4 26.6 1.0
O B:ALA218 2.8 28.2 1.0
O B:GLU192 2.9 29.3 1.0
C B:LEU219 3.1 24.6 1.0
CA B:LEU219 3.4 25.4 1.0
C B:GLU192 3.5 29.4 1.0
C B:VAL194 3.5 28.0 1.0
C B:ALA191 3.6 26.6 1.0
CA B:GLU192 3.8 31.8 1.0
C B:ALA218 3.8 26.8 1.0
N B:VAL194 4.0 26.9 1.0
N B:LEU219 4.1 25.2 1.0
N B:GLU192 4.1 29.0 1.0
N B:GLY220 4.2 24.9 1.0
O B:HOH616 4.3 22.0 1.0
O B:HOH565 4.4 36.3 1.0
CA B:VAL194 4.4 27.1 1.0
N B:ALA193 4.4 27.3 1.0
N B:ASP195 4.4 26.3 1.0
CA B:ASP195 4.5 24.6 1.0
C B:ALA193 4.6 27.8 1.0
CA B:GLY220 4.6 26.7 1.0
O C:HOH708 4.7 43.7 1.0
CD1 B:LEU219 4.7 30.8 1.0
CG2 C:THR186 4.7 26.5 1.0
CB B:LEU219 4.8 25.2 1.0
O C:PRO185 4.8 26.7 1.0
CA B:ALA191 4.8 24.9 1.0

Sodium binding site 3 out of 5 in 5v72

Go back to Sodium Binding Sites List in 5v72
Sodium binding site 3 out of 5 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:25.7
occ:1.00
 O C:VAL194 2.2 27.0 1.0
O C:HOH615 2.2 29.9 1.0
O C:ALA191 2.5 28.9 1.0
O C:HOH715 2.6 39.8 1.0
O C:GLU192 2.6 33.5 1.0
O C:LEU219 2.7 29.4 1.0
O C:ALA218 3.1 27.5 1.0
C C:GLU192 3.2 32.0 1.0
C C:VAL194 3.4 24.9 1.0
C C:LEU219 3.5 29.0 1.0
C C:ALA191 3.6 28.1 1.0
CA C:GLU192 3.7 30.9 1.0
CA C:LEU219 3.8 26.5 1.0
N C:VAL194 3.8 25.8 1.0
C C:ALA218 4.1 25.2 1.0
N C:GLU192 4.1 28.6 1.0
N C:ALA193 4.2 29.2 1.0
O C:HOH704 4.2 46.6 1.0
CA C:VAL194 4.2 26.0 1.0
O C:HOH599 4.3 43.1 1.0
C C:ALA193 4.3 28.5 1.0
O C:HOH647 4.3 27.9 1.0
N C:ASP195 4.3 24.7 1.0
N C:LEU219 4.4 25.4 1.0
CA C:ASP195 4.5 24.7 1.0
N C:GLY220 4.5 30.8 1.0
O C:HOH834 4.6 45.5 1.0
CA C:ALA193 4.7 29.1 1.0
O C:HOH717 4.7 31.7 1.0
CA C:ALA191 4.9 25.6 1.0
CD1 C:LEU219 4.9 26.6 1.0
CA C:GLY220 4.9 29.1 1.0
O C:ALA193 4.9 29.1 1.0

Sodium binding site 4 out of 5 in 5v72

Go back to Sodium Binding Sites List in 5v72
Sodium binding site 4 out of 5 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate


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 Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:33.1
occ:1.00
 O C:GLY229 2.4 28.0 1.0
O7 C:CIT403 2.4 30.0 1.0
O2 C:CIT403 2.4 33.7 1.0
O C:HOH638 2.4 28.4 1.0
O6 C:CIT403 2.4 38.2 1.0
O C:VAL228 2.5 28.8 1.0
C6 C:CIT403 3.1 39.5 1.0
C3 C:CIT403 3.2 35.2 1.0
C C:VAL228 3.3 24.4 1.0
O C:HOH529 3.3 50.8 1.0
C C:GLY229 3.3 26.1 1.0
C1 C:CIT403 3.3 39.4 1.0
CA C:GLY229 3.5 25.4 1.0
N C:GLY229 3.7 24.6 1.0
C2 C:CIT403 3.8 36.8 1.0
CG1 C:VAL255 3.9 20.9 1.0
NE2 C:HIS277 4.0 26.0 1.0
O5 C:CIT403 4.2 40.3 1.0
CA C:VAL228 4.4 22.3 1.0
O1 C:CIT403 4.4 52.3 1.0
O4 C:CIT403 4.5 33.8 1.0
N C:ARG230 4.5 27.2 1.0
C4 C:CIT403 4.6 30.6 1.0
O C:HOH723 4.7 42.3 1.0
CD2 C:HIS277 4.8 24.9 1.0
CE1 C:HIS277 4.8 27.7 1.0
CB C:VAL228 5.0 23.4 1.0

Sodium binding site 5 out of 5 in 5v72

Go back to Sodium Binding Sites List in 5v72
Sodium binding site 5 out of 5 in the Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Citrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:32.6
occ:1.00
 O D:HOH647 2.3 41.4 1.0
O D:VAL194 2.4 45.4 1.0
O D:ALA191 2.5 46.6 1.0
O D:LEU219 2.6 42.8 1.0
O D:GLU192 2.7 47.5 1.0
O D:ALA218 2.8 43.0 1.0
C D:LEU219 3.3 40.9 1.0
C D:GLU192 3.3 46.4 1.0
O D:HOH676 3.3 53.9 1.0
C D:ALA191 3.6 44.4 1.0
CA D:LEU219 3.6 41.5 1.0
CA D:GLU192 3.6 48.8 1.0
C D:VAL194 3.6 41.2 1.0
C D:ALA218 3.8 43.9 1.0
N D:VAL194 4.0 42.4 1.0
N D:GLU192 4.1 46.1 1.0
N D:LEU219 4.1 42.6 1.0
N D:ALA193 4.3 44.6 1.0
N D:GLY220 4.3 39.7 1.0
O D:HOH594 4.3 38.5 1.0
CA D:VAL194 4.5 42.6 1.0
C D:ALA193 4.5 42.7 1.0
O D:HOH661 4.5 49.1 1.0
N D:ASP195 4.6 40.6 1.0
CA D:ASP195 4.7 38.8 1.0
CA D:GLY220 4.7 39.6 1.0
CA D:ALA193 4.9 44.2 1.0
CD1 D:LEU219 4.9 44.4 1.0
OE2 D:GLU192 4.9 66.9 1.0
CA D:ALA191 4.9 42.4 1.0
CB D:LEU219 5.0 41.0 1.0
O D:HOH560 5.0 65.1 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: Mon Aug 18 02:44:28 2025

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