Zinc in PDB 8y00: Structure of A Xylanase Xyl-1 M4 Mutant E175A in Complex with Xylotriose

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

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

Protein crystallography data

The structure of Structure of A Xylanase Xyl-1 M4 Mutant E175A in Complex with Xylotriose, PDB code: 8y00 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) 24.47 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.192, 137.834, 52.822, 90, 97.85, 90
R / Rfree (%) 18.2 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of A Xylanase Xyl-1 M4 Mutant E175A in Complex with Xylotriose (pdb code 8y00). 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 Mutant E175A in Complex with Xylotriose, PDB code: 8y00:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:32.6
occ:1.00
 O A:HOH303 1.6 24.6 1.0
OD1 A:ASP142 2.2 30.6 1.0
O A:HOH304 2.2 28.3 1.0
OD2 A:ASP142 2.7 33.9 1.0
CG A:ASP142 2.8 27.4 1.0
O A:HOH380 3.7 39.6 1.0
O A:HOH385 4.0 53.1 1.0
O A:HIS143 4.1 16.9 1.0
CB A:ASP142 4.3 24.5 1.0
C A:ASP142 5.0 18.3 1.0

Zinc binding site 2 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:28.1
occ:1.00
 ND1 A:HIS143 2.0 21.0 1.0
O A:HOH433 2.1 29.6 1.0
O A:HOH330 2.1 26.6 1.0
O A:HOH427 2.2 19.4 1.0
O A:PHE92 2.4 18.8 1.0
CE1 A:HIS143 2.8 21.5 1.0
CG A:HIS143 3.1 21.2 1.0
CB A:HIS143 3.6 19.5 1.0
C A:PHE92 3.7 16.8 1.0
NE2 A:HIS143 4.0 23.8 1.0
N A:PHE92 4.2 14.5 1.0
CD2 A:HIS143 4.2 21.5 1.0
O A:SER93 4.3 25.7 1.0
CA A:SER93 4.5 16.4 1.0
O A:HOH398 4.5 34.0 1.0
N A:SER93 4.5 16.0 1.0
CA A:PHE92 4.6 16.2 1.0
CD1 A:PHE92 4.8 16.4 1.0
CB A:SER91 4.9 17.2 1.0
C A:SER93 4.9 20.7 1.0
O A:HOH391 5.0 23.6 1.0

Zinc binding site 3 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:39.0
occ:1.00
 O B:HOH428 1.6 25.9 1.0
O B:HOH417 2.1 25.9 1.0
OD1 B:ASP142 2.3 38.7 1.0
OD2 B:ASP142 2.7 40.7 1.0
CG B:ASP142 2.8 33.2 1.0
O B:HIS143 4.1 19.3 1.0
O B:HOH534 4.3 34.6 1.0
CB B:ASP142 4.3 28.0 1.0
O B:HOH593 4.4 31.4 1.0
C B:ASP142 4.9 23.5 1.0

Zinc binding site 4 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:40.7
occ:1.00
 O B:HOH529 1.8 33.7 1.0
ND1 B:HIS143 1.9 24.7 1.0
O B:HOH541 2.2 27.7 1.0
O B:HOH470 2.2 27.3 1.0
O B:HOH575 2.4 33.0 1.0
O B:PHE92 2.6 15.7 1.0
CE1 B:HIS143 2.8 25.0 1.0
CG B:HIS143 3.0 22.7 1.0
CB B:HIS143 3.5 21.4 1.0
C B:PHE92 3.9 15.3 1.0
NE2 B:HIS143 3.9 27.1 1.0
CD2 B:HIS143 4.0 22.5 1.0
N B:PHE92 4.3 15.6 1.0
O B:HOH515 4.5 29.6 1.0
O B:SER93 4.5 30.9 1.0
CA B:SER93 4.7 18.3 1.0
CA B:PHE92 4.8 15.4 1.0
N B:SER93 4.8 17.2 1.0
O B:HOH513 4.9 29.0 1.0
CD1 B:PHE92 5.0 13.8 1.0
CA B:HIS143 5.0 21.1 1.0

Zinc binding site 5 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:36.7
occ:1.00
 O C:HOH402 1.7 30.8 1.0
O C:HOH469 1.8 45.0 1.0
OD1 C:ASP142 2.1 29.4 1.0
OD2 C:ASP142 2.5 35.1 1.0
CG C:ASP142 2.6 28.7 1.0
O B:HOH409 3.8 35.7 1.0
O C:HIS143 4.1 22.4 1.0
CB C:ASP142 4.2 30.3 1.0
O C:HOH425 4.2 36.2 1.0
C C:ASP142 4.9 24.9 1.0
CA C:ASP142 5.0 26.4 1.0

Zinc binding site 6 out of 6 in 8y00

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


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 in Complex with Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:28.7
occ:1.00
 O C:HOH519 2.0 28.0 1.0
ND1 C:HIS143 2.0 21.7 1.0
O C:HOH455 2.1 24.8 1.0
O C:HOH494 2.1 22.9 1.0
O C:PHE92 2.4 22.4 1.0
CE1 C:HIS143 2.9 22.5 1.0
CG C:HIS143 3.1 21.1 1.0
CB C:HIS143 3.6 20.0 1.0
C C:PHE92 3.6 20.0 1.0
O C:HOH552 4.0 41.6 1.0
NE2 C:HIS143 4.1 23.3 1.0
CD2 C:HIS143 4.2 23.7 1.0
N C:PHE92 4.2 18.7 1.0
O C:SER93 4.3 22.8 1.0
CA C:SER93 4.4 19.1 1.0
N C:SER93 4.5 18.9 1.0
CA C:PHE92 4.6 18.6 1.0
O B:HOH584 4.7 40.5 1.0
O C:HOH463 4.8 38.2 1.0
CD1 C:PHE92 4.8 20.8 1.0
O B:HOH411 4.9 44.2 1.0
C C:SER93 4.9 21.4 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 21:54:39 2024

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