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Sodium in PDB 3ivt: Homocitrate Synthase LYS4 Bound to 2-Og

Enzymatic activity of Homocitrate Synthase LYS4 Bound to 2-Og

All present enzymatic activity of Homocitrate Synthase LYS4 Bound to 2-Og:
2.3.3.14;

Protein crystallography data

The structure of Homocitrate Synthase LYS4 Bound to 2-Og, PDB code: 3ivt was solved by S.L.Bulfer, E.M.Scott, J.-F.Couture, L.Pillus, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.47 / 2.67
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 133.731, 133.731, 125.904, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 20.6

Other elements in 3ivt:

The structure of Homocitrate Synthase LYS4 Bound to 2-Og also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Homocitrate Synthase LYS4 Bound to 2-Og (pdb code 3ivt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Homocitrate Synthase LYS4 Bound to 2-Og, PDB code: 3ivt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3ivt

Go back to Sodium Binding Sites List in 3ivt
Sodium binding site 1 out of 2 in the Homocitrate Synthase LYS4 Bound to 2-Og


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:33.2
occ:0.50
O A:ARG214 2.9 44.1 1.0
O A:VAL217 3.0 43.9 1.0
O A:GLY215 3.6 44.6 1.0
C A:GLY215 3.7 44.0 1.0
CA A:GLY215 3.8 43.0 1.0
C A:ARG214 4.0 43.8 1.0
C A:VAL217 4.0 44.0 1.0
O A:HOH482 4.1 66.2 1.0
N A:GLY215 4.4 43.0 1.0
N A:VAL216 4.5 44.2 1.0
N A:VAL217 4.6 43.0 1.0
NE A:ARG214 4.6 41.0 1.0
CA A:SER218 4.6 45.4 1.0
NH2 A:ARG214 4.7 37.7 1.0
N A:SER218 4.7 44.8 1.0
C A:VAL216 4.8 43.5 1.0
CA A:VAL217 4.9 43.4 1.0

Sodium binding site 2 out of 2 in 3ivt

Go back to Sodium Binding Sites List in 3ivt
Sodium binding site 2 out of 2 in the Homocitrate Synthase LYS4 Bound to 2-Og


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Homocitrate Synthase LYS4 Bound to 2-Og within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:25.1
occ:0.50
O B:HOH488 2.4 63.9 1.0
O B:ARG214 2.8 45.4 1.0
O B:VAL217 2.9 46.6 1.0
O B:GLY215 3.6 45.8 1.0
C B:GLY215 3.8 45.5 1.0
CA B:GLY215 3.9 44.7 1.0
C B:ARG214 4.0 44.7 1.0
C B:VAL217 4.0 46.6 1.0
N B:GLY215 4.4 44.2 1.0
N B:VAL216 4.5 45.6 1.0
NE B:ARG214 4.6 43.3 1.0
N B:VAL217 4.6 45.7 1.0
CA B:SER218 4.7 47.5 1.0
NH2 B:ARG214 4.7 42.6 1.0
N B:SER218 4.8 47.1 1.0
C B:VAL216 4.8 45.6 1.0
CA B:VAL217 5.0 45.9 1.0

Reference:

S.L.Bulfer, E.M.Scott, J.F.Couture, L.Pillus, R.C.Trievel. Crystal Structure and Functional Analysis of Homocitrate Synthase, An Essential Enzyme in Lysine Biosynthesis. J.Biol.Chem. V. 284 35769 2009.
ISSN: ISSN 0021-9258
PubMed: 19776021
DOI: 10.1074/JBC.M109.046821
Page generated: Tue Dec 15 06:15:24 2020

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