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

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

All present enzymatic activity of The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) 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) From Streptomyces Sp. 9, PDB code: 3wuf 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 / 2.04
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.315, 82.315, 288.581, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the The Mutant Crystal Structure of B-1,4-Xylanase (XYNAS9_V43P/G44E) From Streptomyces Sp. 9 (pdb code 3wuf). 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) From Streptomyces Sp. 9, PDB code: 3wuf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:29.5
occ:1.00
 OD2 A:ASP312 2.0 24.3 1.0
OE2 A:GLU82 2.1 22.2 1.0
OE2 A:GLU62 2.2 23.6 1.0
OE1 A:GLU82 2.7 21.4 1.0
CD A:GLU82 2.8 22.7 1.0
OE1 A:GLU62 2.8 24.5 1.0
CD A:GLU62 2.8 23.6 1.0
CG A:ASP312 3.0 25.1 1.0
CB A:ASP312 3.5 20.1 1.0
O A:HOH580 3.6 39.2 1.0
CB A:TYR317 3.9 26.4 1.0
O A:TYR317 4.0 27.7 1.0
OD1 A:ASP312 4.1 25.7 1.0
CG A:GLU82 4.2 21.5 1.0
N A:ASP59 4.3 22.4 1.0
O A:HOH614 4.3 31.0 1.0
CG A:GLU62 4.3 23.8 1.0
CB A:ASP59 4.4 22.0 1.0
O A:HOH728 4.4 42.5 1.0
CA A:THR58 4.4 21.0 1.0
OH A:TYR68 4.5 22.8 1.0
O A:HOH531 4.5 20.3 1.0
C A:THR58 4.6 21.1 1.0
CA A:ASP312 4.7 20.0 1.0
C A:TYR317 4.7 26.7 1.0
CG A:TYR317 4.7 27.3 1.0
O A:ALA57 4.8 18.2 1.0
CA A:TYR317 5.0 26.1 1.0

Zinc binding site 2 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:43.2
occ:1.00
 OD1 A:ASP98 2.2 30.9 1.0
CG A:ASP98 2.9 28.3 1.0
OD2 A:ASP98 3.1 24.2 1.0
OG1 A:THR100 3.3 31.9 1.0
O A:HOH525 3.8 36.3 1.0
O A:HOH673 4.0 52.4 1.0
CB A:ASP98 4.4 27.0 1.0
O A:HOH611 4.5 38.0 1.0
CB A:THR100 4.5 27.1 1.0
CG2 A:THR100 4.7 28.8 1.0

Zinc binding site 3 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:73.7
occ:1.00
 OD2 A:ASP107 2.5 37.0 1.0
OD1 A:ASP107 2.6 37.2 1.0
OE2 A:GLU103 2.6 42.3 1.0
CG A:ASP107 2.9 32.9 1.0
CD A:GLU103 3.4 40.8 1.0
CG A:GLU103 3.5 37.6 1.0
NH2 A:ARG157 4.3 32.3 1.0
CB A:ASP107 4.4 28.7 1.0
OE1 A:GLU103 4.5 44.7 1.0
O A:HOH814 4.7 36.7 1.0
O A:GLU103 4.7 25.4 1.0
NH1 A:ARG157 4.8 32.3 1.0
CZ A:ARG157 5.0 31.6 1.0

Zinc binding site 4 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:31.2
occ:1.00
 OD2 A:ASP219 2.1 23.5 1.0
O A:HOH838 2.3 18.7 1.0
CG A:ASP219 2.8 26.5 1.0
OD1 A:ASP219 3.0 22.8 1.0
O A:HOH556 3.7 30.2 1.0
O A:HOH620 3.9 40.3 1.0
CG2 A:ILE214 4.1 23.9 1.0
CB A:ASP219 4.3 24.0 1.0
O A:GLY215 4.5 25.7 1.0
C A:GLY215 4.8 23.5 1.0
N A:GLY215 4.9 23.4 1.0
CA A:GLY215 4.9 23.4 1.0
NH1 A:ARG259 4.9 26.2 1.0
O A:HOH864 4.9 48.4 1.0

Zinc binding site 5 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:27.2
occ:1.00
 OD2 A:ASP334 2.3 31.4 1.0
CG A:ASP334 3.0 27.4 1.0
OD1 A:ASP334 3.3 23.4 1.0
OD2 A:ASP336 4.0 31.7 1.0
CB A:ASP334 4.0 24.2 1.0
O A:HOH884 4.1 49.0 1.0
O A:HOH584 4.1 29.8 1.0
CB A:ALA338 4.3 23.9 1.0
NH1 A:ARG280 4.4 24.5 1.0
CB A:ASP336 4.4 26.6 1.0
CG A:ASP336 4.7 28.5 1.0
O A:HOH697 4.9 54.7 1.0
O A:HOH766 4.9 46.0 1.0
N A:ASP336 5.0 25.2 1.0

Zinc binding site 6 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:24.4
occ:1.00
 ND1 A:HIS344 2.2 19.4 1.0
O A:HOH839 2.3 17.8 1.0
CE1 A:HIS344 3.0 20.5 1.0
CG A:HIS344 3.2 18.2 1.0
O A:HOH711 3.5 46.0 1.0
CB A:HIS344 3.6 21.0 1.0
NE2 A:HIS344 4.2 19.9 1.0
CD2 A:HIS344 4.3 19.5 1.0
CA A:HIS344 4.4 20.7 1.0
O A:HOH517 4.8 22.5 1.0

Zinc binding site 7 out of 7 in 3wuf

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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) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:98.1
occ:1.00
 OD2 A:ASP39 2.7 56.2 1.0
OD1 A:ASP39 3.3 56.5 1.0
CG A:ASP39 3.4 56.1 1.0
OE2 A:GLU45 3.8 35.6 1.0
OE1 A:GLU45 4.0 33.0 1.0
O A:HOH890 4.1 56.4 1.0
CD A:GLU45 4.3 33.8 1.0
O A:HOH885 4.4 65.9 1.0
O A:THR40 4.4 41.6 1.0
CB A:ASP39 4.9 53.8 1.0
O A:HOH818 5.0 50.1 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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