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Zinc in PDB 3wue: The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9

Enzymatic activity of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9

All present enzymatic activity of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9:
3.2.1.8;

Protein crystallography data

The structure of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9, PDB code: 3wue was solved by C.C.Chen, X.Han, P.Lv, T.P.Ko, W.Peng, C.H.Huang, Y.Zheng, J.Gao, Y.Yang, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.15
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.879, 80.879, 289.026, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 (pdb code 3wue). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9, PDB code: 3wue:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3wue

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Zinc binding site 1 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:58.4
occ:1.00
 OD2 A:ASP98 2.2 44.2 1.0
CG A:ASP98 3.0 37.5 1.0
OD1 A:ASP98 3.1 36.9 1.0
O A:HOH575 3.3 62.7 1.0
O A:HOH555 4.0 49.8 1.0
OG1 A:THR100 4.1 45.9 1.0
O A:HOH656 4.3 46.1 1.0
CB A:THR100 4.4 41.7 1.0
CB A:ASP98 4.4 37.9 1.0
CG2 A:THR100 4.9 42.9 1.0

Zinc binding site 2 out of 5 in 3wue

Go back to Zinc Binding Sites List in 3wue
Zinc binding site 2 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:73.1
occ:1.00
 OD2 A:ASP107 2.4 47.6 1.0
O A:HOH686 2.5 57.8 1.0
OD1 A:ASP107 2.5 46.4 1.0
OE1 A:GLU103 2.6 53.3 1.0
CG A:ASP107 2.8 44.2 1.0
O A:HOH543 2.8 52.8 1.0
CD A:GLU103 3.8 51.9 1.0
NH2 A:ARG157 4.1 43.5 1.0
NH1 A:ARG157 4.2 44.3 1.0
CB A:ASP107 4.3 39.6 1.0
O A:GLU103 4.6 35.5 1.0
CB A:GLU103 4.6 42.3 1.0
CG A:GLU103 4.6 47.9 1.0
CZ A:ARG157 4.6 44.0 1.0
OE2 A:GLU103 4.7 54.1 1.0

Zinc binding site 3 out of 5 in 3wue

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Zinc binding site 3 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:42.5
occ:1.00
 OD2 A:ASP219 2.2 42.0 1.0
O A:HOH697 2.3 37.4 1.0
CG A:ASP219 2.9 37.9 1.0
OD1 A:ASP219 3.0 36.4 1.0
O A:HOH706 3.4 77.5 1.0
O A:HOH629 3.9 47.5 1.0
CG2 A:ILE214 4.1 39.9 1.0
CB A:ASP219 4.3 37.5 1.0
O A:GLY215 4.3 39.8 1.0
C A:GLY215 4.6 38.9 1.0
N A:GLY215 4.7 39.2 1.0
CA A:GLY215 4.8 38.2 1.0

Zinc binding site 4 out of 5 in 3wue

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Zinc binding site 4 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:39.6
occ:1.00
 O A:HOH713 2.2 15.9 1.0
OD2 A:ASP334 2.2 40.2 1.0
CG A:ASP334 3.0 37.0 1.0
OD1 A:ASP334 3.4 34.6 1.0
OD2 A:ASP336 4.0 41.1 1.0
CB A:ASP334 4.1 33.5 1.0
CB A:ALA338 4.2 33.9 1.0
NH1 A:ARG280 4.4 37.3 1.0
CB A:ASP336 4.5 39.8 1.0
CG A:ASP336 4.7 41.0 1.0

Zinc binding site 5 out of 5 in 3wue

Go back to Zinc Binding Sites List in 3wue
Zinc binding site 5 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:37.9
occ:1.00
 ND1 A:HIS344 2.1 29.5 1.0
O A:HOH714 2.3 31.7 1.0
CE1 A:HIS344 3.0 29.3 1.0
CG A:HIS344 3.1 29.8 1.0
CB A:HIS344 3.5 28.9 1.0
NE2 A:HIS344 4.2 32.1 1.0
CD2 A:HIS344 4.2 30.1 1.0
CA A:HIS344 4.4 30.0 1.0

Reference:

C.C.Chen, H.Luo, X.Han, P.Lv, T.P.Ko, W.Peng, C.H.Huang, K.Wang, J.Gao, Y.Zheng, Y.Yang, J.Zhang, B.Yao, R.T.Guo. Structural Perspectives of An Engineered Beta-1,4-Xylanase with Enhanced Thermostability. J.Biotechnol. V.189C 175 2014.
ISSN: ISSN 0168-1656
PubMed: 25193708
DOI: 10.1016/J.JBIOTEC.2014.08.030
Page generated: Sat Oct 26 18:16:51 2024

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