Zinc in PDB 8xzz: Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose

Enzymatic activity of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose

All present enzymatic activity of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose:
3.2.1.8;

Protein crystallography data

The structure of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose, PDB code: 8xzz was solved by W.L.Xiang, J.-W.Huang, Y.Yang, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.27 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.074, 137.54, 52.848, 90, 97.83, 90
R / Rfree (%) 16.1 / 19.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose (pdb code 8xzz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose, PDB code: 8xzz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8xzz

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Zinc binding site 1 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:35.7
occ:1.00
 O A:HOH402 1.7 21.4 1.0
O A:HOH537 2.4 32.9 1.0
OD1 A:ASP142 2.5 29.4 1.0
OD2 A:ASP142 2.6 31.0 1.0
CG A:ASP142 2.9 25.9 1.0
O A:HOH424 3.5 31.5 1.0
O A:HIS143 4.1 15.1 1.0
CB A:ASP142 4.4 18.1 1.0

Zinc binding site 2 out of 6 in 8xzz

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Zinc binding site 2 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:21.6
occ:1.00
 ND1 A:HIS143 2.0 14.9 1.0
O A:HOH526 2.0 20.0 1.0
O A:HOH552 2.2 14.4 1.0
O A:HOH467 2.2 21.2 1.0
O A:PHE92 2.4 13.3 1.0
CE1 A:HIS143 2.8 14.9 1.0
CG A:HIS143 3.1 17.0 1.0
CB A:HIS143 3.6 15.1 1.0
C A:PHE92 3.7 14.1 1.0
NE2 A:HIS143 4.0 19.1 1.0
CD2 A:HIS143 4.1 16.3 1.0
O C:HOH463 4.1 37.2 1.0
N A:PHE92 4.2 10.1 1.0
O A:SER93 4.4 24.0 1.0
O C:HOH468 4.5 34.5 1.0
CA A:SER93 4.5 11.9 1.0
N A:SER93 4.6 11.2 1.0
CA A:PHE92 4.6 12.7 1.0
O A:HOH482 4.6 27.8 1.0
O A:HOH590 4.8 36.0 1.0
CD1 A:PHE92 4.9 15.3 1.0
O A:HOH481 4.9 18.6 1.0
C A:SER93 5.0 16.8 1.0

Zinc binding site 3 out of 6 in 8xzz

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Zinc binding site 3 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:39.7
occ:1.00
 OD2 B:ASP142 2.3 35.0 1.0
OD1 B:ASP142 2.7 42.0 1.0
CG B:ASP142 2.8 30.4 1.0
O B:HIS143 4.1 15.5 1.0
CB B:ASP142 4.3 23.2 1.0
O B:HOH313 4.4 28.4 1.0
C B:ASP142 4.9 19.1 1.0

Zinc binding site 4 out of 6 in 8xzz

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Zinc binding site 4 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:36.9
occ:1.00
 ND1 B:HIS143 2.1 23.0 1.0
O B:HOH451 2.1 27.5 1.0
O B:HOH449 2.2 21.0 1.0
O B:HOH392 2.4 27.1 1.0
O B:PHE92 2.6 12.8 1.0
O B:HOH478 2.7 36.0 1.0
CE1 B:HIS143 3.0 20.8 1.0
CG B:HIS143 3.2 17.1 1.0
CB B:HIS143 3.6 17.7 1.0
C B:PHE92 3.9 12.1 1.0
O B:HOH491 4.1 34.8 1.0
NE2 B:HIS143 4.1 21.9 1.0
CD2 B:HIS143 4.2 19.6 1.0
N B:PHE92 4.3 10.1 1.0
O B:SER93 4.5 27.8 1.0
O B:HOH447 4.5 28.9 1.0
CA B:SER93 4.7 12.9 1.0
CA B:PHE92 4.7 10.9 1.0
N B:SER93 4.8 10.0 1.0
O B:HOH406 4.9 21.4 1.0
CD1 B:PHE92 5.0 12.9 1.0

Zinc binding site 5 out of 6 in 8xzz

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Zinc binding site 5 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:44.9
occ:1.00
 O D:HOH301 1.7 31.6 1.0
O D:HOH441 2.3 35.4 1.0
OD1 D:ASP142 2.5 35.9 1.0
OD2 D:ASP142 2.7 39.0 1.0
CG D:ASP142 3.0 34.4 1.0
O D:HOH392 3.6 33.4 1.0
O D:HOH319 4.0 30.3 1.0
O D:HIS143 4.1 18.0 1.0
CB D:ASP142 4.5 28.5 1.0

Zinc binding site 6 out of 6 in 8xzz

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Zinc binding site 6 out of 6 in the Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of A Xylanase Xyl-1 M4 E175A in Complex with Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:23.6
occ:1.00
 ND1 D:HIS143 2.0 16.8 1.0
O D:HOH374 2.1 25.2 1.0
O D:HOH430 2.1 19.3 1.0
O D:HOH315 2.2 20.2 1.0
O D:PHE92 2.4 16.1 1.0
CE1 D:HIS143 2.8 17.2 1.0
CG D:HIS143 3.1 17.6 1.0
C D:PHE92 3.6 15.3 1.0
CB D:HIS143 3.6 16.2 1.0
O D:HOH467 3.8 37.0 1.0
O B:HOH342 4.0 30.5 1.0
NE2 D:HIS143 4.0 21.8 1.0
N D:PHE92 4.1 13.0 1.0
CD2 D:HIS143 4.2 19.5 1.0
O D:SER93 4.3 19.4 1.0
CA D:SER93 4.4 13.7 1.0
N D:SER93 4.5 13.5 1.0
CA D:PHE92 4.5 14.1 1.0
O D:HOH417 4.6 30.1 1.0
CE B:MET0 4.7 42.2 1.0
O D:HOH401 4.8 26.4 1.0
CD1 D:PHE92 4.8 18.2 1.0
CB D:SER91 4.9 15.0 1.0
C D:SER93 4.9 16.4 1.0

Reference:

Y.Wu, Y.Yang, G.Lu, W.L.Xiang, T.Y.Sun, K.W.Chen, X.Lv, Y.F.Gui, R.Q.Zeng, Y.K.Du, C.H.Fu, J.W.Huang, C.C.Chen, R.T.Guo, L.J.Yu. Unleashing the Power of Evolution in Xylanase Engineering: Investigating the Role of Distal Mutation Regulation. J.Agric.Food Chem. V. 72 18201 2024.
ISSN: ESSN 1520-5118
PubMed: 39082219
DOI: 10.1021/ACS.JAFC.4C03245
Page generated: Tue Dec 10 21:54:45 2024

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