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Zinc in PDB 5a7m: The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)

Enzymatic activity of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)

All present enzymatic activity of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1):
3.2.1.37;

Protein crystallography data

The structure of The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1), PDB code: 5a7m 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) 204.12 / 1.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.911, 203.724, 82.112, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 19.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Zinc atom in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1) (pdb code 5a7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 22 binding sites of Zinc where determined in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1), PDB code: 5a7m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 22 in 5a7m

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Zinc binding site 1 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1901

b:14.6
occ:1.00
O A:HOH2086 1.9 13.2 1.0
ND1 A:HIS34 2.0 17.0 1.0
OD2 A:ASP31 2.1 11.9 1.0
CG A:ASP31 2.8 12.4 1.0
OD1 A:ASP31 2.9 11.8 1.0
CE1 A:HIS34 3.0 17.5 1.0
CG A:HIS34 3.0 16.9 1.0
CB A:HIS34 3.4 16.3 1.0
NE2 A:HIS34 4.1 18.0 1.0
CD2 A:HIS34 4.1 17.6 1.0
CB A:ASP31 4.2 12.3 1.0
O A:HOH2087 4.2 29.4 1.0
N A:HIS34 4.3 16.7 1.0
CA A:HIS34 4.5 16.4 1.0
O A:HOH2022 4.8 33.2 1.0
CB A:GLU33 4.8 21.5 1.0

Zinc binding site 2 out of 22 in 5a7m

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Zinc binding site 2 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1902

b:47.7
occ:1.00
O A:HOH2947 2.1 48.2 1.0
O A:HOH2090 2.3 45.7 1.0
NE2 A:HIS34 2.3 18.0 1.0
O A:HOH2095 2.4 45.5 1.0
O A:HOH2096 2.5 17.9 1.0
O A:HOH2091 2.6 26.3 1.0
CE1 A:HIS34 3.1 17.5 1.0
O A:HOH2092 3.3 44.3 1.0
CD2 A:HIS34 3.4 17.6 1.0
OE1 A:GLU33 3.5 37.0 1.0
ND1 A:HIS34 4.3 17.0 1.0
CG A:HIS34 4.5 16.9 1.0
CD A:GLU33 4.6 33.1 1.0
CB A:GLU33 4.7 21.5 1.0
CG A:GLU33 5.0 27.5 1.0

Zinc binding site 3 out of 22 in 5a7m

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Zinc binding site 3 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:20.2
occ:1.00
OXT A:ACT1923 2.0 15.2 1.0
OD2 A:ASP95 2.0 12.7 1.0
O A:HOH2193 2.1 19.5 1.0
O A:HOH2191 2.1 28.4 1.0
O A:ACT1923 2.6 16.7 1.0
C A:ACT1923 2.6 16.4 1.0
CG A:ASP95 2.7 12.0 1.0
OD1 A:ASP95 2.7 12.4 1.0
O A:TYR430 4.1 11.4 1.0
CH3 A:ACT1923 4.1 15.9 1.0
CA A:TYR429 4.1 10.7 1.0
CB A:ASP95 4.2 11.6 1.0
O A:HOH2610 4.2 9.3 1.0
N A:TYR430 4.3 10.9 1.0
O A:HOH2192 4.3 35.2 1.0
CG A:ARG96 4.4 11.2 1.0
C A:TYR429 4.4 10.6 1.0
CD1 A:TYR429 4.6 11.2 1.0
N A:ARG96 4.7 10.6 1.0
C A:TYR430 4.7 11.4 1.0
N A:TYR429 4.8 10.9 1.0

Zinc binding site 4 out of 22 in 5a7m

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Zinc binding site 4 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1904

b:21.8
occ:1.00
O A:HOH2246 1.9 25.0 1.0
NE2 A:HIS128 2.1 10.9 1.0
O A:HOH2243 2.1 21.9 1.0
O A:HOH2245 2.2 17.7 1.0
O A:HOH2948 2.2 23.1 1.0
O A:HOH2244 2.5 25.0 1.0
CD2 A:HIS128 3.0 10.2 1.0
CE1 A:HIS128 3.1 10.8 1.0
O A:HOH2255 3.8 35.2 1.0
CG A:HIS128 4.1 9.9 1.0
ND1 A:HIS128 4.2 10.2 1.0
O A:HOH2256 4.4 11.2 1.0
O A:HOH2118 4.5 30.3 1.0
O A:HOH2329 4.5 39.8 1.0
O A:HOH2114 4.6 28.8 1.0
O A:HOH2115 4.9 35.6 1.0

Zinc binding site 5 out of 22 in 5a7m

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Zinc binding site 5 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1907

b:16.9
occ:1.00
O A:HOH2378 2.0 25.6 1.0
OD1 A:ASP225 2.0 15.9 1.0
O A:HOH2374 2.1 18.9 1.0
ND1 A:HIS302 2.1 10.6 1.0
CG A:ASP225 2.8 15.0 1.0
OD2 A:ASP225 2.9 15.6 1.0
CE1 A:HIS302 3.0 10.6 1.0
ZN A:ZN1908 3.0 35.0 1.0
CG A:HIS302 3.2 10.8 1.0
O A:HOH2436 3.3 24.3 1.0
CA A:HIS302 3.6 12.4 1.0
O A:GLY223 3.6 11.5 1.0
O A:HOH2380 3.6 26.4 0.8
CB A:HIS302 3.6 11.2 1.0
OG A:SER259 3.9 10.6 1.0
O A:HIS302 4.0 12.6 1.0
O A:HOH2486 4.1 8.8 0.2
NE2 A:HIS302 4.2 10.1 1.0
CB A:ASP225 4.2 13.2 1.0
C A:HIS302 4.3 13.2 1.0
CD2 A:HIS302 4.3 10.5 1.0
O A:HOH2379 4.3 18.1 1.0
C A:GLY223 4.3 11.7 1.0
CB A:SER259 4.4 9.3 1.0
N A:HIS302 4.6 12.3 1.0
CA A:ASP225 4.7 11.6 1.0
O A:PHE224 4.7 10.2 1.0
N A:ASP225 4.7 11.3 1.0
CA A:GLY223 4.7 11.6 1.0
C A:PHE224 4.8 11.3 1.0

Zinc binding site 6 out of 22 in 5a7m

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Zinc binding site 6 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1908

b:35.0
occ:1.00
O A:HOH2378 2.1 25.6 1.0
OD2 A:ASP225 2.3 15.6 1.0
O A:HOH2380 2.3 26.4 0.8
O A:HOH2379 2.4 18.1 1.0
O A:HOH2949 2.5 36.5 1.0
ZN A:ZN1907 3.0 16.9 1.0
CG A:ASP225 3.2 15.0 1.0
OD1 A:ASP225 3.6 15.9 1.0
O A:HOH2374 3.8 18.9 1.0
O A:HOH2488 3.9 32.5 1.0
O A:HOH2486 3.9 8.8 0.2
O A:HOH2436 4.0 24.3 1.0
O A:HIS302 4.2 12.6 1.0
CB A:ASP225 4.4 13.2 1.0
O A:HOH2447 4.7 17.6 1.0
O A:HOH2164 4.9 28.9 1.0

Zinc binding site 7 out of 22 in 5a7m

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Zinc binding site 7 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1909

b:29.4
occ:0.50
ZN A:ZN1909 0.0 29.4 0.5
ZN A:ZN1909 1.5 22.5 0.5
O A:HOH2462 2.0 34.1 1.0
OE2 B:GLU278 2.1 11.7 0.5
O A:HOH2950 2.3 40.4 1.0
OE1 B:GLU278 2.3 10.6 0.5
OE2 A:GLU278 2.4 13.7 0.5
OE1 B:GLU278 2.4 12.2 0.5
O A:HOH2456 2.5 13.4 0.2
OE2 B:GLU278 2.5 10.5 0.5
CD B:GLU278 2.6 11.7 0.5
CD B:GLU278 2.6 10.7 0.5
O A:HOH2468 3.0 35.6 0.8
OE2 A:GLU278 3.1 14.2 0.5
CD A:GLU278 3.4 13.3 0.5
OE1 A:GLU278 3.7 14.1 0.5
CD A:GLU278 3.8 13.7 0.5
O A:HOH2464 3.8 39.1 0.2
CG B:GLU278 4.0 10.7 0.5
OE1 A:GLU278 4.1 14.8 0.5
CG B:GLU278 4.1 11.5 0.5
OG1 B:THR274 4.1 9.6 1.0
O A:HOH2468 4.2 4.5 0.2
OG1 A:THR274 4.2 9.0 1.0
CB A:GLN273 4.3 9.2 0.5
O A:HOH2458 4.4 3.0 0.5
CB A:GLN273 4.5 9.9 0.5
OE1 A:GLN273 4.5 12.2 0.5
CA B:THR274 4.7 9.5 1.0
CG A:GLU278 4.7 12.8 0.5
CB B:THR274 4.8 9.6 1.0
CG2 B:THR274 4.9 9.7 1.0
O B:HOH2478 4.9 24.1 1.0
N A:THR274 4.9 8.7 1.0
CG A:GLU278 4.9 13.4 0.5
O A:HOH2470 5.0 16.1 1.0

Zinc binding site 8 out of 22 in 5a7m

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Zinc binding site 8 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1909

b:22.5
occ:0.50
ZN A:ZN1909 0.0 22.5 0.5
ZN A:ZN1909 1.5 29.4 0.5
O A:HOH2468 1.8 35.6 0.8
O A:HOH2462 2.0 34.1 1.0
OE2 A:GLU278 2.1 13.7 0.5
OE2 A:GLU278 2.2 14.2 0.5
OE1 A:GLU278 2.4 14.1 0.5
OE2 B:GLU278 2.5 11.7 0.5
CD A:GLU278 2.6 13.3 0.5
CD A:GLU278 2.7 13.7 0.5
OE1 A:GLU278 2.8 14.8 0.5
O A:HOH2950 2.8 40.4 1.0
O A:HOH2468 2.9 4.5 0.2
O A:HOH2464 3.2 39.1 0.2
OE1 B:GLU278 3.4 10.6 0.5
CD B:GLU278 3.4 11.7 0.5
OE2 B:GLU278 3.5 10.5 0.5
CD B:GLU278 3.6 10.7 0.5
OE1 B:GLU278 3.7 12.2 0.5
O A:HOH2456 3.8 13.4 0.2
CG A:GLU278 4.0 12.8 0.5
CG A:GLU278 4.1 13.4 0.5
OG1 B:THR274 4.1 9.6 1.0
OG1 A:THR274 4.2 9.0 1.0
CB B:GLN273 4.4 12.2 1.0
O A:HOH2470 4.4 16.1 1.0
CG B:GLU278 4.7 10.7 0.5
O A:HOH2458 4.7 3.0 0.5
CG B:GLU278 4.8 11.5 0.5
CA A:THR274 4.8 8.8 1.0
N B:THR274 4.9 9.8 1.0
CB A:THR274 4.9 9.1 1.0
CA B:THR274 5.0 9.5 1.0

Zinc binding site 9 out of 22 in 5a7m

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Zinc binding site 9 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1911

b:17.7
occ:0.75
OE2 A:GLU334 1.8 12.4 0.2
O A:HOH2496 1.9 10.3 0.8
ND1 A:HIS331 2.0 13.2 1.0
OE1 A:GLU334 2.1 21.7 0.8
O A:HOH2517 2.2 22.7 0.8
CD A:GLU334 2.6 12.3 0.2
CE1 A:HIS331 2.9 14.2 1.0
CD A:GLU334 2.9 20.6 0.8
OE1 A:GLU334 2.9 11.9 0.2
OE2 A:GLU334 3.0 24.3 0.8
CG A:HIS331 3.1 13.5 1.0
CB A:HIS331 3.5 13.1 1.0
O A:HOH2496 3.6 2.9 0.2
CG A:GLU334 4.0 12.6 0.2
NE2 A:HIS331 4.0 13.9 0.8
CD2 A:HIS331 4.1 13.5 0.8
CA A:HIS331 4.3 11.9 1.0
CG A:GLU334 4.3 18.6 0.8
CB A:GLN308 4.4 16.8 1.0
O A:TRP330 4.5 10.4 1.0
N A:SER309 4.5 14.8 1.0
CB A:SER309 4.6 13.6 0.5
CB A:SER309 4.7 14.7 0.5
CB A:GLU334 4.7 13.0 0.2
CB A:GLU334 4.8 15.9 0.8
CA A:SER309 5.0 14.5 0.5
CA A:SER309 5.0 13.9 0.5

Zinc binding site 10 out of 22 in 5a7m

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Zinc binding site 10 out of 22 in the The Structure of Hypocrea Jecorina Beta-Xylosidase XYL3A (BXL1)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1915

b:7.2
occ:0.50
O A:HOH2836 1.9 23.2 1.0
OE2 A:GLU671 2.0 17.9 1.0
O A:HOH2837 2.0 18.1 1.0
O A:HOH2839 2.0 15.9 0.5
CD A:GLU671 2.8 18.4 1.0
OE1 A:GLU671 3.0 19.8 1.0
NZ A:LYS705 3.2 28.8 1.0
O A:HOH2414 3.8 42.9 1.0
OD2 A:ASP703 4.2 20.6 1.0
CG A:GLU671 4.3 17.2 1.0
CE A:LYS705 4.3 26.9 1.0
O A:HOH2415 4.3 40.8 1.0
CB A:ASP703 4.6 18.0 1.0
CG A:LYS705 4.8 20.9 1.0
O A:HOH2838 4.9 26.7 1.0
CG A:ASP703 4.9 20.2 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: Wed Dec 16 06:01:38 2020

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