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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

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