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Zinc in PDB 3wug: The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9

Enzymatic activity of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9

All present enzymatic activity of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9:
3.2.1.8;

Protein crystallography data

The structure of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9, PDB code: 3wug was solved by C.C.Chen, X.Han, P.Lv, T.P.Ko, W.Peng, C.H.Huang, Y.Zheng, J.Gao, Y.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 / 1.88
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.798, 80.798, 288.589, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 (pdb code 3wug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9, PDB code: 3wug:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3wug

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Zinc binding site 1 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:38.4
occ:1.00
 OD2 A:ASP312 2.0 23.7 1.0
OE2 A:GLU62 2.2 24.6 1.0
OE1 A:GLU82 2.3 33.4 1.0
O A:HOH739 2.7 46.0 1.0
CD A:GLU62 2.9 26.6 1.0
OE1 A:GLU62 2.9 28.8 1.0
CG A:ASP312 3.0 23.1 1.0
CD A:GLU82 3.3 34.4 1.0
CB A:ASP312 3.5 21.4 1.0
O A:TYR317 3.6 30.3 1.0
OE2 A:GLU82 3.6 37.2 1.0
CB A:TYR317 3.8 27.5 1.0
OD1 A:ASP312 4.1 22.9 1.0
O A:HOH639 4.3 40.5 1.0
O A:HOH535 4.3 23.4 1.0
N A:ASP59 4.3 22.4 1.0
CG A:GLU62 4.3 25.4 1.0
CB A:ASP59 4.4 23.9 1.0
C A:TYR317 4.4 28.0 1.0
CA A:THR58 4.5 21.5 1.0
O A:HOH688 4.5 40.2 1.0
CG A:GLU82 4.5 31.1 1.0
C A:THR58 4.7 22.9 1.0
OH A:TYR68 4.8 24.7 1.0
CG A:TYR317 4.8 27.0 1.0
CA A:ASP312 4.8 19.9 1.0
CA A:TYR317 4.8 27.0 1.0

Zinc binding site 2 out of 7 in 3wug

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Zinc binding site 2 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:42.0
occ:1.00
 OD2 A:ASP98 2.2 30.8 1.0
O A:HOH802 2.8 52.0 1.0
CG A:ASP98 3.0 28.1 1.0
OD1 A:ASP98 3.1 26.3 1.0
OG1 A:THR100 4.0 36.1 1.0
O A:HOH563 4.2 37.8 1.0
O A:HOH610 4.3 33.1 1.0
CB A:ASP98 4.4 26.5 1.0
CB A:THR100 4.4 30.6 1.0

Zinc binding site 3 out of 7 in 3wug

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Zinc binding site 3 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:57.4
occ:1.00
 OD1 A:ASP107 2.4 34.4 1.0
O A:HOH804 2.4 58.7 1.0
OE1 A:GLU103 2.5 42.0 1.0
OD2 A:ASP107 2.5 36.4 1.0
O A:HOH787 2.7 59.2 1.0
CG A:ASP107 2.8 33.4 1.0
CD A:GLU103 3.7 39.8 1.0
NH2 A:ARG157 4.0 35.1 1.0
CB A:ASP107 4.3 30.8 1.0
NH1 A:ARG157 4.3 32.7 1.0
OE2 A:GLU103 4.5 44.7 1.0
CZ A:ARG157 4.6 32.2 1.0
O A:GLU103 4.7 27.4 1.0
CG A:GLU103 4.7 38.1 1.0
CB A:GLU103 4.8 31.9 1.0

Zinc binding site 4 out of 7 in 3wug

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Zinc binding site 4 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:80.1
occ:1.00
 ND1 A:HIS153 2.1 37.7 1.0
O A:HOH786 2.6 54.8 1.0
CE1 A:HIS153 2.8 37.9 1.0
CG A:HIS153 3.3 33.4 1.0
O A:HOH763 3.4 56.8 1.0
O A:HOH764 3.6 56.1 1.0
CB A:HIS153 3.8 30.4 1.0
O A:HOH728 3.8 57.3 1.0
NE2 A:HIS153 4.0 37.6 1.0
O A:HOH634 4.1 56.0 1.0
CA A:HIS153 4.2 27.2 1.0
CE2 A:TYR99 4.2 34.4 1.0
CD2 A:HIS153 4.3 35.6 1.0
O A:HOH582 4.4 36.4 1.0
CD2 A:TYR99 4.5 33.8 1.0

Zinc binding site 5 out of 7 in 3wug

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Zinc binding site 5 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:30.9
occ:1.00
 OD2 A:ASP219 2.1 28.7 1.0
O A:HOH738 2.4 29.1 1.0
CG A:ASP219 2.9 28.8 1.0
OD1 A:ASP219 3.0 25.9 1.0
O A:HOH664 3.4 47.7 1.0
O A:HOH692 4.0 38.4 1.0
CG2 A:ILE214 4.1 29.9 1.0
CB A:ASP219 4.3 25.9 1.0
O A:GLY215 4.4 28.2 1.0
C A:GLY215 4.6 27.0 1.0
N A:GLY215 4.8 27.5 1.0
CA A:GLY215 4.8 26.9 1.0
NH1 A:ARG259 4.9 28.2 1.0

Zinc binding site 6 out of 7 in 3wug

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Zinc binding site 6 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 6 of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:26.7
occ:1.00
 OD2 A:ASP334 2.2 26.9 1.0
O A:HOH735 2.2 9.8 1.0
O A:HOH736 2.2 27.0 1.0
CG A:ASP334 2.9 26.3 1.0
OD1 A:ASP334 3.2 24.7 1.0
OD2 A:ASP336 4.0 31.7 1.0
CB A:ALA338 4.1 21.7 1.0
CB A:ASP334 4.1 24.1 1.0
O A:HOH557 4.3 30.8 1.0
CB A:ASP336 4.4 28.4 1.0
NH1 A:ARG280 4.4 24.6 1.0
CG A:ASP336 4.7 31.0 1.0
O A:HOH601 4.8 37.4 1.0

Zinc binding site 7 out of 7 in 3wug

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Zinc binding site 7 out of 7 in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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 7 of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) with Xylobiose From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:25.6
occ:1.00
 ND1 A:HIS344 2.1 21.3 1.0
O A:HOH737 2.3 23.0 1.0
CE1 A:HIS344 3.0 23.8 1.0
CG A:HIS344 3.1 22.9 1.0
CB A:HIS344 3.5 22.1 1.0
O A:HOH667 4.0 38.3 1.0
NE2 A:HIS344 4.1 24.2 1.0
CD2 A:HIS344 4.2 22.3 1.0
CA A:HIS344 4.5 22.3 1.0
O A:HOH585 4.8 32.6 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 18:17:36 2024

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