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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

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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

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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

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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

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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 Dec 15 11:43:05 2020

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