Atomistry » Sodium » PDB 3ma9-3mo9 » 3mi3
Atomistry »
  Sodium »
    PDB 3ma9-3mo9 »
      3mi3 »

Sodium in PDB 3mi3: Homocitrate Synthase LYS4 Bound to Lysine

Enzymatic activity of Homocitrate Synthase LYS4 Bound to Lysine

All present enzymatic activity of Homocitrate Synthase LYS4 Bound to Lysine:
2.3.3.14;

Protein crystallography data

The structure of Homocitrate Synthase LYS4 Bound to Lysine, PDB code: 3mi3 was solved by S.L.Bulfer, E.M.Scott, L.Pillus, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.69 / 2.38
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 135.637, 135.637, 122.928, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 20.3

Other elements in 3mi3:

The structure of Homocitrate Synthase LYS4 Bound to Lysine 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 Lysine (pdb code 3mi3). 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 Lysine, PDB code: 3mi3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3mi3

Go back to Sodium Binding Sites List in 3mi3
Sodium binding site 1 out of 2 in the Homocitrate Synthase LYS4 Bound to Lysine


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 Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:28.4
occ:0.50
O A:HOH602 2.3 50.9 1.0
O A:VAL217 2.9 44.7 1.0
O A:ARG214 3.0 45.2 1.0
O A:GLY215 3.6 44.2 1.0
C A:VAL217 3.9 44.9 1.0
C A:GLY215 3.9 43.3 1.0
CA A:GLY215 4.1 42.9 1.0
C A:ARG214 4.1 44.5 1.0
CA A:SER218 4.5 46.8 1.0
N A:VAL217 4.5 44.9 1.0
NH2 A:ARG214 4.5 41.0 1.0
N A:SER218 4.6 45.9 1.0
N A:VAL216 4.6 44.5 1.0
N A:GLY215 4.6 43.7 1.0
C A:VAL216 4.7 44.4 1.0
NE A:ARG214 4.7 43.2 1.0
CA A:VAL217 4.8 44.2 1.0

Sodium binding site 2 out of 2 in 3mi3

Go back to Sodium Binding Sites List in 3mi3
Sodium binding site 2 out of 2 in the Homocitrate Synthase LYS4 Bound to Lysine


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 Lysine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:25.2
occ:0.50
O B:HOH737 2.5 53.2 1.0
O B:VAL217 2.9 46.6 1.0
O B:ARG214 2.9 45.7 1.0
O B:GLY215 3.3 47.1 1.0
C B:GLY215 3.8 45.3 1.0
C B:VAL217 3.8 46.4 1.0
CA B:GLY215 4.0 44.5 1.0
C B:ARG214 4.0 45.7 1.0
N B:VAL217 4.4 45.8 1.0
N B:GLY215 4.5 45.2 1.0
CA B:SER218 4.5 46.9 0.5
N B:VAL216 4.6 45.7 1.0
N B:SER218 4.6 46.5 1.0
NH2 B:ARG214 4.6 41.9 1.0
CA B:SER218 4.6 46.4 0.5
C B:VAL216 4.6 45.2 1.0
CA B:VAL217 4.7 45.8 1.0
OG B:SER218 4.7 48.2 0.5
NE B:ARG214 4.8 45.4 1.0
O B:VAL216 5.0 44.6 1.0

Reference:

S.L.Bulfer, E.M.Scott, L.Pillus, R.C.Trievel. Structural Basis For L-Lysine Feedback Inhibition of Homocitrate Synthase J.Biol.Chem. V. 285 10446 2010.
ISSN: ISSN 0021-9258
PubMed: 20089861
Page generated: Tue Dec 15 06:17:36 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy