Atomistry » Sodium » PDB 5v0e-5vb8 » 5v72
Atomistry »
  Sodium »
    PDB 5v0e-5vb8 »
      5v72 »

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: Tue Oct 8 00:45:04 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy