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Sodium in PDB 1a9y: Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose

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

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

Protein crystallography data

The structure of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose, PDB code: 1a9y 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 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.000, 85.000, 106.700, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / n/a

Sodium Binding Sites:

The binding sites of Sodium atom in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose (pdb code 1a9y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose, PDB code: 1a9y:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 1a9y

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Sodium binding site 1 out of 4 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose


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- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:25.9
occ:1.00
O A:GLN194 2.3 32.8 1.0
O A:HOH593 2.4 30.4 1.0
O A:HOH494 2.6 22.5 1.0
O A:HOH652 2.7 35.4 1.0
C A:GLN194 3.5 26.6 1.0
N A:GLN194 3.7 20.9 1.0
CA A:GLN194 4.0 19.5 1.0
O A:HOH560 4.1 30.3 1.0
CB A:GLN194 4.2 28.5 1.0
O A:HOH558 4.2 28.2 1.0
OD1 A:ASN35 4.4 44.9 1.0
O A:HOH696 4.5 23.3 1.0
N A:GLY195 4.6 23.9 1.0
O A:HOH930 4.6 55.4 1.0
O A:ILE196 4.7 28.3 1.0
C A:PRO193 4.7 32.7 1.0
CA A:GLY195 4.9 16.3 1.0
O A:HOH495 4.9 19.0 1.0

Sodium binding site 2 out of 4 in 1a9y

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Sodium binding site 2 out of 4 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose


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- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na411

b:17.9
occ:1.00
O A:GLN334 2.1 32.5 1.0
O A:HOH576 2.5 30.6 1.0
O A:HOH432 2.5 24.2 1.0
O A:HOH638 2.5 39.8 1.0
O A:HOH895 2.7 51.8 1.0
O A:HOH896 2.9 66.5 1.0
C A:GLN334 3.2 33.0 1.0
O A:HOH894 3.4 49.5 1.0
O A:TYR336 3.7 34.7 1.0
CA A:GLN334 4.1 34.4 1.0
N A:GLY335 4.2 22.1 1.0
NE2 A:GLN334 4.3 0.0 1.0
CA A:GLY335 4.4 22.1 1.0
O A:HOH776 4.4 40.4 1.0
CB A:GLN334 4.4 0.0 1.0
OD1 A:ASP338 4.5 88.2 1.0
NZ A:LYS37 4.5 39.2 1.0
C A:GLY335 4.5 34.8 1.0
OD2 A:ASP192 4.6 20.3 1.0
N A:TYR336 4.6 21.5 1.0
NE2 A:GLN194 4.7 26.1 1.0
OD1 A:ASP192 4.7 29.5 1.0
C A:TYR336 4.8 25.8 1.0
OE1 A:GLN194 4.8 34.4 1.0
CE A:LYS37 4.9 23.5 1.0
O A:HOH827 5.0 57.6 1.0

Sodium binding site 3 out of 4 in 1a9y

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Sodium binding site 3 out of 4 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose


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- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na412

b:28.3
occ:1.00
O A:HOH528 2.2 31.8 1.0
O A:HOH755 2.4 36.9 1.0
O A:HOH773 2.4 68.5 1.0
O A:HOH525 2.5 27.4 1.0
O A:HOH738 2.8 42.5 1.0
O A:HOH513 4.2 24.4 1.0
ND2 A:ASN285 4.3 22.9 1.0
O A:HOH550 4.5 37.3 1.0
O A:HOH945 4.6 64.5 1.0
CB A:HIS287 4.6 19.2 1.0
OG A:SER214 4.6 16.8 1.0
CB A:SER214 4.7 10.4 1.0
OD1 A:ASN285 4.7 24.1 1.0
OD2 A:ASP213 4.8 23.1 1.0
CG A:ASN285 5.0 22.1 1.0
ND1 A:HIS287 5.0 18.9 1.0

Sodium binding site 4 out of 4 in 1a9y

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Sodium binding site 4 out of 4 in the Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Udp-Galactose 4-Epimerase Mutant S124A/Y149F Complexed with Udp- Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na413

b:13.8
occ:1.00
O A:HOH635 2.2 50.1 1.0
OE1 A:GLN91 2.3 29.0 1.0
O A:HOH452 2.3 22.4 1.0
O A:HOH741 2.8 60.5 1.0
CD A:GLN91 3.3 19.8 1.0
NE2 A:GLN91 3.7 26.2 1.0
O A:HOH589 3.9 67.9 1.0
O A:HOH753 4.1 33.2 1.0
CA A:GLN91 4.2 12.6 1.0
O A:HOH900 4.2 57.6 1.0
CG A:GLN91 4.5 11.4 1.0
CB A:GLN91 4.6 16.7 1.0
O A:VAL90 4.7 19.4 1.0
O A:GLN91 4.9 22.5 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 05:21:44 2020

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