Zinc in PDB 8xzy: Structure of A Xylanase Xyl-1 M4 Mutant E175A

Enzymatic activity of Structure of A Xylanase Xyl-1 M4 Mutant E175A

All present enzymatic activity of Structure of A Xylanase Xyl-1 M4 Mutant E175A:
3.2.1.8;

Protein crystallography data

The structure of Structure of A Xylanase Xyl-1 M4 Mutant E175A, PDB code: 8xzy 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) 23.29 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.231, 137.536, 52.857, 90, 97.66, 90
R / Rfree (%) 18.1 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Xylanase Xyl-1 M4 Mutant E175A (pdb code 8xzy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of A Xylanase Xyl-1 M4 Mutant E175A, PDB code: 8xzy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8xzy

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Zinc binding site 1 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn200

b:37.3
occ:1.00
 O A:HOH303 1.4 23.1 1.0
OD2 A:ASP142 2.3 32.6 1.0
O A:HOH419 2.4 33.8 1.0
OD1 A:ASP142 2.4 32.1 1.0
CG A:ASP142 2.7 26.5 1.0
O A:HIS143 4.1 14.9 1.0
O A:HOH376 4.1 30.7 1.0
CB A:ASP142 4.2 23.5 1.0
C A:ASP142 4.9 18.0 1.0
CA A:ASP142 4.9 21.6 1.0

Zinc binding site 2 out of 7 in 8xzy

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Zinc binding site 2 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:24.7
occ:1.00
 ND1 A:HIS143 1.9 18.9 1.0
O A:HOH412 2.0 24.3 1.0
O A:HOH368 2.1 24.7 1.0
O A:HOH435 2.2 18.7 1.0
O A:PHE92 2.4 17.1 1.0
CE1 A:HIS143 2.7 20.1 1.0
CG A:HIS143 3.0 20.0 1.0
CB A:HIS143 3.5 18.4 1.0
C A:PHE92 3.6 16.7 1.0
NE2 A:HIS143 3.9 19.7 1.0
CD2 A:HIS143 4.1 19.8 1.0
N A:PHE92 4.1 13.7 1.0
O A:SER93 4.3 24.7 1.0
O A:HOH474 4.4 35.1 1.0
CA A:SER93 4.5 17.5 1.0
N A:SER93 4.5 16.6 1.0
CA A:PHE92 4.5 14.0 1.0
O A:HOH339 4.8 24.7 1.0
O A:HOH483 4.8 35.2 1.0
CD1 A:PHE92 4.8 17.3 1.0
C A:SER93 4.9 20.1 1.0
CB A:SER91 4.9 16.6 1.0
O A:HOH396 4.9 24.7 1.0

Zinc binding site 3 out of 7 in 8xzy

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Zinc binding site 3 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn200

b:40.4
occ:1.00
 O B:HOH302 1.4 24.1 1.0
O B:HOH304 1.8 36.4 1.0
O B:HOH318 2.2 29.2 1.0
OD2 B:ASP142 2.3 32.7 1.0
O B:HOH450 2.3 35.0 1.0
OD1 B:ASP142 2.3 29.2 1.0
CG B:ASP142 2.6 25.3 1.0
O B:HIS143 4.0 17.1 1.0
CB B:ASP142 4.1 25.4 1.0
O B:HOH402 4.4 27.6 1.0
C B:ASP142 4.8 21.3 1.0
CA B:ASP142 4.9 22.4 1.0

Zinc binding site 4 out of 7 in 8xzy

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Zinc binding site 4 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:37.5
occ:1.00
 ND1 B:HIS143 2.0 20.2 1.0
O B:HOH456 2.2 33.6 1.0
O B:HOH410 2.3 29.8 1.0
O B:HOH442 2.3 18.2 1.0
O B:PHE92 2.8 13.9 1.0
CE1 B:HIS143 2.8 21.0 1.0
CG B:HIS143 3.0 21.3 1.0
CB B:HIS143 3.4 19.9 1.0
NE2 B:HIS143 4.0 23.1 1.0
C B:PHE92 4.1 14.0 1.0
CD2 B:HIS143 4.1 19.5 1.0
O B:HOH478 4.4 53.7 1.0
N B:PHE92 4.4 11.4 1.0
O B:HOH407 4.5 32.5 1.0
O B:HOH394 4.6 25.1 1.0
CA B:HIS143 4.9 20.2 1.0
CA B:PHE92 4.9 11.7 1.0

Zinc binding site 5 out of 7 in 8xzy

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Zinc binding site 5 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn200

b:72.0
occ:1.00
 ND1 C:HIS143 2.1 24.6 1.0
O C:HOH428 2.4 40.4 1.0
CE1 C:HIS143 3.0 25.8 1.0
O C:HOH349 3.0 39.1 1.0
CG C:HIS143 3.0 24.1 1.0
O C:PHE92 3.1 13.3 1.0
O C:HOH417 3.3 44.1 1.0
CB C:HIS143 3.4 22.1 1.0
NE2 C:HIS143 4.1 28.3 1.0
CD2 C:HIS143 4.1 24.1 1.0
O C:HOH405 4.3 36.4 1.0
C C:PHE92 4.3 15.8 1.0
O C:HOH431 4.5 51.9 1.0
O C:HOH375 4.6 24.5 1.0
N C:PHE92 4.6 14.8 1.0
CA C:HIS143 4.8 21.5 1.0

Zinc binding site 6 out of 7 in 8xzy

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Zinc binding site 6 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


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 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn200

b:38.8
occ:1.00
 O D:HOH301 1.7 27.1 1.0
O D:HOH388 2.0 43.4 1.0
O D:HOH426 2.2 34.3 1.0
OD1 D:ASP142 2.2 30.5 1.0
O D:HOH314 2.3 30.1 1.0
OD2 D:ASP142 2.3 34.8 1.0
CG D:ASP142 2.6 30.4 1.0
CB D:ASP142 4.1 26.7 1.0
O D:HIS143 4.2 20.1 1.0
O D:HOH377 4.2 35.1 1.0
O D:HOH354 4.3 49.2 1.0
O D:HOH461 4.8 46.1 1.0
C D:ASP142 4.9 22.3 1.0
CA D:ASP142 4.9 25.9 1.0

Zinc binding site 7 out of 7 in 8xzy

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Zinc binding site 7 out of 7 in the Structure of A Xylanase Xyl-1 M4 Mutant E175A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of A Xylanase Xyl-1 M4 Mutant E175A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:31.4
occ:1.00
 O D:HOH379 1.9 25.0 1.0
ND1 D:HIS143 2.0 20.2 1.0
O D:HOH414 2.1 25.4 1.0
O D:PHE92 2.5 17.7 1.0
CE1 D:HIS143 2.8 21.9 1.0
CG D:HIS143 3.1 23.1 1.0
CB D:HIS143 3.6 22.5 1.0
C D:PHE92 3.7 18.3 1.0
NE2 D:HIS143 4.0 24.6 1.0
CD2 D:HIS143 4.1 23.3 1.0
N D:PHE92 4.2 17.1 1.0
O D:SER93 4.3 25.3 1.0
O D:HOH406 4.5 40.3 1.0
CA D:SER93 4.6 17.4 1.0
N D:SER93 4.6 17.4 1.0
CA D:PHE92 4.6 16.9 1.0
CD1 D:PHE92 4.8 18.3 1.0
O D:HOH353 5.0 31.9 1.0
C D:SER93 5.0 21.4 1.0
O B:HOH483 5.0 41.7 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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