Atomistry » Sodium » PDB 4tmw-4u9k » 4tvc
Atomistry »
  Sodium »
    PDB 4tmw-4u9k »
      4tvc »

Sodium in PDB 4tvc: N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides

Enzymatic activity of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides

All present enzymatic activity of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides:
2.4.1.5;

Protein crystallography data

The structure of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides, PDB code: 4tvc was solved by Y.Brison, M.Remaud-Simeon, L.Mourey, S.Tranier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.20 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.310, 100.140, 186.240, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.5

Other elements in 4tvc:

The structure of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides also contains other interesting chemical elements:

Iodine (I) 3 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides (pdb code 4tvc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides, PDB code: 4tvc:

Sodium binding site 1 out of 1 in 4tvc

Go back to Sodium Binding Sites List in 4tvc
Sodium binding site 1 out of 1 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na3001

b:33.9
occ:1.00
 O A:HOH3841 2.7 41.7 1.0
OH A:TYR2231 2.7 32.6 1.0
O A:HOH3720 2.8 44.8 1.0
O A:HOH3291 2.8 25.5 1.0
O A:PHE2204 2.8 21.3 1.0
O A:MET2190 3.0 17.5 1.0
CZ A:TYR2231 3.5 27.2 1.0
CE1 A:TYR2231 3.7 23.0 1.0
C A:PHE2204 4.0 18.6 1.0
CB A:ASN2203 4.0 16.5 1.0
C A:MET2190 4.1 19.9 1.0
CA A:ASP2205 4.4 18.8 1.0
CB A:MET2190 4.4 19.3 1.0
OD1 A:ASP2205 4.5 21.6 1.0
CA A:MET2190 4.5 19.5 1.0
O A:HOH3986 4.6 43.3 1.0
CE2 A:TYR2231 4.6 25.4 1.0
N A:ASP2205 4.6 17.5 1.0
O A:HOH3998 4.7 45.8 1.0
ND2 A:ASN2203 4.8 20.0 1.0
C A:ASN2203 4.8 17.9 1.0
O A:ASN2203 4.8 17.0 1.0
O A:HOH3251 4.8 28.9 1.0
CG A:ASN2203 4.9 17.5 1.0
CD1 A:TYR2231 4.9 23.0 1.0
O A:HOH4019 4.9 51.9 1.0
N A:PHE2204 5.0 17.8 1.0
SD A:MET2190 5.0 37.9 1.0

Reference:

Y.Brison, Y.Malbert, G.Czaplicki, L.Mourey, M.Remaud-Simeon, S.Tranier. Structural Insights Into the Carbohydrate Binding Ability of An Alpha-(12) Branching Sucrase From Glycoside Hydrolase Family 70. J.Biol.Chem. V. 291 7527 2016.
ISSN: ESSN 1083-351X
PubMed: 26865636
DOI: 10.1074/JBC.M115.688796
Page generated: Mon Oct 7 18:30:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy