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Sodium in PDB 2uw1: Ivy Desaturase Structure

Enzymatic activity of Ivy Desaturase Structure

All present enzymatic activity of Ivy Desaturase Structure:
1.14.99.6;

Protein crystallography data

The structure of Ivy Desaturase Structure, PDB code: 2uw1 was solved by J.E.Guy, E.Whittle, D.Kumaran, Y.Lindqvist, J.Shanklin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.122, 61.863, 201.002, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.9

Other elements in 2uw1:

The structure of Ivy Desaturase Structure also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ivy Desaturase Structure (pdb code 2uw1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ivy Desaturase Structure, PDB code: 2uw1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2uw1

Go back to Sodium Binding Sites List in 2uw1
Sodium binding site 1 out of 2 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ivy Desaturase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1361

b:40.8
occ:1.00
O A:HOH2112 2.2 23.0 1.0
O B:HOH2125 2.3 24.2 1.0
OE1 A:GLU101 2.3 34.7 1.0
O A:HOH2121 2.4 21.2 1.0
O A:HOH2068 2.5 29.8 1.0
O B:HOH2129 3.0 31.1 1.0
NA B:NA1361 3.2 33.5 1.0
OD1 A:ASP143 3.4 30.4 1.0
CD A:GLU101 3.4 33.9 1.0
O B:HOH2127 3.8 30.3 1.0
OE2 A:GLU101 4.0 36.0 1.0
OD1 A:ASN139 4.0 24.5 1.0
O A:HOH2113 4.0 38.3 1.0
O B:HOH2084 4.2 27.8 1.0
N A:ASP143 4.3 23.8 1.0
OD1 B:ASP143 4.3 21.7 0.5
C A:GLY142 4.5 23.5 1.0
O A:ASN139 4.5 22.9 1.0
CA A:GLU101 4.5 24.9 1.0
CA A:GLY142 4.5 23.6 1.0
CG A:ASP143 4.6 27.9 1.0
OD1 B:ASN139 4.6 22.9 1.0
CG A:GLU101 4.6 28.6 1.0
O A:HOH2066 4.6 17.2 1.0
O A:GLU101 4.6 24.4 1.0
O B:HOH2128 4.7 22.7 1.0
CB A:GLU101 4.7 25.4 1.0
O B:HOH2124 4.9 18.0 1.0
CA A:ASP143 4.9 24.5 1.0

Sodium binding site 2 out of 2 in 2uw1

Go back to Sodium Binding Sites List in 2uw1
Sodium binding site 2 out of 2 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ivy Desaturase Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1361

b:33.5
occ:1.00
O B:HOH2124 2.2 18.0 1.0
O A:HOH2121 2.2 21.2 1.0
O B:HOH2127 2.3 30.3 1.0
O B:HOH2125 2.3 24.2 1.0
O B:HOH2084 2.3 27.8 1.0
OE1 B:GLU101 2.3 30.9 1.0
NA A:NA1361 3.2 40.8 1.0
CD B:GLU101 3.4 30.6 1.0
OE2 B:GLU101 3.7 32.8 1.0
OD1 B:ASP143 3.7 21.7 0.5
OD1 B:ASN139 4.0 22.9 1.0
O B:HOH2129 4.1 31.1 1.0
O A:HOH2068 4.2 29.8 1.0
OD1 A:ASP143 4.2 30.4 1.0
O A:HOH2113 4.4 38.3 1.0
N B:ASP143 4.5 23.2 1.0
OD1 A:ASN139 4.5 24.5 1.0
O B:HOH2123 4.5 18.1 1.0
O A:HOH2122 4.6 19.6 1.0
CA B:GLU101 4.6 24.5 1.0
O B:ASN139 4.6 22.1 1.0
CG B:GLU101 4.6 27.1 1.0
O B:GLU101 4.6 25.0 1.0
C B:GLY142 4.7 23.7 1.0
CA B:GLY142 4.7 23.4 1.0
CG B:ASP143 4.8 22.4 0.5
CB B:GLU101 4.8 24.8 1.0
O A:HOH2112 4.9 23.0 1.0

Reference:

J.E.Guy, E.Whittle, D.Kumaran, Y.Lindqvist, J.Shanklin. The Crystal Structure of the Ivy {Delta}4-16:0-Acp Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity. J.Biol.Chem. V. 282 19863 2007.
ISSN: ISSN 0021-9258
PubMed: 17463003
DOI: 10.1074/JBC.M702520200
Page generated: Tue Dec 15 05:56:11 2020

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