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Sodium in PDB 1a9z: Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose

Enzymatic activity of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose

All present enzymatic activity of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose:
5.1.3.2;

Protein crystallography data

The structure of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose, PDB code: 1a9z was solved by J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.900, 83.900, 108.100, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose (pdb code 1a9z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose, PDB code: 1a9z:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 1a9z

Go back to Sodium Binding Sites List in 1a9z
Sodium binding site 1 out of 3 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na420

b:30.0
occ:1.00
O A:GLN194 2.3 36.2 1.0
O A:HOH703 2.4 50.5 1.0
O A:HOH569 2.5 31.3 1.0
O A:HOH957 2.8 71.1 1.0
O A:HOH727 2.9 38.2 1.0
C A:GLN194 3.4 29.9 1.0
N A:GLN194 3.8 22.2 1.0
CA A:GLN194 4.0 18.5 1.0
CB A:GLN194 4.0 22.9 1.0
N A:GLY195 4.5 32.8 1.0
O A:HOH834 4.6 47.4 1.0
O A:ILE196 4.7 28.1 1.0
O A:HOH518 4.7 25.4 1.0
O A:HOH720 4.7 24.4 1.0
O A:HOH803 4.7 50.9 1.0
CA A:GLY195 4.8 29.9 1.0
OD1 A:ASN35 4.8 30.6 1.0
C A:PRO193 4.8 33.6 1.0
O A:HOH879 4.9 54.5 1.0
O A:HOH565 4.9 42.2 1.0
O A:HOH645 5.0 49.5 1.0

Sodium binding site 2 out of 3 in 1a9z

Go back to Sodium Binding Sites List in 1a9z
Sodium binding site 2 out of 3 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na421

b:28.5
occ:1.00
OE1 A:GLN91 2.2 35.5 1.0
O A:HOH510 2.4 27.2 1.0
O A:HOH704 2.7 81.1 1.0
CD A:GLN91 3.2 26.4 1.0
NE2 A:GLN91 3.8 41.7 1.0
O A:HOH730 3.8 44.0 1.0
CA A:GLN91 4.3 32.5 1.0
CG A:GLN91 4.4 24.5 1.0
CB A:GLN91 4.6 23.9 1.0
O A:VAL90 4.7 24.5 1.0
O A:GLN91 4.9 25.9 1.0

Sodium binding site 3 out of 3 in 1a9z

Go back to Sodium Binding Sites List in 1a9z
Sodium binding site 3 out of 3 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na422

b:28.4
occ:1.00
O A:GLN334 2.3 51.7 1.0
O A:HOH597 2.4 53.4 1.0
O A:HOH515 2.5 42.3 1.0
O A:HOH608 2.7 44.7 1.0
O A:HOH946 3.3 83.8 1.0
C A:GLN334 3.3 44.7 1.0
O A:HOH829 3.5 44.7 1.0
O A:TYR336 3.9 26.9 1.0
CA A:GLN334 4.1 60.8 1.0
N A:GLY335 4.2 40.0 1.0
CB A:GLN334 4.4 48.2 1.0
NZ A:LYS37 4.4 29.3 1.0
CA A:GLY335 4.4 26.4 1.0
NE2 A:GLN194 4.5 44.4 1.0
OD1 A:ASP192 4.5 20.7 1.0
OD2 A:ASP192 4.6 23.1 1.0
NE2 A:GLN334 4.6 0.0 1.0
OE1 A:GLN194 4.6 35.5 1.0
OD1 A:ASP338 4.7 0.0 1.0
C A:GLY335 4.7 25.8 1.0
N A:TYR336 4.7 35.0 1.0
O A:HOH868 4.8 58.0 1.0
C A:TYR336 5.0 32.2 1.0
CG A:ASP192 5.0 31.3 1.0

Reference:

J.B.Thoden, H.M.Holden. Dramatic Differences in the Binding of Udp-Galactose and Udp-Glucose to Udp-Galactose 4-Epimerase From Escherichia Coli. Biochemistry V. 37 11469 1998.
ISSN: ISSN 0006-2960
PubMed: 9708982
DOI: 10.1021/BI9808969
Page generated: Tue Dec 15 05:21:45 2020

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