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

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

All present enzymatic activity of The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9, PDB code: 3wub 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 / 2.08
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 80.910, 80.910, 289.302, 90.00, 90.00, 120.00
R / Rfree (%) 19.6 / 22.1

Zinc Binding Sites:

The binding sites of Zinc atom in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) From Streptomyces Sp. 9 (pdb code 3wub). 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) From Streptomyces Sp. 9, PDB code: 3wub:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3wub

Go back to Zinc Binding Sites List in 3wub
Zinc binding site 1 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:75.2
occ:1.00
 OD2 A:ASP107 2.5 45.0 1.0
OD1 A:ASP107 2.5 42.6 1.0
O A:HOH666 2.6 65.6 1.0
OE1 A:GLU103 2.7 52.7 1.0
CG A:ASP107 2.8 41.2 1.0
O A:HOH665 3.0 73.6 1.0
CD A:GLU103 3.9 50.8 1.0
NH2 A:ARG157 4.0 40.1 1.0
NH1 A:ARG157 4.1 39.8 1.0
CB A:ASP107 4.3 37.0 1.0
CZ A:ARG157 4.5 39.1 1.0
OE2 A:GLU103 4.7 53.5 1.0
O A:GLU103 4.8 32.1 1.0
CG A:GLU103 4.8 45.8 1.0
CB A:GLU103 4.8 38.9 1.0

Zinc binding site 2 out of 5 in 3wub

Go back to Zinc Binding Sites List in 3wub
Zinc binding site 2 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:33.5
occ:1.00
 NE2 A:HIS149 2.2 32.3 1.0
OD1 A:ASP145 2.2 30.7 1.0
O A:HOH816 2.3 28.9 1.0
CG A:ASP145 2.9 30.7 1.0
OD2 A:ASP145 2.9 31.1 1.0
CD2 A:HIS149 3.0 31.5 1.0
CE1 A:HIS149 3.2 32.7 1.0
O A:HOH589 3.3 46.2 1.0
CG A:HIS149 4.2 33.0 1.0
O A:HOH712 4.2 57.8 1.0
ND1 A:HIS149 4.3 33.4 1.0
CB A:ASP145 4.3 26.3 1.0
CA A:ASP145 4.9 27.9 1.0
O A:ASP145 5.0 25.9 1.0

Zinc binding site 3 out of 5 in 3wub

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Zinc binding site 3 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:37.9
occ:1.00
 OD2 A:ASP219 2.2 35.8 1.0
O A:HOH661 2.4 31.4 1.0
CG A:ASP219 2.9 30.9 1.0
OD1 A:ASP219 3.0 29.6 1.0
O A:HOH604 3.9 44.1 1.0
CG2 A:ILE214 4.2 34.6 1.0
CB A:ASP219 4.3 30.1 1.0
O A:GLY215 4.5 33.8 1.0
C A:GLY215 4.7 32.9 1.0
CA A:GLY215 4.8 32.5 1.0
N A:GLY215 4.9 33.0 1.0
NH1 A:ARG259 5.0 35.1 1.0

Zinc binding site 4 out of 5 in 3wub

Go back to Zinc Binding Sites List in 3wub
Zinc binding site 4 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:34.9
occ:1.00
 OD2 A:ASP334 2.2 36.2 1.0
O A:HOH662 2.2 12.9 1.0
O A:HOH663 2.2 40.7 1.0
CG A:ASP334 3.0 34.0 1.0
OD1 A:ASP334 3.3 30.6 1.0
OD2 A:ASP336 4.0 38.0 1.0
CB A:ASP334 4.1 30.4 1.0
CB A:ALA338 4.2 28.4 1.0
O A:HOH626 4.2 44.1 1.0
NH1 A:ARG280 4.3 31.8 1.0
CB A:ASP336 4.4 34.8 1.0
O A:HOH744 4.6 55.4 1.0
CG A:ASP336 4.7 37.5 1.0

Zinc binding site 5 out of 5 in 3wub

Go back to Zinc Binding Sites List in 3wub
Zinc binding site 5 out of 5 in the The Wild Type Crystal Structure of B-1,4-Xylanase (XYNAS9) 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) From Streptomyces Sp. 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:55.2
occ:1.00
 OD2 A:ASP98 2.2 36.9 1.0
CG A:ASP98 2.9 32.6 1.0
OD1 A:ASP98 3.0 28.9 1.0
O A:HOH664 3.1 61.2 1.0
O A:HOH567 3.9 53.8 1.0
OG1 A:THR100 4.0 44.5 1.0
CB A:THR100 4.2 39.0 1.0
CB A:ASP98 4.4 31.9 1.0
O A:HOH586 4.5 36.5 1.0
CG2 A:THR100 4.8 41.0 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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