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Iodine 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:

Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 3 binding sites of Iodine where determined in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with Gluco-Oligosaccharides, PDB code: 4tvc:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 4tvc

Go back to Iodine Binding Sites List in 4tvc
Iodine binding site 1 out of 3 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 Iodine with other atoms in the I 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:I2075

b:0.4
occ:0.50
 I1 A:TYI2075 0.0 0.4 0.5
CE1 A:TYI2075 2.1 69.2 1.0
CD1 A:TYI2075 3.0 56.9 1.0
CZ A:TYI2075 3.1 64.6 1.0
OH A:TYI2075 3.3 68.4 1.0
CG A:TYI2075 4.3 47.2 1.0
CE2 A:TYI2075 4.6 60.3 1.0
O A:HOH3121 4.8 41.7 1.0
CD2 A:TYI2075 4.9 52.2 1.0

Iodine binding site 2 out of 3 in 4tvc

Go back to Iodine Binding Sites List in 4tvc
Iodine binding site 2 out of 3 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 Iodine with other atoms in the I binding site number 2 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:I2075

b:77.9
occ:0.50
 I2 A:TYI2075 0.0 77.9 0.5
CE2 A:TYI2075 2.1 60.3 1.0
CD2 A:TYI2075 3.1 52.2 1.0
CZ A:TYI2075 3.3 64.6 1.0
O A:HOH3443 3.4 43.1 1.0
OH A:TYI2075 3.5 68.4 1.0
OD1 A:ASP2076 4.3 38.5 1.0
CG A:GLN2079 4.4 42.5 1.0
CB A:GLN2079 4.4 37.0 1.0
CG A:TYI2075 4.4 47.2 1.0
O A:HOH3211 4.4 39.7 1.0
OE1 A:GLN2079 4.5 50.4 1.0
CE1 A:TYI2075 4.6 69.2 1.0
CD A:GLN2079 4.8 47.1 1.0

Iodine binding site 3 out of 3 in 4tvc

Go back to Iodine Binding Sites List in 4tvc
Iodine binding site 3 out of 3 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 Iodine with other atoms in the I binding site number 3 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:I2712

b:80.7
occ:0.50
 IE A:IYR2712 0.0 80.7 0.5
CE A:IYR2712 2.1 43.2 1.0
CF A:IYR2712 3.0 37.6 1.0
OF A:IYR2712 3.0 49.4 1.0
CD A:IYR2712 3.1 34.4 1.0
CB A:ASP2133 4.2 32.8 1.0
CG A:IYR2712 4.3 36.2 1.0
NE1 A:TRP2135 4.3 26.6 1.0
CG2 A:VAL2711 4.3 25.7 1.0
CA A:ASP2133 4.4 28.1 1.0
CC A:IYR2712 4.4 29.4 1.0
CZ2 A:TRP2135 4.4 26.3 1.0
CE2 A:TRP2135 4.7 27.3 1.0
O A:GLY2132 4.7 29.8 1.0
CH A:IYR2712 4.8 31.3 1.0
N A:ASP2133 5.0 29.2 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: Sun Aug 11 19:58:07 2024

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