Atomistry » Sodium » PDB 2mat-2oj0 » 2o5w
Atomistry »
  Sodium »
    PDB 2mat-2oj0 »
      2o5w »

Sodium in PDB 2o5w: Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate

Protein crystallography data

The structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate, PDB code: 2o5w was solved by S.B.Gabelli, M.A.Bianchet, L.M.Amzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.416, 42.909, 108.328, 90.00, 115.19, 90.00
R / Rfree (%) 19.5 / 28.7

Other elements in 2o5w:

The structure of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate also contains other interesting chemical elements:

Samarium (Sm) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate (pdb code 2o5w). 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 the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate, PDB code: 2o5w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2o5w

Go back to Sodium Binding Sites List in 2o5w
Sodium binding site 1 out of 2 in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na171

b:44.8
occ:1.00
OPP A:PPV163 2.2 78.5 1.0
OE2 A:GLU60 2.5 42.5 1.0
O A:THR40 2.6 22.5 1.0
SM A:SM170 2.9 76.7 1.0
P1 A:PPV163 3.0 79.5 1.0
O11 A:PPV163 3.1 79.1 1.0
OE1 A:GLU56 3.2 34.8 1.0
O22 A:PPV163 3.2 77.3 1.0
P2 A:PPV163 3.3 77.2 1.0
O31 A:PPV163 3.3 79.1 1.0
CD A:GLU60 3.5 41.2 1.0
C A:THR40 3.7 22.3 1.0
CD A:GLU56 3.9 34.7 1.0
CA A:GLY41 3.9 23.3 1.0
O12 A:PPV163 3.9 77.4 1.0
OE1 A:GLU117 4.0 41.8 1.0
OE2 A:GLU56 4.0 34.6 1.0
CG A:GLU60 4.1 39.3 1.0
N A:GLY41 4.2 22.8 1.0
O21 A:PPV163 4.4 79.7 1.0
OE1 A:GLU60 4.5 41.5 1.0
O32 A:PPV163 4.5 77.0 1.0
OG1 A:THR40 4.5 21.6 1.0
CA A:THR40 4.8 22.0 1.0
N A:THR40 5.0 21.7 1.0

Sodium binding site 2 out of 2 in 2o5w

Go back to Sodium Binding Sites List in 2o5w
Sodium binding site 2 out of 2 in the Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the E. Coli Dihydroneopterin Triphosphate Pyrophosphohydrolase in Complex with Sm+3 and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na171

b:53.1
occ:1.00
OE2 C:GLU60 2.2 46.4 1.0
O31 C:PPV163 2.2 65.3 1.0
O C:THR40 2.5 28.9 1.0
O22 C:PPV163 2.8 71.4 1.0
SM C:SM170 2.9 77.0 1.0
CD C:GLU60 3.4 43.1 1.0
P1 C:PPV163 3.4 70.1 1.0
OE1 C:GLU117 3.4 47.7 1.0
OE1 C:GLU56 3.5 47.5 1.0
C C:THR40 3.6 28.8 1.0
O11 C:PPV163 3.6 69.4 1.0
P2 C:PPV163 3.7 71.6 1.0
O32 C:PPV163 3.9 71.7 1.0
CA C:GLY41 3.9 30.4 1.0
CG C:GLU60 3.9 40.1 1.0
OPP C:PPV163 4.0 70.5 1.0
N C:GLY41 4.2 29.4 1.0
OG1 C:THR40 4.3 28.4 1.0
OE1 C:GLU60 4.4 43.5 1.0
CD C:GLU56 4.4 39.0 1.0
CD C:GLU117 4.6 47.3 1.0
O21 C:PPV163 4.6 69.6 1.0
CA C:THR40 4.7 28.1 1.0
N C:THR40 4.8 27.5 1.0
OE2 C:GLU56 4.9 38.9 1.0
OE2 C:GLU117 5.0 47.4 1.0

Reference:

S.B.Gabelli, M.A.Bianchet, W.Xu, C.A.Dunn, Z.D.Niu, L.M.Amzel, M.J.Bessman. Structure and Function of the E. Coli Dihydroneopterin Triphosphate Pyrophosphatase: A Nudix Enzyme Involved in Folate Biosynthesis. Structure V. 15 1014 2007.
ISSN: ISSN 0969-2126
PubMed: 17698004
DOI: 10.1016/J.STR.2007.06.018
Page generated: Tue Dec 15 05:52:14 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