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Zinc in PDB 4pud: Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site

Enzymatic activity of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site

All present enzymatic activity of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site:
3.2.1.8;

Protein crystallography data

The structure of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site, PDB code: 4pud was solved by R.D.Dann, H.V.Solomon, S.Lansky, A.Ben-David, N.Lavid, R.Salama, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.394, 61.664, 89.321, 90.00, 119.37, 90.00
R / Rfree (%) 14.6 / 18.3

Other elements in 4pud:

The structure of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site (pdb code 4pud). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site, PDB code: 4pud:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 4pud

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Zinc binding site 1 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn406

b:26.4
occ:1.00
 O A:HOH746 2.0 26.1 1.0
OD2 A:ASP21 2.0 22.9 1.0
O A:HOH795 2.1 26.6 1.0
ZN A:ZN415 2.1 51.8 0.6
O A:HOH745 2.1 23.9 1.0
O A:HOH772 2.1 21.8 1.0
CG A:ASP21 3.0 22.8 1.0
OD1 A:ASP21 3.3 24.4 1.0
O A:HOH572 4.1 30.2 1.0
O A:HOH694 4.2 39.9 1.0
O A:PHE52 4.2 20.2 1.0
O A:HOH646 4.2 42.0 1.0
O A:LYS49 4.3 22.8 1.0
O A:HOH637 4.3 44.3 1.0
CB A:ASP21 4.4 20.2 1.0
O A:ARG50 4.5 22.7 1.0
O A:HOH828 4.5 57.7 1.0
OE1 A:GLN22 4.5 33.7 1.0
CB A:ASN53 4.7 21.2 1.0
CG A:GLN22 4.7 25.8 1.0
C A:PHE52 4.8 19.7 1.0
C A:ARG50 5.0 20.9 1.0

Zinc binding site 2 out of 9 in 4pud

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Zinc binding site 2 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:40.7
occ:0.75
 ZN A:ZN417 2.2 24.0 0.9
O A:HOH561 3.2 27.7 1.0
OD1 A:ASP365 3.3 23.1 1.0
NE2 A:HIS11 3.4 22.1 1.0
O A:HOH845 3.4 45.9 1.0
OD2 A:ASP365 3.6 22.1 1.0
CG A:ASP365 3.7 23.8 1.0
CE1 A:HIS11 3.8 24.6 1.0
CE2 A:TYR281 4.2 24.9 1.0
CD A:PRO364 4.2 24.6 1.0
CD2 A:HIS11 4.5 21.3 1.0
CG A:PRO364 4.6 25.3 1.0
CD2 A:TYR281 4.7 25.4 1.0
CB A:ASP365 4.9 24.9 1.0
CZ A:TYR281 4.9 25.5 1.0

Zinc binding site 3 out of 9 in 4pud

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Zinc binding site 3 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn410

b:28.4
occ:0.85
 CL A:CL408 1.9 45.9 1.0
NE2 A:HIS322 2.0 35.7 1.0
O A:HOH843 2.0 29.9 1.0
OE1 A:GLU58 2.2 34.2 1.0
OE2 A:GLU58 2.5 42.3 1.0
CE1 A:HIS322 2.6 40.7 1.0
CD A:GLU58 2.6 32.6 1.0
CD2 A:HIS322 3.2 32.4 1.0
O3B A:XYP401 3.6 33.9 1.0
OE2 A:GLU35 3.8 35.3 1.0
ND1 A:HIS322 3.8 41.6 1.0
CG A:GLU35 4.1 26.1 1.0
CG A:GLU58 4.1 30.4 1.0
CG A:HIS322 4.1 31.1 1.0
O A:HOH524 4.2 22.7 1.0
CD A:GLU35 4.4 32.2 1.0
O A:HOH652 4.5 39.9 1.0
ND2 A:ASN59 4.5 31.2 1.0
CB A:GLU58 4.8 23.9 1.0
N A:TRP324 4.8 22.6 1.0
C3B A:XYP401 4.9 43.1 1.0

Zinc binding site 4 out of 9 in 4pud

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Zinc binding site 4 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:23.1
occ:0.60
 OD1 A:ASP297 2.2 26.9 1.0
O A:ALA374 2.3 25.2 1.0
OD1 A:ASP377 2.3 27.5 1.0
O A:LYS379 2.3 34.4 1.0
O A:HOH532 2.4 25.0 1.0
O A:HOH531 2.4 27.0 1.0
CL A:CL414 2.4 43.9 0.9
CG A:ASP297 3.4 28.3 1.0
CG A:ASP377 3.4 30.3 1.0
C A:ALA374 3.5 27.0 1.0
C A:LYS379 3.5 46.0 1.0
OD2 A:ASP377 3.7 28.3 1.0
O A:HOH833 4.2 56.1 1.0
CB A:ASP297 4.2 24.4 1.0
N A:LYS379 4.2 39.3 1.0
OXT A:LYS379 4.3 45.8 1.0
CA A:ALA374 4.3 23.5 1.0
OD2 A:ASP297 4.3 36.2 1.0
NZ A:LYS301 4.3 49.1 1.0
O A:HOH583 4.4 25.8 1.0
CA A:ASP297 4.4 22.1 1.0
N A:ILE375 4.4 23.3 1.0
CA A:LYS379 4.5 44.2 1.0
CA A:ILE375 4.5 21.8 1.0
O A:ASP297 4.6 23.4 1.0
CE A:LYS301 4.6 49.2 1.0
O A:ASP377 4.7 21.9 1.0
CB A:ASP377 4.8 32.4 1.0
CB A:ALA374 4.9 26.5 1.0
C A:ASP297 4.9 22.0 1.0
C A:ASP377 4.9 32.1 1.0

Zinc binding site 5 out of 9 in 4pud

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Zinc binding site 5 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn412

b:38.8
occ:0.60
 O A:GLU27 2.3 23.8 1.0
O A:ILE310 2.3 23.2 1.0
O A:SER307 2.3 26.4 1.0
O A:HOH533 2.4 31.0 1.0
O A:HOH624 2.5 29.3 1.0
O A:HOH588 2.6 31.0 1.0
C A:ILE310 3.4 24.3 1.0
C A:GLU27 3.4 26.2 1.0
C A:SER307 3.5 28.2 1.0
CA A:SER311 4.0 23.2 1.0
N A:SER311 4.1 23.4 1.0
CA A:SER307 4.2 25.2 1.0
CA A:PHE28 4.2 22.6 1.0
O A:HOH596 4.2 36.7 1.0
N A:PHE28 4.3 25.0 1.0
CB A:PHE28 4.3 23.3 1.0
CB A:SER307 4.3 23.4 1.0
N A:ILE310 4.4 24.6 1.0
O A:HOH816 4.4 48.0 1.0
CA A:GLU27 4.5 21.5 1.0
CA A:ILE310 4.5 24.1 1.0
N A:ASP308 4.5 29.1 1.0
CA A:ASP308 4.6 32.5 1.0
O A:HOH744 4.6 53.0 1.0
CD2 A:PHE28 4.7 24.2 1.0
O A:HOH576 4.8 35.9 1.0
C A:SER311 4.8 18.4 1.0
C A:ASP308 4.9 32.5 1.0
O A:ASN26 5.0 23.8 1.0
CG A:PHE28 5.0 21.3 1.0
O A:SER311 5.0 18.9 1.0

Zinc binding site 6 out of 9 in 4pud

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Zinc binding site 6 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn413

b:38.6
occ:0.70
 OD2 A:ASP282 2.0 53.9 1.0
O A:HOH844 2.2 46.5 1.0
O A:HOH760 2.4 41.1 1.0
CG A:ASP282 2.8 37.3 1.0
OD1 A:ASP282 3.0 34.4 1.0
O A:HOH837 3.6 56.7 1.0
CL A:CL409 3.9 52.4 0.7
CB A:ASP282 4.3 29.3 1.0
O A:HOH590 4.3 33.4 1.0
CB A:THR280 4.5 25.7 1.0
N A:ASP282 4.7 23.4 1.0
ZN A:ZN416 4.8 76.8 0.6
CG2 A:THR280 4.8 30.9 1.0

Zinc binding site 7 out of 9 in 4pud

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Zinc binding site 7 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn415

b:51.8
occ:0.60
 ZN A:ZN406 2.1 26.4 1.0
O A:LYS49 2.8 22.8 1.0
O A:PHE52 2.8 20.2 1.0
O A:HOH746 2.8 26.1 1.0
O A:HOH745 2.9 23.9 1.0
OD2 A:ASP21 3.0 22.9 1.0
O A:HOH772 3.1 21.8 1.0
O A:HOH572 3.3 30.2 1.0
O A:HOH828 3.3 57.7 1.0
O A:HOH522 3.4 25.8 1.0
C A:LYS49 3.6 22.6 1.0
C A:PHE52 3.7 19.7 1.0
O A:LEU48 3.8 24.1 1.0
N A:PHE52 3.9 19.7 1.0
CG A:ASP21 3.9 22.8 1.0
C A:ARG50 4.0 20.9 1.0
O A:ARG50 4.1 22.7 1.0
OD1 A:ASP21 4.1 24.4 1.0
O A:HOH637 4.2 44.3 1.0
O A:HOH795 4.2 26.6 1.0
N A:HIS51 4.3 18.7 1.0
CA A:LYS49 4.3 21.5 1.0
CA A:PHE52 4.4 19.1 1.0
N A:ARG50 4.4 22.1 1.0
C A:HIS51 4.5 20.5 1.0
CA A:ARG50 4.5 21.0 1.0
N A:ASN53 4.5 19.9 1.0
CA A:ASN53 4.8 19.1 1.0
CA A:HIS51 4.8 17.1 1.0
CB A:ASN53 4.8 21.2 1.0
C A:LEU48 4.8 21.3 1.0

Zinc binding site 8 out of 9 in 4pud

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Zinc binding site 8 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn416

b:76.8
occ:0.60
 OD1 A:ASP282 2.2 34.4 1.0
CL A:CL409 2.2 52.4 0.7
CG A:ASP282 3.1 37.3 1.0
O A:HOH845 3.2 45.9 1.0
CA A:ASP282 3.2 26.2 1.0
N A:ASP282 3.4 23.4 1.0
CB A:ASP282 3.6 29.3 1.0
CD2 A:TYR281 3.9 25.4 1.0
C A:TYR281 4.0 24.6 1.0
OD2 A:ASP282 4.2 53.9 1.0
CB A:TYR281 4.3 24.8 1.0
O A:TYR281 4.4 23.4 1.0
CG A:TYR281 4.5 22.7 1.0
C A:ASP282 4.6 26.3 1.0
ZN A:ZN413 4.8 38.6 0.7
CA A:TYR281 4.8 24.2 1.0
CE2 A:TYR281 4.8 24.9 1.0
O A:ASP282 5.0 27.9 1.0

Zinc binding site 9 out of 9 in 4pud

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Zinc binding site 9 out of 9 in the Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn417

b:24.0
occ:0.90
 OD1 A:ASP365 1.9 23.1 1.0
NE2 A:HIS11 2.0 22.1 1.0
ZN A:ZN407 2.2 40.7 0.8
CG A:ASP365 2.8 23.8 1.0
CD2 A:HIS11 3.0 21.3 1.0
OD2 A:ASP365 3.0 22.1 1.0
CE1 A:HIS11 3.0 24.6 1.0
O A:HOH546 4.0 30.2 1.0
CD A:LYS367 4.1 24.3 1.0
ND1 A:HIS11 4.1 22.9 1.0
CG A:HIS11 4.1 23.1 1.0
CB A:ASP365 4.2 24.9 1.0
CB A:LYS367 4.5 20.3 1.0
O A:HOH561 4.5 27.7 1.0
NZ A:LYS367 4.7 32.0 1.0
O A:HOH845 4.8 45.9 1.0
CG A:LYS367 4.8 22.6 1.0

Reference:

R.D.Dann, H.V.Solomon, S.Lansky, A.Ben-David, N.Lavid, R.Salama, Y.Shoham, G.Shoham. Extracellulr Xylanase From Geobacillus Stearothermophilus: E159Q Mutant, with Xylopentaose in Active Site. To Be Published.
Page generated: Wed Aug 20 21:33:41 2025

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