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Sodium in PDB 5v7g: Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate

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

All present enzymatic activity of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate:
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 Nadph and Oxalate, PDB code: 5v7g was solved by I.G.Shabalin, D.V.Mason, K.B.Handing, J.Kutner, D.Matelska, D.R.Cooper, 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) 37.07 / 1.75
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 178.209, 178.209, 133.799, 90.00, 90.00, 120.00
R / Rfree (%) 15 / 18

Other elements in 5v7g:

The structure of Crystal Structure of Nadph-Dependent Glyoxylate/Hydroxypyruvate Reductase SMC04462 (Smghrb) From Sinorhizobium Meliloti in Complex with Nadph and Oxalate 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 Nadph and Oxalate (pdb code 5v7g). 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 Nadph and Oxalate, PDB code: 5v7g:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5v7g

Go back to Sodium Binding Sites List in 5v7g
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 Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:38.4
occ:1.00
 O A:HOH754 2.4 61.9 1.0
O A:ALA191 2.4 27.8 1.0
O A:VAL194 2.5 36.4 1.0
O A:LEU219 2.5 34.7 1.0
O A:ALA218 2.6 34.0 1.0
O A:GLU192 2.6 35.7 1.0
C A:LEU219 3.2 31.6 1.0
C A:GLU192 3.2 37.3 1.0
CA A:LEU219 3.5 38.1 1.0
C A:ALA191 3.5 28.3 1.0
CA A:GLU192 3.6 37.1 1.0
C A:ALA218 3.6 33.2 1.0
C A:VAL194 3.6 34.9 1.0
N A:VAL194 3.9 44.1 1.0
N A:LEU219 4.0 33.7 1.0
N A:GLU192 4.0 27.8 1.0
O A:HOH612 4.1 41.1 1.0
N A:ALA193 4.2 30.5 1.0
N A:GLY220 4.2 34.1 1.0
CA A:VAL194 4.4 31.3 1.0
O A:HOH660 4.5 35.8 1.0
C A:ALA193 4.5 38.0 1.0
N A:ASP195 4.6 29.5 1.0
CD1 A:LEU219 4.7 28.1 1.0
CA A:GLY220 4.7 36.9 1.0
CA A:ASP195 4.7 26.3 1.0
O A:HOH879 4.8 35.9 1.0
CA A:ALA191 4.8 33.0 1.0
CA A:ALA193 4.8 38.4 1.0
CB A:LEU219 4.8 38.6 1.0
CA A:ALA218 5.0 34.0 1.0

Sodium binding site 2 out of 4 in 5v7g

Go back to Sodium Binding Sites List in 5v7g
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 Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:34.4
occ:1.00
 O B:HOH725 2.4 49.4 1.0
O B:ALA191 2.4 35.0 1.0
O B:VAL194 2.4 33.5 1.0
O B:LEU219 2.5 36.6 1.0
O B:GLU192 2.6 35.3 1.0
O B:ALA218 2.6 34.1 1.0
C B:GLU192 3.2 35.1 1.0
C B:LEU219 3.2 34.1 1.0
CA B:LEU219 3.5 40.4 1.0
C B:ALA191 3.5 34.1 1.0
CA B:GLU192 3.6 38.0 1.0
C B:VAL194 3.6 27.8 1.0
C B:ALA218 3.6 43.1 1.0
O B:HOH577 3.7 66.6 1.0
N B:VAL194 3.9 36.9 1.0
N B:GLU192 4.0 32.9 1.0
N B:LEU219 4.0 44.4 1.0
N B:ALA193 4.1 34.3 1.0
N B:GLY220 4.3 47.1 1.0
O B:HOH589 4.3 37.2 1.0
CA B:VAL194 4.4 26.4 1.0
C B:ALA193 4.4 38.8 1.0
N B:ASP195 4.6 33.2 1.0
O B:HOH594 4.6 51.3 1.0
CA B:ASP195 4.7 21.5 1.0
CD1 B:LEU219 4.7 38.1 1.0
CA B:GLY220 4.7 50.0 1.0
CA B:ALA193 4.8 37.1 1.0
CA B:ALA191 4.8 34.1 1.0
OE1 B:GLU192 4.8 80.6 1.0
CB B:LEU219 4.9 32.7 1.0

Sodium binding site 3 out of 4 in 5v7g

Go back to Sodium Binding Sites List in 5v7g
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 Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na404

b:26.6
occ:1.00
 O C:HOH778 2.4 40.0 1.0
O C:VAL194 2.4 24.2 1.0
O C:ALA191 2.4 25.7 1.0
O C:LEU219 2.5 27.8 1.0
O C:ALA218 2.6 30.1 1.0
O C:GLU192 2.7 30.6 1.0
C C:LEU219 3.1 28.3 1.0
C C:GLU192 3.3 30.7 1.0
CA C:LEU219 3.4 28.2 1.0
C C:ALA191 3.5 28.3 1.0
C C:VAL194 3.6 26.2 1.0
C C:ALA218 3.6 35.3 1.0
CA C:GLU192 3.6 34.0 1.0
O C:HOH510 3.9 39.0 1.0
N C:VAL194 3.9 24.3 1.0
N C:LEU219 3.9 27.9 1.0
N C:GLU192 4.0 25.9 1.0
N C:GLY220 4.2 34.4 1.0
N C:ALA193 4.2 25.9 1.0
CA C:VAL194 4.4 28.8 1.0
O C:HOH780 4.4 42.4 1.0
C C:ALA193 4.5 27.5 1.0
N C:ASP195 4.5 18.7 1.0
O C:HOH625 4.6 32.3 1.0
CD1 C:LEU219 4.6 32.2 1.0
CA C:ASP195 4.6 17.3 1.0
CA C:GLY220 4.7 26.2 1.0
CA C:ALA191 4.7 30.6 1.0
CB C:LEU219 4.7 21.1 1.0
CA C:ALA193 4.9 23.5 1.0
OE1 C:GLU192 4.9 77.6 1.0
CA C:ALA218 5.0 31.3 1.0

Sodium binding site 4 out of 4 in 5v7g

Go back to Sodium Binding Sites List in 5v7g
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 Nadph and Oxalate


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 Nadph and Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na405

b:29.8
occ:1.00
 O D:HOH754 2.4 41.7 1.0
O D:ALA191 2.4 27.4 1.0
O D:VAL194 2.4 24.4 1.0
O D:LEU219 2.5 29.6 1.0
O D:ALA218 2.6 26.7 1.0
O D:GLU192 2.7 31.9 1.0
C D:LEU219 3.1 28.6 1.0
C D:GLU192 3.2 32.6 1.0
CA D:LEU219 3.4 29.0 1.0
C D:ALA191 3.5 32.0 1.0
C D:VAL194 3.6 27.2 1.0
CA D:GLU192 3.6 30.0 1.0
C D:ALA218 3.6 29.4 1.0
O D:HOH524 3.9 55.1 1.0
N D:VAL194 3.9 29.9 1.0
N D:GLU192 4.0 28.8 1.0
N D:LEU219 4.0 33.6 1.0
N D:ALA193 4.1 30.4 1.0
N D:GLY220 4.2 25.4 1.0
CA D:VAL194 4.4 27.7 1.0
O D:HOH859 4.4 59.0 1.0
O D:HOH615 4.4 29.4 1.0
C D:ALA193 4.5 33.0 1.0
N D:ASP195 4.6 24.0 1.0
CD1 D:LEU219 4.6 28.6 1.0
CA D:ASP195 4.7 21.2 1.0
CA D:ALA191 4.7 27.2 1.0
CA D:GLY220 4.7 32.1 1.0
CB D:LEU219 4.8 25.3 1.0
CA D:ALA193 4.8 28.3 1.0
O D:HOH890 4.8 36.1 1.0
OE1 D:GLU192 4.9 65.3 1.0
CA D:ALA218 5.0 27.1 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: Tue Oct 8 00:45:20 2024

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