Atomistry » Sodium » PDB 5uka-5v0d » 5ur0
Atomistry »
  Sodium »
    PDB 5uka-5v0d »
      5ur0 »

Sodium in PDB 5ur0: Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi

Enzymatic activity of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi

All present enzymatic activity of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi:
1.2.1.12;

Protein crystallography data

The structure of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi, PDB code: 5ur0 was solved by A.T.P.Machado, M.Silva, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.743, 94.552, 90.932, 90.00, 99.96, 90.00
R / Rfree (%) 15.4 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi (pdb code 5ur0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi, PDB code: 5ur0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ur0

Go back to Sodium Binding Sites List in 5ur0
Sodium binding site 1 out of 4 in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.1
occ:1.00
 O A:VAL26 2.2 29.7 1.0
O A:SER20 2.3 22.6 1.0
O A:HOH753 2.4 27.0 1.0
O A:ARG23 2.4 33.1 1.0
O A:HOH732 2.5 29.1 1.0
O A:HOH759 3.3 56.6 1.0
C A:VAL26 3.4 28.0 1.0
C A:SER20 3.5 22.9 1.0
C A:ARG23 3.6 34.1 1.0
CA A:GLU27 4.0 27.8 1.0
O A:HOH635 4.1 24.8 1.0
N A:GLU27 4.2 27.2 1.0
O A:HOH816 4.2 52.2 1.0
CA A:LEU21 4.2 25.9 1.0
CB A:GLU27 4.3 30.2 1.0
N A:LEU21 4.3 23.6 1.0
O A:HOH567 4.3 29.9 1.0
CA A:THR24 4.3 38.0 1.0
N A:VAL26 4.4 29.3 1.0
N A:ARG23 4.4 33.3 1.0
N A:THR24 4.4 35.6 1.0
CA A:SER20 4.5 21.8 1.0
C A:LEU21 4.5 27.5 1.0
CA A:VAL26 4.5 28.2 1.0
CG2 A:VAL26 4.5 27.8 1.0
CA A:ARG23 4.6 34.2 1.0
C A:THR24 4.7 37.3 1.0
O A:LEU21 4.7 29.0 1.0
CB A:SER20 4.7 22.0 1.0
CG A:ARG23 4.8 35.2 1.0
N A:ASP25 5.0 35.1 1.0

Sodium binding site 2 out of 4 in 5ur0

Go back to Sodium Binding Sites List in 5ur0
Sodium binding site 2 out of 4 in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:29.9
occ:1.00
 O B:HOH750 2.3 25.4 1.0
O B:ARG23 2.3 31.9 1.0
O B:SER20 2.3 23.2 1.0
O B:VAL26 2.3 30.8 1.0
O B:HOH743 2.6 38.6 1.0
C B:SER20 3.5 23.5 1.0
C B:ARG23 3.5 33.5 1.0
C B:VAL26 3.5 28.9 1.0
CA B:GLU27 4.0 27.7 1.0
O B:HOH665 4.1 30.2 1.0
O B:HOH620 4.1 23.3 1.0
O B:HOH731 4.2 39.4 1.0
CB B:GLU27 4.2 30.6 1.0
CA B:LEU21 4.3 27.1 1.0
N B:GLU27 4.3 27.8 1.0
CA B:THR24 4.3 37.0 1.0
N B:LEU21 4.3 24.5 1.0
N B:ARG23 4.3 31.2 1.0
N B:THR24 4.3 35.6 1.0
N B:VAL26 4.4 29.4 1.0
CA B:SER20 4.4 22.7 1.0
C B:LEU21 4.5 29.1 1.0
CA B:ARG23 4.5 33.6 1.0
O B:HOH821 4.6 43.1 1.0
CA B:VAL26 4.6 28.6 1.0
C B:THR24 4.6 37.2 1.0
CG B:ARG23 4.7 32.7 0.3
O B:LEU21 4.7 31.4 1.0
CB B:SER20 4.7 23.2 1.0
CG B:ARG23 4.7 32.6 0.7
N B:ASP25 4.9 35.4 1.0
N B:GLU22 5.0 28.7 1.0

Sodium binding site 3 out of 4 in 5ur0

Go back to Sodium Binding Sites List in 5ur0
Sodium binding site 3 out of 4 in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:30.5
occ:1.00
 O C:SER20 2.3 23.4 1.0
O C:VAL26 2.3 30.0 1.0
O C:ARG23 2.3 32.0 1.0
O C:HOH743 2.4 25.8 1.0
O C:HOH727 2.4 39.4 1.0
O C:HOH724 2.8 93.9 1.0
C C:SER20 3.5 22.7 1.0
C C:VAL26 3.5 29.9 1.0
C C:ARG23 3.5 35.0 1.0
O C:HOH780 4.0 52.8 1.0
CA C:GLU27 4.1 29.6 1.0
O C:HOH568 4.1 22.2 1.0
CB C:GLU27 4.2 32.2 1.0
O C:HOH571 4.2 32.7 1.0
CA C:THR24 4.3 39.1 1.0
CA C:LEU21 4.3 25.6 1.0
N C:GLU27 4.3 28.6 1.0
N C:LEU21 4.3 23.6 1.0
N C:ARG23 4.3 33.8 1.0
N C:THR24 4.4 38.0 1.0
N C:VAL26 4.4 33.8 1.0
CA C:SER20 4.5 21.8 1.0
C C:LEU21 4.5 28.8 1.0
CA C:ARG23 4.5 34.9 1.0
CA C:VAL26 4.6 31.1 1.0
C C:THR24 4.6 38.6 1.0
CG2 C:VAL26 4.7 28.5 1.0
O C:LEU21 4.7 29.3 1.0
CB C:SER20 4.7 21.8 1.0
CG C:ARG23 4.7 33.8 1.0
N C:ASP25 4.9 36.2 1.0
N C:GLU22 5.0 31.2 1.0

Sodium binding site 4 out of 4 in 5ur0

Go back to Sodium Binding Sites List in 5ur0
Sodium binding site 4 out of 4 in the Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystallographic Structure of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:27.0
occ:1.00
 O D:SER20 2.3 21.3 1.0
O D:VAL26 2.3 29.9 1.0
O D:ARG23 2.3 28.4 1.0
O D:HOH738 2.4 32.0 1.0
O D:HOH769 2.5 25.4 1.0
O D:HOH699 2.9 53.4 1.0
C D:SER20 3.5 21.4 1.0
C D:ARG23 3.5 29.8 1.0
C D:VAL26 3.5 28.4 1.0
O D:HOH803 4.0 36.3 1.0
CA D:GLU27 4.1 26.5 1.0
O D:HOH634 4.2 19.1 1.0
O D:HOH606 4.2 32.6 1.0
CA D:LEU21 4.2 26.3 1.0
CA D:THR24 4.3 34.2 1.0
CB D:GLU27 4.3 28.8 1.0
N D:LEU21 4.3 23.0 1.0
N D:GLU27 4.3 27.0 1.0
N D:ARG23 4.3 29.6 1.0
N D:THR24 4.3 31.9 1.0
C D:LEU21 4.4 28.7 1.0
N D:VAL26 4.4 29.8 1.0
CA D:SER20 4.5 19.6 1.0
CA D:ARG23 4.5 30.6 1.0
CA D:VAL26 4.6 28.4 1.0
O D:LEU21 4.6 30.1 1.0
CG2 D:VAL26 4.6 24.8 1.0
C D:THR24 4.6 34.7 1.0
CB D:SER20 4.8 20.2 1.0
CG D:ARG23 4.8 28.9 1.0
N D:GLU22 4.9 29.2 1.0
N D:ASP25 5.0 33.4 1.0

Reference:

A.T.P.Machado, M.Silva, J.Iulek. Structural Studies of Glyceraldehyde-3-Phosphate Dehydrogenase From Naegleria Gruberi, the First One From Phylum Percolozoa. Biochim. Biophys. Acta V.1866 581 2018.
ISSN: ISSN 0006-3002
PubMed: 29501559
DOI: 10.1016/J.BBAPAP.2018.02.006
Page generated: Tue Oct 8 00:38:58 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy