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

Iodine in PDB 2dfb: Xylanase II From Tricoderma Reesei at 100K

Enzymatic activity of Xylanase II From Tricoderma Reesei at 100K

All present enzymatic activity of Xylanase II From Tricoderma Reesei at 100K:
3.2.1.8;

Protein crystallography data

The structure of Xylanase II From Tricoderma Reesei at 100K, PDB code: 2dfb was solved by K.Harata, T.Akiba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.80 / 1.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.970, 58.510, 69.800, 90.00, 90.00, 90.00
R / Rfree (%) 10.8 / 12.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Xylanase II From Tricoderma Reesei at 100K (pdb code 2dfb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Xylanase II From Tricoderma Reesei at 100K, PDB code: 2dfb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 1 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I192

b:10.9
occ:1.00
 O A:HOH206 3.5 13.6 1.0
O A:HOH202 3.5 11.7 1.0
N A:SER146 3.6 10.8 1.0
OG A:SER146 3.9 13.8 1.0
CB A:ARG145 4.1 10.3 1.0
CA A:ARG145 4.1 10.6 1.0
O A:HOH232 4.2 17.6 1.0
N A:SER147 4.3 11.0 1.0
C A:ARG145 4.4 10.5 1.0
CA A:SER146 4.5 11.4 1.0
C A:SER146 4.7 11.1 1.0
CB A:SER146 4.8 12.4 1.0

Iodine binding site 2 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 2 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I193

b:17.4
occ:0.58
 NE A:ARG119 3.5 23.6 1.0
O A:HOH475 3.5 34.2 0.5
NH2 A:ARG119 3.7 43.2 1.0
O A:ARG119 3.9 12.8 1.0
C A:THR120 3.9 11.5 1.0
CZ A:ARG119 3.9 30.6 1.0
O A:HOH427 4.0 35.4 1.0
CA A:THR120 4.0 11.9 1.0
CE1 A:TYR135 4.1 15.9 1.0
N A:GLN121 4.1 13.3 1.0
O A:HOH224 4.2 16.1 1.0
C A:ARG119 4.2 11.6 1.0
CB A:GLN121 4.3 14.4 1.0
CG A:ARG119 4.3 13.2 1.0
CD1 A:TYR135 4.3 14.2 1.0
N A:THR120 4.3 11.5 1.0
O A:THR120 4.3 12.6 1.0
O A:HOH405 4.4 41.8 1.0
CD A:ARG119 4.4 16.1 1.0
O A:HOH271 4.4 19.5 1.0
CB A:ARG119 4.6 12.7 1.0
CA A:GLN121 4.8 12.8 1.0
O A:HOH276 4.9 18.8 1.0

Iodine binding site 3 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 3 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I194

b:14.0
occ:0.27
 O A:PRO68 3.4 15.0 1.0
N A:GLY70 3.7 11.8 1.0
CA A:GLY94 3.9 11.3 1.0
CG2 A:THR95 4.0 12.3 1.0
C A:GLY94 4.0 11.0 1.0
C A:PRO68 4.1 12.2 1.0
N A:THR95 4.1 11.1 1.0
CA A:ASN69 4.1 12.4 1.0
O A:GLY70 4.2 11.1 1.0
N A:ASN69 4.4 11.9 1.0
C A:ASN69 4.5 11.4 1.0
CG A:PRO68 4.5 14.1 1.0
O A:HOH435 4.5 45.6 1.0
O A:HOH363 4.6 29.7 1.0
CA A:GLY70 4.6 11.9 1.0
O A:GLY94 4.7 12.2 1.0
CB A:PRO68 4.8 13.5 1.0
CA A:THR95 4.8 11.2 1.0
C A:GLY70 4.8 10.8 1.0
CB A:THR95 5.0 11.5 1.0

Iodine binding site 4 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 4 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I195

b:16.1
occ:0.22
 OG A:SER65 3.1 19.8 0.3
OG A:SER184 3.3 17.1 1.0
N A:ALA185 3.8 11.1 1.0
CA A:ALA185 3.9 11.1 1.0
CB A:SER65 3.9 15.7 1.0
CB A:SER184 3.9 13.7 1.0
ND2 A:ASN67 3.9 18.6 1.0
C A:SER184 3.9 11.6 1.0
C A:ALA185 4.0 10.8 1.0
O A:SER184 4.1 12.8 1.0
N A:SER186 4.2 11.0 1.0
O A:HOH313 4.3 25.8 1.0
O A:SER65 4.4 11.7 1.0
CB A:SER186 4.5 14.1 1.0
CA A:SER184 4.6 12.3 1.0
O A:ALA185 4.6 11.8 1.0
C A:SER65 4.6 11.2 1.0
OG A:SER65 4.8 16.9 0.7
CA A:SER65 4.9 11.9 1.0
CG A:ASN67 5.0 14.5 1.0
CA A:SER186 5.0 11.6 1.0

Iodine binding site 5 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 5 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I196

b:21.4
occ:0.33
 NE2 A:GLN125 3.5 26.8 1.0
N A:VAL123 3.5 14.9 1.0
O A:HOH395 3.8 35.4 0.9
NH1 A:ARG122 4.0 20.5 1.0
CA A:ARG122 4.1 12.8 1.0
O A:HOH463 4.2 37.4 1.0
O A:GLN121 4.3 17.2 1.0
CG A:GLN125 4.3 16.1 1.0
O A:VAL123 4.3 16.3 1.0
C A:ARG122 4.3 13.2 1.0
CB A:VAL123 4.3 17.1 1.0
CD A:GLN125 4.4 18.9 1.0
CA A:VAL123 4.4 15.2 1.0
O A:HOH418 4.4 38.1 0.7
CD A:ARG122 4.6 16.2 1.0
O A:HOH383 4.7 46.1 1.0
CG2 A:VAL123 4.7 20.6 1.0
CZ A:ARG122 4.8 18.2 1.0
C A:VAL123 4.8 15.2 1.0
CB A:ARG122 4.9 13.1 1.0

Iodine binding site 6 out of 6 in 2dfb

Go back to Iodine Binding Sites List in 2dfb
Iodine binding site 6 out of 6 in the Xylanase II From Tricoderma Reesei at 100K


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Xylanase II From Tricoderma Reesei at 100K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I197

b:23.2
occ:0.26
 OE1 A:GLN34 2.0 18.6 0.7
NE2 A:GLN34 2.7 30.5 0.3
CD A:GLN34 2.8 16.0 0.7
NE2 A:GLN34 2.9 29.1 0.7
OG A:SER36 3.1 17.1 0.6
OG A:SER36 3.5 14.7 0.4
CD A:GLN34 3.6 20.6 0.3
CA A:GLY30 3.6 13.2 1.0
CG A:GLN34 3.7 14.6 0.3
N A:GLY30 3.8 12.6 1.0
O A:THR28 3.8 15.9 1.0
N A:SER36 3.9 11.6 1.0
CB A:SER36 3.9 14.6 1.0
C A:PHE35 4.1 10.7 1.0
C A:ASN29 4.2 12.8 1.0
CG A:GLN34 4.2 14.1 0.7
CA A:PHE35 4.2 11.3 1.0
CG2 A:THR28 4.4 16.0 1.0
O A:ASN29 4.4 17.0 1.0
CA A:SER36 4.5 11.6 1.0
C A:THR28 4.6 12.4 1.0
N A:PHE35 4.6 11.5 1.0
O A:PHE35 4.6 11.9 1.0
CB A:THR28 4.6 13.2 1.0
OE1 A:GLN34 4.7 33.6 0.3
C A:GLN34 4.8 10.8 1.0
O A:GLN34 4.8 11.5 1.0
CB A:GLN34 4.8 15.3 0.7
CB A:GLN34 4.9 11.9 0.3
C A:GLY30 5.0 13.5 1.0
CD A:PRO31 5.0 19.0 1.0

Reference:

N.Watanabe, T.Akiba, R.Kanai, K.Harata. Structure of An Orthorhombic Form of Xylanase II From Trichoderma Reesei and Analysis of Thermal Displacement. Acta Crystallogr.,Sect.D V. 62 784 2006.
ISSN: ISSN 0907-4449
PubMed: 16790934
DOI: 10.1107/S0907444906017379
Page generated: Sun Aug 11 13:45:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy