Atomistry » Iodine » PDB 2axe-2fwh » 2d97
Atomistry »
  Iodine »
    PDB 2axe-2fwh »
      2d97 »

Iodine in PDB 2d97: Structure of Vil-Xylanase

Enzymatic activity of Structure of Vil-Xylanase

All present enzymatic activity of Structure of Vil-Xylanase:
3.2.1.8;

Protein crystallography data

The structure of Structure of Vil-Xylanase, PDB code: 2d97 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) 18.98 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.347, 38.585, 57.162, 90.00, 110.31, 90.00
R / Rfree (%) 19.8 / 22.8

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Vil-Xylanase (pdb code 2d97). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Structure of Vil-Xylanase, PDB code: 2d97:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 2d97

Go back to Iodine Binding Sites List in 2d97
Iodine binding site 1 out of 5 in the Structure of Vil-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-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I9

b:34.1
occ:0.24
IE A:IYR9 0.0 34.1 0.2
CE A:IYR9 2.1 22.6 1.0
CD A:IYR9 3.0 20.1 1.0
CF A:IYR9 3.1 22.0 1.0
OF A:IYR9 3.3 20.2 1.0
CC A:IYR9 4.3 19.2 1.0
CG A:IYR9 4.4 19.8 1.0
CH A:IYR9 4.8 18.6 1.0

Iodine binding site 2 out of 5 in 2d97

Go back to Iodine Binding Sites List in 2d97
Iodine binding site 2 out of 5 in the Structure of Vil-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-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I73

b:38.8
occ:0.29
IE A:IYR73 0.0 38.8 0.3
CE A:IYR73 2.1 29.7 1.0
CF A:IYR73 3.0 30.1 1.0
CD A:IYR73 3.1 27.2 1.0
OF A:IYR73 3.2 32.6 1.0
CE2 A:TYR88 3.5 23.1 1.0
CD2 A:TYR88 3.5 22.5 1.0
OG A:SER75 3.6 23.6 1.0
CB A:GLU177 3.8 16.0 1.0
CG1 A:VAL46 4.2 18.5 1.0
CG A:TYR77 4.2 16.5 1.0
CB A:TYR77 4.2 12.1 1.0
CD1 A:TYR77 4.3 18.1 1.0
CG A:IYR73 4.4 27.0 1.0
CC A:IYR73 4.4 23.2 1.0
CG A:GLU177 4.6 16.7 1.0
CG2 A:VAL46 4.7 18.2 1.0
O A:ALA175 4.7 12.6 1.0
CB A:ALA175 4.7 14.7 1.0
CD2 A:TYR77 4.8 14.5 1.0
CZ A:TYR88 4.8 23.6 1.0
N A:GLU177 4.8 12.7 1.0
CH A:IYR73 4.9 23.6 1.0
CA A:GLU177 4.9 15.9 1.0
CG A:TYR88 4.9 20.3 1.0
CE1 A:TYR77 4.9 20.6 1.0
CB A:SER75 4.9 19.5 1.0
O A:IYR73 5.0 14.9 1.0

Iodine binding site 3 out of 5 in 2d97

Go back to Iodine Binding Sites List in 2d97
Iodine binding site 3 out of 5 in the Structure of Vil-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-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:42.3
occ:0.75
I1 A:TYI135 0.0 42.3 0.8
CE1 A:TYI135 2.1 38.2 1.0
CZ A:TYI135 3.0 39.6 1.0
CD1 A:TYI135 3.0 34.4 1.0
OH A:TYI135 3.2 40.4 1.0
O A:HOH277 3.3 45.9 1.0
NE A:ARG119 3.6 39.7 1.0
CD A:ARG119 3.8 35.1 1.0
CG A:ARG119 3.9 31.9 1.0
N A:GLN121 4.2 23.2 1.0
CB A:GLN121 4.2 24.9 1.0
CE2 A:TYI135 4.3 39.8 1.0
CZ A:ARG119 4.3 41.9 1.0
C A:THR120 4.3 22.6 1.0
CG A:TYI135 4.3 31.9 1.0
CA A:THR120 4.5 22.4 1.0
CA A:GLN121 4.7 22.6 1.0
N A:THR120 4.8 21.7 1.0
NH1 A:ARG119 4.8 43.6 1.0
O A:THR120 4.8 21.3 1.0
CD2 A:TYI135 4.8 36.5 1.0
C A:ARG119 5.0 23.1 1.0

Iodine binding site 4 out of 5 in 2d97

Go back to Iodine Binding Sites List in 2d97
Iodine binding site 4 out of 5 in the Structure of Vil-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-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I135

b:48.3
occ:0.35
I2 A:TYI135 0.0 48.3 0.3
CE2 A:TYI135 2.1 39.8 1.0
CD2 A:TYI135 3.0 36.5 1.0
CZ A:TYI135 3.0 39.6 1.0
OH A:TYI135 3.2 40.4 1.0
CG A:TYI135 4.3 31.9 1.0
CE1 A:TYI135 4.3 38.2 1.0
NE2 A:GLN121 4.8 30.2 1.0
CD1 A:TYI135 4.9 34.4 1.0

Iodine binding site 5 out of 5 in 2d97

Go back to Iodine Binding Sites List in 2d97
Iodine binding site 5 out of 5 in the Structure of Vil-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-Xylanase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I179

b:40.2
occ:0.52
IE A:IYR179 0.0 40.2 0.5
CE A:IYR179 2.1 32.2 1.0
CF A:IYR179 3.0 32.3 1.0
CD A:IYR179 3.0 28.9 1.0
OF A:IYR179 3.1 34.7 1.0
O A:HOH233 3.6 30.9 1.0
OD1 A:ASN44 4.0 19.3 1.0
CB A:ASN44 4.0 15.2 1.0
CG A:ASN44 4.2 18.6 1.0
CG A:IYR179 4.3 30.1 1.0
CE1 A:PHE180 4.3 16.8 1.0
CC A:IYR179 4.4 27.0 1.0
CH A:IYR179 4.8 26.8 1.0
CD1 A:PHE180 4.9 14.8 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 Jan 24 17:23:28 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy