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Iodine in PDB 4tvd: N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose

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

All present enzymatic activity of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose:
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 D-Glucose, PDB code: 4tvd 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) 47.70 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.770, 98.980, 181.910, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 22.3

Other elements in 4tvd:

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

Calcium (Ca) 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 D-Glucose (pdb code 4tvd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose, PDB code: 4tvd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 4tvd

Go back to Iodine Binding Sites List in 4tvd
Iodine binding site 1 out of 5 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2075

b:85.7
occ:0.50
 I1 A:TYI2075 0.0 85.7 0.5
CE1 A:TYI2075 2.1 69.6 1.0
CD1 A:TYI2075 3.0 64.5 1.0
CZ A:TYI2075 3.1 70.5 1.0
OH A:TYI2075 3.2 77.7 1.0
CG A:TYI2075 4.3 60.4 1.0
CE2 A:TYI2075 4.4 67.3 1.0
CD2 A:TYI2075 4.9 61.4 1.0

Iodine binding site 2 out of 5 in 4tvd

Go back to Iodine Binding Sites List in 4tvd
Iodine binding site 2 out of 5 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2075

b:71.7
occ:0.50
 I2 A:TYI2075 0.0 71.7 0.5
CE2 A:TYI2075 2.1 67.3 1.0
CZ A:TYI2075 3.0 70.5 1.0
CD2 A:TYI2075 3.1 61.4 1.0
OH A:TYI2075 3.1 77.7 1.0
CG A:GLN2079 4.1 71.9 1.0
OE1 A:GLN2079 4.2 80.2 1.0
CD A:GLN2079 4.3 73.3 1.0
CG A:TYI2075 4.4 60.4 1.0
CE1 A:TYI2075 4.4 69.6 1.0
OD1 A:ASP2076 4.4 53.9 1.0
CB A:GLN2079 4.5 62.4 1.0
CD1 A:TYI2075 4.9 64.5 1.0

Iodine binding site 3 out of 5 in 4tvd

Go back to Iodine Binding Sites List in 4tvd
Iodine binding site 3 out of 5 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose


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 D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2712

b:64.0
occ:0.50
 IE A:IYR2712 0.0 64.0 0.5
CE A:IYR2712 2.0 39.6 1.0
OF A:IYR2712 2.9 48.6 1.0
CF A:IYR2712 2.9 41.0 1.0
CD A:IYR2712 3.1 35.1 1.0
CB A:ASP2133 4.0 33.8 1.0
CG A:IYR2712 4.2 40.5 1.0
CA A:ASP2133 4.2 35.0 1.0
CG2 A:VAL2711 4.3 34.7 1.0
NE1 A:TRP2135 4.3 43.0 1.0
CC A:IYR2712 4.3 33.6 1.0
CZ2 A:TRP2135 4.6 44.7 1.0
CH A:IYR2712 4.7 35.6 1.0
CE2 A:TRP2135 4.8 42.8 1.0
O A:GLY2132 4.8 37.2 1.0
N A:ASP2133 4.9 32.8 1.0

Iodine binding site 4 out of 5 in 4tvd

Go back to Iodine Binding Sites List in 4tvd
Iodine binding site 4 out of 5 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2764

b:82.5
occ:0.50
 IE A:IYR2764 0.0 82.5 0.5
CE A:IYR2764 2.1 79.6 1.0
CD A:IYR2764 3.0 72.8 1.0
CF A:IYR2764 3.2 82.1 1.0
OF A:IYR2764 3.4 82.5 1.0
O6 A:BGC2910 3.7 57.5 1.0
OH A:TYR2762 3.8 40.1 1.0
C6 A:BGC2910 3.8 46.4 1.0
O5 A:BGC2910 4.2 46.9 1.0
CC A:IYR2764 4.4 60.2 1.0
CG A:IYR2764 4.5 72.6 1.0
C5 A:BGC2910 4.6 43.5 1.0
OG A:SER2779 4.7 43.9 1.0
CH A:IYR2764 5.0 62.2 1.0

Iodine binding site 5 out of 5 in 4tvd

Go back to Iodine Binding Sites List in 4tvd
Iodine binding site 5 out of 5 in the N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of N-Terminally Truncated Dextransucrase Dsr-E From Leuconostoc Mesenteroides Nrrl B-1299 in Complex with D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I2767

b:95.0
occ:0.50
 IE A:IYR2767 0.0 95.0 0.5
CE A:IYR2767 2.1 65.3 1.0
CD A:IYR2767 3.0 57.4 1.0
CF A:IYR2767 3.2 61.2 1.0
OF A:IYR2767 3.4 56.7 1.0
NZ A:LYS2765 3.6 35.7 1.0
CG A:PRO2774 3.8 37.2 1.0
CE A:LYS2765 4.1 36.9 1.0
CC A:IYR2767 4.3 53.6 1.0
CG A:IYR2767 4.4 55.4 1.0
CH A:IYR2767 4.9 54.1 1.0
CD A:PRO2774 4.9 37.0 1.0
CB A:PRO2774 4.9 40.3 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 19:58:08 2024

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