Atomistry » Sodium » PDB 2r25-2uyz » 2rk7
Atomistry »
  Sodium »
    PDB 2r25-2uyz »
      2rk7 »

Sodium in PDB 2rk7: The Structure of Rat Cytosolic Pepck in Complex with Oxalate

Enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Oxalate

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Oxalate:
4.1.1.32;

Protein crystallography data

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate, PDB code: 2rk7 was solved by S.M.Sullivan, R.M.Stiffin, G.M.Carlson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.82 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.011, 118.945, 86.506, 90.00, 106.95, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 2rk7:

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate (pdb code 2rk7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate, PDB code: 2rk7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2rk7

Go back to Sodium Binding Sites List in 2rk7
Sodium binding site 1 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:15.8
occ:1.00
O A:LEU79 2.3 12.7 1.0
O A:ASN208 2.3 6.9 1.0
O A:HOH5865 2.4 25.3 1.0
O A:HOH5645 2.4 15.9 1.0
O A:HOH6093 2.5 33.0 1.0
C A:LEU79 3.4 11.9 1.0
C A:ASN208 3.5 6.8 1.0
N A:LEU79 3.8 11.9 1.0
O A:VAL65 3.8 14.5 1.0
CA A:LEU79 4.0 12.0 1.0
CB A:ASN208 4.1 7.3 1.0
CB A:LEU79 4.1 11.7 1.0
O A:GLY64 4.2 15.1 1.0
O A:ASN209 4.3 4.8 1.0
CA A:ASN208 4.3 7.3 1.0
C A:ASN209 4.3 5.3 1.0
CB A:ASN209 4.5 5.8 1.0
N A:ASN209 4.5 6.4 1.0
N A:THR80 4.5 12.0 1.0
C A:VAL65 4.6 14.4 1.0
CB A:TRP210 4.6 4.5 1.0
CA A:ASN209 4.6 5.7 1.0
N A:TRP210 4.8 4.6 1.0
CA A:THR80 4.8 11.9 1.0
CA A:VAL65 4.8 14.4 1.0
C A:ALA78 4.9 12.2 1.0
CE3 A:TRP210 5.0 4.5 1.0

Sodium binding site 2 out of 2 in 2rk7

Go back to Sodium Binding Sites List in 2rk7
Sodium binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:18.2
occ:1.00
O B:HOH5939 2.1 13.8 1.0
O B:ASN208 2.3 8.2 1.0
O B:HOH5726 2.3 21.1 1.0
O B:HOH5645 2.3 16.1 1.0
O B:LEU79 2.5 14.4 1.0
C B:ASN208 3.5 8.2 1.0
C B:LEU79 3.6 13.7 1.0
O B:VAL65 3.7 14.4 1.0
N B:LEU79 3.8 13.7 1.0
CA B:LEU79 4.1 13.6 1.0
CB B:ASN208 4.1 8.7 1.0
O B:GLY64 4.1 14.2 1.0
CB B:ASN209 4.2 7.7 1.0
O B:ASN209 4.2 6.9 1.0
C B:ASN209 4.2 6.6 1.0
CB B:LEU79 4.3 13.9 1.0
CA B:ASN208 4.3 8.5 1.0
N B:ASN209 4.4 7.7 1.0
C B:VAL65 4.4 14.1 1.0
CA B:ASN209 4.5 7.4 1.0
CA B:VAL65 4.6 14.4 1.0
CB B:TRP210 4.7 4.6 1.0
N B:TRP210 4.7 6.0 1.0
N B:THR80 4.7 13.5 1.0
C B:ALA78 4.9 13.2 1.0

Reference:

R.M.Stiffin, S.M.Sullivan, G.M.Carlson, T.Holyoak. Differential Inhibition of Cytosolic Pepck By Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition. Biochemistry V. 47 2099 2008.
ISSN: ISSN 0006-2960
PubMed: 18197707
DOI: 10.1021/BI7020662
Page generated: Tue Dec 15 05:55:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy