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Zinc in PDB 5ae6: The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose

Enzymatic activity of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose

All present enzymatic activity of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose:
3.2.1.37;

Protein crystallography data

The structure of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose, PDB code: 5ae6 was solved by N.E.Mikkelsen, M.Gudmundsson, S.Karkehabadi, H.Hansson, M.Sandgren, E.Larenas, C.Mitchinson, B.Keleman, T.Kaper, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 202.44 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.244, 202.443, 82.441, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose (pdb code 5ae6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose, PDB code: 5ae6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 5ae6

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Zinc binding site 1 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1901

b:25.4
occ:1.00
 OD2 A:ASP31 2.1 21.2 1.0
ND1 A:HIS34 2.1 23.7 1.0
O A:HOH2044 2.2 17.3 1.0
CG A:ASP31 2.8 20.8 1.0
OD1 A:ASP31 2.9 19.6 1.0
CE1 A:HIS34 3.1 24.0 1.0
CG A:HIS34 3.1 24.0 1.0
CB A:HIS34 3.5 23.7 1.0
NE2 A:HIS34 4.2 24.1 1.0
CD2 A:HIS34 4.2 24.0 1.0
N A:HIS34 4.3 24.3 1.0
CB A:ASP31 4.3 20.8 1.0
CA A:HIS34 4.4 23.6 1.0
CB A:GLU33 4.8 30.3 1.0

Zinc binding site 2 out of 14 in 5ae6

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Zinc binding site 2 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1902

b:62.7
occ:0.50
 O A:HOH2503 2.1 17.6 0.5
O A:HOH2504 2.2 24.7 0.5
NE2 A:HIS34 2.3 24.1 1.0
CE1 A:HIS34 3.0 24.0 1.0
CD2 A:HIS34 3.5 24.0 1.0
ND1 A:HIS34 4.2 23.7 1.0
CG A:HIS34 4.5 24.0 1.0
O A:HOH2449 4.6 45.7 1.0
CB A:GLU33 4.8 30.3 1.0

Zinc binding site 3 out of 14 in 5ae6

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Zinc binding site 3 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:21.7
occ:1.00
 O A:HOH2135 1.9 21.8 1.0
O A:HOH2133 2.0 28.9 1.0
NE2 A:HIS128 2.1 20.3 1.0
O A:HOH2134 2.3 20.0 1.0
O A:HOH2505 2.3 16.3 1.0
O A:HOH2132 2.4 24.5 1.0
CD2 A:HIS128 3.0 19.5 1.0
CE1 A:HIS128 3.2 20.3 1.0
O A:HOH2140 4.1 21.2 1.0
CG A:HIS128 4.2 19.8 1.0
O A:HOH2056 4.2 24.4 1.0
O A:HOH2057 4.2 21.5 1.0
ND1 A:HIS128 4.3 19.9 1.0

Zinc binding site 4 out of 14 in 5ae6

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Zinc binding site 4 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1906

b:46.3
occ:0.50
 ZN A:ZN1906 0.0 46.3 0.5
O A:HOH2191 1.7 19.7 0.5
O A:HOH2186 1.7 33.5 0.5
O A:HOH2188 2.2 27.2 0.5
O A:HOH2190 2.3 25.3 0.5
NE2 A:HIS198 2.5 22.4 0.5
NE2 A:HIS198 2.5 20.9 0.5
CE1 A:HIS198 2.6 22.1 0.5
O A:HOH2187 2.8 25.7 0.5
ZN A:ZN1906 3.1 47.9 0.5
OE2 A:GLU197 3.3 36.0 1.0
CE1 A:HIS198 3.3 21.0 0.5
CD2 A:HIS198 3.6 20.7 0.5
CD2 A:HIS198 3.9 21.8 0.5
ND1 A:HIS198 3.9 21.8 0.5
O A:HOH2187 4.1 14.2 0.5
CD A:GLU197 4.1 33.3 1.0
ND1 A:HIS198 4.4 20.6 0.5
OE1 A:GLU197 4.5 34.5 1.0
CG A:HIS198 4.5 21.5 0.5
CG A:HIS198 4.6 20.5 0.5

Zinc binding site 5 out of 14 in 5ae6

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Zinc binding site 5 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1906

b:47.9
occ:0.50
 ZN A:ZN1906 0.0 47.9 0.5
CE1 A:HIS198 2.1 21.0 0.5
O A:HOH2190 2.3 25.3 0.5
O A:HOH2188 2.3 27.2 0.5
NE2 A:HIS198 2.4 20.9 0.5
O A:HOH2506 2.4 32.3 1.0
NE2 A:HIS198 2.7 22.4 0.5
ZN A:ZN1906 3.1 46.3 0.5
CD2 A:HIS198 3.2 21.8 0.5
ND1 A:HIS198 3.3 20.6 0.5
O A:HOH2058 3.4 38.4 1.0
O A:HOH2191 3.5 19.7 0.5
CD2 A:HIS198 3.7 20.7 0.5
CE1 A:HIS198 3.7 22.1 0.5
CG A:HIS198 4.1 20.5 0.5
OE2 A:GLU197 4.2 36.0 1.0
O A:HOH2307 4.2 29.3 1.0
O A:HOH2305 4.3 22.3 1.0
CG A:HIS198 4.3 21.5 0.5
ND1 A:HIS198 4.5 21.8 0.5
O A:HOH2186 4.6 33.5 0.5
O A:HOH2189 4.7 27.1 1.0

Zinc binding site 6 out of 14 in 5ae6

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Zinc binding site 6 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1911

b:31.8
occ:0.50
 OE1 A:GLU334 1.9 26.8 1.0
ND1 A:HIS331 2.1 21.1 1.0
O A:HOH2285 2.3 16.9 0.5
O A:HOH2276 2.6 17.0 1.0
CD A:GLU334 2.7 26.4 1.0
OE2 A:GLU334 2.8 29.2 1.0
CE1 A:HIS331 2.9 20.9 1.0
CG A:HIS331 3.2 20.9 1.0
CB A:HIS331 3.7 19.6 1.0
NE2 A:HIS331 4.0 20.9 1.0
CG A:GLU334 4.1 24.7 1.0
CD2 A:HIS331 4.2 20.9 1.0
CB A:GLN308 4.3 21.0 1.0
CA A:HIS331 4.4 19.4 1.0
N A:SER309 4.4 18.2 1.0
O A:TRP330 4.5 18.2 1.0
CB A:GLU334 4.7 22.2 1.0
CB A:SER309 4.7 17.6 0.5
CB A:SER309 4.7 18.0 0.5
O A:HOH2277 4.7 22.2 1.0
NE2 A:GLN308 4.9 23.2 1.0
CA A:SER309 5.0 18.2 0.5
CA A:SER309 5.0 18.1 0.5

Zinc binding site 7 out of 14 in 5ae6

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Zinc binding site 7 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1901

b:23.3
occ:1.00
 O B:HOH2043 1.9 21.4 1.0
OD2 B:ASP31 1.9 17.9 1.0
ND1 B:HIS34 2.1 17.7 1.0
O B:HOH2044 2.2 20.4 1.0
CG B:ASP31 2.7 18.2 1.0
OD1 B:ASP31 2.8 17.4 1.0
CE1 B:HIS34 2.9 17.6 1.0
CG B:HIS34 3.2 17.8 1.0
CB B:HIS34 3.6 17.6 1.0
NE2 B:HIS34 4.1 17.8 1.0
CB B:ASP31 4.1 18.0 1.0
CD2 B:HIS34 4.2 17.8 1.0
N B:HIS34 4.4 18.8 1.0
CB B:GLU33 4.6 22.9 1.0
CA B:HIS34 4.6 18.1 1.0
OE1 B:GLU33 4.7 27.0 1.0

Zinc binding site 8 out of 14 in 5ae6

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Zinc binding site 8 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1904

b:22.5
occ:1.00
 O B:HOH2130 1.9 29.4 1.0
NE2 B:HIS128 2.1 16.6 1.0
O B:HOH2128 2.2 22.5 1.0
O B:HOH2129 2.2 19.5 1.0
O B:HOH2127 2.3 31.9 1.0
O B:HOH2439 2.4 24.2 1.0
CD2 B:HIS128 3.0 16.1 1.0
O B:HOH2440 3.1 39.0 1.0
CE1 B:HIS128 3.2 16.3 1.0
CG B:HIS128 4.2 16.5 1.0
O B:HOH2053 4.2 23.1 1.0
ND1 B:HIS128 4.3 16.3 1.0
O B:HOH2054 4.3 25.9 1.0
O B:HOH2134 4.4 17.1 1.0

Zinc binding site 9 out of 14 in 5ae6

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Zinc binding site 9 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1906

b:39.4
occ:0.50
 ZN B:ZN1906 0.0 39.4 0.5
O B:HOH2175 1.9 21.1 0.5
O B:HOH2174 2.2 24.0 0.5
O B:HOH2171 2.2 26.6 0.5
CE1 B:HIS198 2.2 20.5 0.5
NE2 B:HIS198 2.5 20.9 0.5
NE2 B:HIS198 2.6 20.9 0.5
ZN B:ZN1906 2.9 51.8 0.5
CD2 B:HIS198 3.3 20.6 0.5
CE1 B:HIS198 3.4 21.0 0.5
ND1 B:HIS198 3.5 20.3 0.5
OE1 B:GLU197 3.7 35.6 1.0
CD2 B:HIS198 3.9 20.4 0.5
CG B:HIS198 4.3 20.4 0.5
CD B:GLU197 4.3 34.0 1.0
CG B:HIS198 4.5 20.5 0.5
ND1 B:HIS198 4.5 20.3 0.5
OE2 B:GLU197 4.6 37.5 1.0

Zinc binding site 10 out of 14 in 5ae6

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Zinc binding site 10 out of 14 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) in Complex with 4-Thioxylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1906

b:51.8
occ:0.50
 ZN B:ZN1906 0.0 51.8 0.5
O B:HOH2175 1.8 21.1 0.5
CE1 B:HIS198 2.2 21.0 0.5
NE2 B:HIS198 2.4 20.9 0.5
NE2 B:HIS198 2.4 20.9 0.5
O B:HOH2172 2.7 35.4 1.0
ZN B:ZN1906 2.9 39.4 0.5
CD2 B:HIS198 3.2 20.4 0.5
O B:HOH2171 3.3 26.6 0.5
CE1 B:HIS198 3.4 20.5 0.5
ND1 B:HIS198 3.5 20.3 0.5
CD2 B:HIS198 3.8 20.6 0.5
CG B:HIS198 4.3 20.5 0.5
CG B:HIS198 4.3 20.4 0.5
ND1 B:HIS198 4.4 20.3 0.5
O B:HOH2275 4.5 18.0 1.0
O B:HOH2277 4.5 25.9 1.0
O B:HOH2174 4.6 24.0 0.5
O B:HOH2173 4.9 18.7 1.0
OE2 B:GLU197 4.9 37.5 1.0

Reference:

N.E.Mikkelsen, M.Gudmundsson, S.Karkehabadi, M.Sandgren, E.Larenas, C.Mitchinson, B.Keleman, T.Kaper, H.Hansson. Th Crystal Structure of A Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, XYL3A From Hypocrea Jecorina To Be Published.
Page generated: Thu Aug 21 00:41:02 2025

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