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Sodium in PDB 4ywb: Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid

Enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid

All present enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid, PDB code: 4ywb was solved by M.D.Balan, T.A.Johnson, W.R.Lotosky, M.J.Mcleod, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.21 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.124, 118.732, 86.393, 90.00, 107.27, 90.00
R / Rfree (%) 17.3 / 21

Other elements in 4ywb:

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid (pdb code 4ywb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid, PDB code: 4ywb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ywb

Go back to Sodium Binding Sites List in 4ywb
Sodium binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:24.8
occ:1.00
O A:ASN208 2.2 22.0 1.0
O A:LEU79 2.3 22.8 1.0
O A:HOH1304 2.3 36.5 1.0
O A:HOH1062 2.4 25.4 1.0
O A:HOH999 2.4 23.3 1.0
C A:ASN208 3.4 23.8 1.0
C A:LEU79 3.4 22.5 1.0
N A:LEU79 3.8 22.5 1.0
CA A:LEU79 4.0 21.6 1.0
O A:VAL65 4.0 21.9 1.0
CB A:ASN208 4.0 27.1 1.0
CB A:LEU79 4.0 24.6 1.0
CA A:ASN208 4.2 24.2 1.0
O A:HOH1437 4.2 42.1 1.0
CB A:ASN209 4.2 25.3 1.0
O A:ASN209 4.3 21.2 1.0
O A:GLY64 4.3 28.6 1.0
C A:ASN209 4.3 23.6 1.0
N A:ASN209 4.3 25.1 1.0
CA A:ASN209 4.5 24.7 1.0
N A:THR80 4.5 20.3 1.0
CB A:TRP210 4.6 21.0 1.0
C A:VAL65 4.7 23.1 1.0
N A:TRP210 4.7 22.4 1.0
CA A:THR80 4.9 20.2 1.0
CA A:VAL65 4.9 24.0 1.0
C A:ALA78 4.9 21.7 1.0

Sodium binding site 2 out of 2 in 4ywb

Go back to Sodium Binding Sites List in 4ywb
Sodium binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Oxalic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na703

b:22.1
occ:1.00
O C:ASN208 2.2 21.3 1.0
O C:LEU79 2.2 20.1 1.0
O C:HOH1306 2.2 33.2 1.0
O C:HOH1050 2.3 22.2 1.0
O C:HOH1087 2.4 21.9 1.0
C C:LEU79 3.4 17.6 1.0
C C:ASN208 3.4 19.9 1.0
N C:LEU79 3.8 18.4 1.0
CA C:LEU79 3.9 18.9 1.0
CB C:ASN208 3.9 22.5 1.0
O C:VAL65 4.0 22.1 1.0
CB C:LEU79 4.1 19.4 1.0
O C:HOH1404 4.1 39.8 1.0
CA C:ASN208 4.2 21.3 1.0
CB C:ASN209 4.3 23.1 1.0
O C:GLY64 4.3 27.9 1.0
C C:ASN209 4.4 19.6 1.0
N C:ASN209 4.4 21.5 1.0
O C:ASN209 4.5 20.3 1.0
N C:THR80 4.5 18.4 1.0
CA C:ASN209 4.6 20.8 1.0
CB C:TRP210 4.7 17.1 1.0
C C:VAL65 4.7 20.4 1.0
N C:TRP210 4.8 20.0 1.0
CA C:THR80 4.8 18.1 1.0
CA C:VAL65 4.9 20.9 1.0
C C:ALA78 5.0 18.3 1.0

Reference:

M.D.Balan, M.J.Mcleod, W.R.Lotosky, M.Ghaly, T.Holyoak. Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase By 3-Mercaptopicolinic Acid. Biochemistry V. 54 5878 2015.
ISSN: ISSN 0006-2960
PubMed: 26322521
DOI: 10.1021/ACS.BIOCHEM.5B00822
Page generated: Tue Dec 15 10:04:46 2020

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