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Iodine in PDB 2d98: Structure of Vil (Extra Ki/I2 Added)-Xylanase

Enzymatic activity of Structure of Vil (Extra Ki/I2 Added)-Xylanase

All present enzymatic activity of Structure of Vil (Extra Ki/I2 Added)-Xylanase:
3.2.1.8;

Protein crystallography data

The structure of Structure of Vil (Extra Ki/I2 Added)-Xylanase, PDB code: 2d98 was solved by H.Miyatake, T.Hasegawa, A.Yamano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.10 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.191, 38.564, 56.794, 90.00, 110.18, 90.00
R / Rfree (%) 20.9 / 25.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Vil (Extra Ki/I2 Added)-Xylanase (pdb code 2d98). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Structure of Vil (Extra Ki/I2 Added)-Xylanase, PDB code: 2d98:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 2d98

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Iodine binding site 1 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9

b:36.6
occ:0.24
 IE A:IYR9 0.0 36.6 0.2
CE A:IYR9 2.1 25.9 1.0
CD A:IYR9 3.0 24.1 1.0
CF A:IYR9 3.1 25.3 1.0
OF A:IYR9 3.3 25.8 1.0
CC A:IYR9 4.3 22.2 1.0
CG A:IYR9 4.4 23.4 1.0
CH A:IYR9 4.9 21.1 1.0

Iodine binding site 2 out of 9 in 2d98

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Iodine binding site 2 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I73

b:35.2
occ:0.44
 IE A:IYR73 0.0 35.2 0.4
CE A:IYR73 2.1 30.0 1.0
CF A:IYR73 3.0 29.6 1.0
CD A:IYR73 3.1 27.5 1.0
OF A:IYR73 3.1 31.0 1.0
CE2 A:TYR88 3.5 24.5 1.0
CD2 A:TYR88 3.5 22.1 1.0
OG A:SER75 3.7 26.4 1.0
CB A:GLU177 3.8 18.9 1.0
CG A:TYR77 4.1 20.1 1.0
CB A:TYR77 4.2 18.3 1.0
CG1 A:VAL46 4.2 21.3 1.0
CD1 A:TYR77 4.3 22.2 1.0
CG A:IYR73 4.3 27.8 1.0
CC A:IYR73 4.4 23.5 1.0
CD2 A:TYR77 4.5 21.0 1.0
CB A:ALA175 4.6 16.6 1.0
CG A:GLU177 4.6 20.8 1.0
CG2 A:VAL46 4.6 22.7 1.0
CE1 A:TYR77 4.8 22.8 1.0
CZ A:TYR88 4.8 23.9 1.0
O A:ALA175 4.9 14.4 1.0
N A:GLU177 4.9 18.5 1.0
CH A:IYR73 4.9 23.7 1.0
CG A:TYR88 4.9 21.3 1.0
CA A:GLU177 4.9 18.6 1.0

Iodine binding site 3 out of 9 in 2d98

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Iodine binding site 3 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I96

b:55.1
occ:0.56
 IE A:IYR96 0.0 55.1 0.6
CE A:IYR96 2.1 51.9 1.0
CF A:IYR96 3.0 52.4 1.0
CD A:IYR96 3.0 48.4 1.0
OF A:IYR96 3.2 54.6 1.0
CB A:THR100 3.6 30.1 1.0
O A:ASN97 4.0 32.2 1.0
O A:PRO98 4.1 26.3 1.0
OG1 A:THR100 4.1 30.1 1.0
O A:THR100 4.1 30.9 1.0
CG A:IYR96 4.3 51.3 1.0
N A:THR100 4.3 30.8 1.0
CC A:IYR96 4.4 45.6 1.0
C A:PRO98 4.4 29.1 1.0
CA A:THR100 4.4 30.0 1.0
CG2 A:THR100 4.4 31.2 1.0
CA A:PRO98 4.4 28.9 1.0
C A:THR100 4.6 30.9 1.0
CH A:IYR96 4.9 48.4 1.0
C A:ASN97 4.9 30.8 1.0

Iodine binding site 4 out of 9 in 2d98

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Iodine binding site 4 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:45.2
occ:0.85
 I1 A:TYI135 0.0 45.2 0.8
CE1 A:TYI135 2.1 41.0 1.0
CZ A:TYI135 3.0 42.1 1.0
CD1 A:TYI135 3.0 37.0 1.0
OH A:TYI135 3.1 42.2 1.0
NE A:ARG119 3.5 44.6 1.0
CZ A:ARG119 3.9 46.6 1.0
CD A:ARG119 4.0 39.5 1.0
N A:GLN121 4.0 27.7 1.0
CB A:GLN121 4.1 29.4 1.0
NH1 A:ARG119 4.2 47.7 1.0
C A:THR120 4.2 26.6 1.0
CG A:ARG119 4.3 34.7 1.0
CE2 A:TYI135 4.3 42.0 1.0
CG A:TYI135 4.3 34.2 1.0
CA A:THR120 4.4 27.3 1.0
CA A:GLN121 4.5 28.5 1.0
NH2 A:ARG119 4.7 49.6 1.0
N A:THR120 4.7 27.2 1.0
O A:THR120 4.7 24.1 1.0
CD2 A:TYI135 4.8 38.3 1.0

Iodine binding site 5 out of 9 in 2d98

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Iodine binding site 5 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:49.0
occ:0.44
 I2 A:TYI135 0.0 49.0 0.4
CE2 A:TYI135 2.1 42.0 1.0
CZ A:TYI135 3.0 42.1 1.0
CD2 A:TYI135 3.0 38.3 1.0
OH A:TYI135 3.2 42.2 1.0
CE1 A:TYI135 4.3 41.0 1.0
CG A:TYI135 4.4 34.2 1.0
CD1 A:TYI135 4.9 37.0 1.0
OE1 A:GLN121 5.0 36.5 1.0

Iodine binding site 6 out of 9 in 2d98

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Iodine binding site 6 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I171

b:47.7
occ:0.45
 I1 A:TYI171 0.0 47.7 0.5
CE1 A:TYI171 2.1 42.3 1.0
CD1 A:TYI171 2.9 38.3 1.0
CZ A:TYI171 3.0 42.8 1.0
CE2 A:TYR77 3.0 24.1 1.0
OH A:TYI171 3.2 46.6 1.0
CD2 A:TYR77 3.3 21.0 1.0
CD1 A:TRP79 3.8 16.3 1.0
NE1 A:TRP79 3.8 16.1 1.0
CZ A:TYR77 3.8 22.9 1.0
CD1 A:ILE173 4.2 17.6 1.0
CG A:TYI171 4.2 35.6 1.0
OH A:TYR77 4.3 26.1 1.0
CE2 A:TYI171 4.3 42.9 1.0
CG A:TYR77 4.3 20.1 1.0
OG A:SER16 4.5 20.1 1.0
O A:TYR77 4.5 18.2 1.0
CG1 A:ILE173 4.5 16.5 1.0
CA A:GLY78 4.5 16.6 1.0
CE1 A:TYR77 4.7 22.8 1.0
CB A:SER16 4.7 19.3 1.0
O A:HOH225 4.7 29.3 1.0
CD2 A:TYI171 4.8 39.8 1.0
C A:TYR77 4.8 17.6 1.0
N A:GLY78 4.9 16.8 1.0
CD1 A:TYR77 4.9 22.2 1.0

Iodine binding site 7 out of 9 in 2d98

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Iodine binding site 7 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I171

b:46.4
occ:0.37
 I2 A:TYI171 0.0 46.4 0.4
CE2 A:TYI171 2.1 42.9 1.0
CZ A:TYI171 3.1 42.8 1.0
CD2 A:TYI171 3.1 39.8 1.0
OH A:TYI171 3.2 46.6 1.0
CG2 A:ILE128 3.9 20.9 1.0
OD2 A:ASP170 4.0 24.3 1.0
CE1 A:TYI171 4.4 42.3 1.0
CG2 A:THR7 4.4 20.0 1.0
CG A:TYI171 4.4 35.6 1.0
CB A:ILE128 4.4 20.8 1.0
NE2 A:GLN52 4.6 23.5 1.0
CZ A:PHE14 4.7 18.5 1.0
CD1 A:TYI171 4.9 38.3 1.0

Iodine binding site 8 out of 9 in 2d98

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Iodine binding site 8 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I179

b:37.0
occ:0.57
 IE A:IYR179 0.0 37.0 0.6
CE A:IYR179 2.1 33.5 1.0
CF A:IYR179 3.0 34.0 1.0
CD A:IYR179 3.0 31.5 1.0
OF A:IYR179 3.2 37.2 1.0
CB A:ASN44 4.0 23.2 1.0
OD1 A:ASN44 4.0 28.5 1.0
CG A:ASN44 4.2 24.7 1.0
CE1 A:PHE180 4.2 19.8 1.0
CG A:IYR179 4.3 32.6 1.0
CC A:IYR179 4.4 29.6 1.0
CD1 A:PHE180 4.8 17.3 1.0
CH A:IYR179 4.8 31.6 1.0

Iodine binding site 9 out of 9 in 2d98

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Iodine binding site 9 out of 9 in the Structure of Vil (Extra Ki/I2 Added)-Xylanase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of Vil (Extra Ki/I2 Added)-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I200

b:51.3
occ:0.67
 O A:GLY24 3.3 31.5 1.0
OG1 A:THR26 3.5 26.1 1.0
C A:GLY24 3.5 30.9 1.0
O A:ASN38 3.6 23.3 1.0
N A:VAL25 3.8 28.8 1.0
CA A:GLY24 4.0 34.0 1.0
N A:SER40 4.1 19.4 1.0
ND2 A:ASN38 4.1 38.4 1.0
N A:THR26 4.1 23.7 1.0
OG A:SER40 4.1 24.9 1.0
CA A:VAL25 4.1 24.8 1.0
C A:VAL25 4.1 25.2 1.0
CA A:TRP39 4.2 20.4 1.0
CB A:THR26 4.3 23.5 1.0
C A:ASN38 4.4 23.3 1.0
C A:TRP39 4.5 19.2 1.0
CB A:SER40 4.6 20.7 1.0
N A:TRP39 4.7 21.6 1.0
O A:VAL25 4.7 23.1 1.0
CA A:THR26 4.8 23.3 1.0
CA A:SER40 5.0 19.6 1.0

Reference:

H.Miyatake, T.Hasegawa, A.Yamano. New Methods to Prepare Iodinated Derivatives By Vaporizing Iodine Labelling (Vil) and Hydrogen Peroxide Vil (Hyper-Vil) Acta Crystallogr.,Sect.D V. 62 280 2006.
ISSN: ISSN 0907-4449
PubMed: 16510975
DOI: 10.1107/S0907444905041909
Page generated: Sun Dec 13 19:23:40 2020

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