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Zinc in PDB 4prw: Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose

Enzymatic activity of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose

All present enzymatic activity of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose:
3.2.1.8;

Protein crystallography data

The structure of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose, PDB code: 4prw 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) 43.07 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.800, 61.670, 89.350, 90.00, 119.38, 90.00
R / Rfree (%) 15.1 / 19.4

Other elements in 4prw:

The structure of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose (pdb code 4prw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose, PDB code: 4prw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4prw

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Zinc binding site 1 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn407

b:16.8
occ:0.60
 O A:ALA374 2.3 17.3 1.0
OD1 A:ASP297 2.3 19.0 1.0
OD1 A:ASP377 2.3 21.8 1.0
O A:HOH957 2.4 20.0 1.0
O A:LYS379 2.4 31.6 1.0
O A:HOH585 2.4 22.2 1.0
O A:HOH953 2.4 20.0 1.0
CG A:ASP297 3.4 24.2 1.0
CG A:ASP377 3.4 22.7 1.0
C A:ALA374 3.4 19.2 1.0
C A:LYS379 3.5 40.4 1.0
OD2 A:ASP377 3.7 23.3 1.0
CB A:ASP297 4.2 19.6 1.0
OXT A:LYS379 4.2 41.4 1.0
NZ A:LYS301 4.3 40.0 1.0
O A:HOH748 4.3 40.0 1.0
N A:LYS379 4.3 34.3 1.0
CA A:ALA374 4.3 17.6 1.0
OD2 A:ASP297 4.3 31.6 1.0
CA A:ASP297 4.4 18.0 1.0
N A:ILE375 4.4 14.7 1.0
CA A:ILE375 4.5 14.3 1.0
O A:HOH889 4.5 46.3 1.0
O A:HOH520 4.5 17.2 1.0
CA A:LYS379 4.5 37.4 1.0
O A:ASP297 4.5 16.5 1.0
O A:ASP377 4.6 17.5 1.0
CE A:LYS301 4.8 40.3 1.0
C A:ASP377 4.8 23.4 1.0
CB A:ASP377 4.8 24.5 1.0
CB A:ALA374 4.9 20.0 1.0
C A:ASP297 4.9 15.4 1.0

Zinc binding site 2 out of 6 in 4prw

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Zinc binding site 2 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:18.2
occ:1.00
 OD2 A:ASP21 2.0 19.1 1.0
O A:HOH771 2.1 20.9 1.0
O A:HOH954 2.1 18.6 1.0
O A:HOH809 2.1 18.2 1.0
O A:HOH615 2.1 18.9 1.0
O A:HOH550 2.2 16.2 1.0
CG A:ASP21 3.0 17.7 1.0
OD1 A:ASP21 3.3 17.9 1.0
O A:HOH570 4.1 21.1 1.0
O A:HOH698 4.1 40.7 1.0
O A:HOH665 4.2 33.8 1.0
O A:PHE52 4.2 13.3 1.0
O A:HOH671 4.2 35.1 1.0
O A:LYS49 4.2 16.0 1.0
O A:HOH709 4.3 46.3 1.0
O A:ARG50 4.4 17.1 1.0
CB A:ASP21 4.4 14.9 1.0
OE1 A:GLN22 4.5 28.1 1.0
CB A:ASN53 4.6 15.3 1.0
CG A:GLN22 4.8 18.7 1.0
C A:PHE52 4.8 13.4 1.0
C A:ARG50 5.0 15.0 1.0

Zinc binding site 3 out of 6 in 4prw

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Zinc binding site 3 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:17.7
occ:1.00
 OD2 A:ASP365 1.9 18.6 1.0
NE2 A:HIS11 2.1 15.3 1.0
CL A:CL412 2.2 22.3 1.0
CG A:ASP365 2.8 17.0 1.0
CD2 A:HIS11 3.0 15.3 1.0
OD1 A:ASP365 3.1 14.6 1.0
CE1 A:HIS11 3.1 15.4 1.0
O A:HOH601 4.0 23.0 1.0
CD A:LYS367 4.1 19.5 1.0
CG A:HIS11 4.2 16.4 1.0
ND1 A:HIS11 4.2 15.0 1.0
CB A:ASP365 4.2 17.8 1.0
CB A:LYS367 4.6 15.6 1.0
O A:HOH518 4.6 19.9 1.0
O A:HOH962 4.6 41.6 1.0
NZ A:LYS367 4.8 23.9 1.0
CG A:LYS367 4.8 17.4 1.0

Zinc binding site 4 out of 6 in 4prw

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Zinc binding site 4 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn411

b:29.9
occ:0.60
 OD2 A:ASP282 2.1 41.7 1.0
O A:HOH963 2.2 38.2 1.0
O A:HOH672 2.4 45.0 1.0
O A:HOH959 2.5 35.1 1.0
CG A:ASP282 2.9 29.9 1.0
OD1 A:ASP282 3.0 24.0 1.0
O A:HOH944 3.4 47.6 1.0
CB A:ASP282 4.3 21.5 1.0
O A:HOH559 4.3 23.6 1.0
CB A:THR280 4.6 19.9 1.0
O A:HOH960 4.7 34.8 1.0
N A:ASP282 4.7 17.5 1.0
CG2 A:THR280 4.9 22.2 1.0

Zinc binding site 5 out of 6 in 4prw

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Zinc binding site 5 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn413

b:16.7
occ:0.70
 CL A:CL414 1.9 34.8 1.0
O A:HOH961 2.0 24.1 1.0
NE2 A:HIS322 2.0 24.4 1.0
OE2 A:GLU58 2.3 26.2 1.0
OE1 A:GLU58 2.5 29.7 1.0
CE1 A:HIS322 2.6 31.4 1.0
CD A:GLU58 2.7 29.2 1.0
CD2 A:HIS322 3.2 23.1 1.0
O2B A:XYP402 3.7 29.9 1.0
OE2 A:GLU35 3.8 28.9 1.0
ND1 A:HIS322 3.9 32.0 1.0
O A:HOH536 4.1 15.3 1.0
CG A:GLU35 4.1 20.1 1.0
CG A:HIS322 4.1 21.4 1.0
CG A:GLU58 4.2 24.1 1.0
O A:HOH812 4.4 51.1 1.0
O A:HOH616 4.5 33.2 1.0
CD A:GLU35 4.5 22.1 1.0
ND2 A:ASN59 4.6 21.9 1.0
CB A:GLU58 4.8 18.6 1.0
O A:HOH773 4.8 47.3 1.0
N A:TRP324 4.9 14.6 1.0
O3B A:XYP402 4.9 33.2 1.0
O A:HOH805 4.9 58.9 1.0
C2B A:XYP402 4.9 34.5 1.0
O A:HOH543 5.0 23.4 1.0

Zinc binding site 6 out of 6 in 4prw

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Zinc binding site 6 out of 6 in the Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn415

b:25.6
occ:0.50
 O A:SER307 2.2 20.9 1.0
O A:GLU27 2.3 18.1 1.0
O A:ILE310 2.3 18.2 1.0
O A:HOH576 2.5 28.9 1.0
O A:HOH551 2.5 21.6 1.0
C A:SER307 3.4 21.7 1.0
C A:GLU27 3.4 17.0 1.0
C A:ILE310 3.5 16.9 1.0
O A:HOH578 4.0 30.5 1.0
CA A:SER311 4.0 13.8 1.0
CA A:SER307 4.2 21.1 1.0
N A:SER311 4.2 16.1 1.0
N A:PHE28 4.2 17.2 1.0
CB A:SER307 4.3 19.8 1.0
CA A:PHE28 4.3 16.1 1.0
CB A:PHE28 4.3 16.3 1.0
N A:ILE310 4.3 17.7 1.0
N A:ASP308 4.4 22.6 1.0
CA A:GLU27 4.4 16.3 1.0
O A:HOH737 4.5 41.3 1.0
CA A:ILE310 4.5 16.4 1.0
CA A:ASP308 4.5 28.7 1.0
O A:HOH752 4.7 42.5 1.0
CD2 A:PHE28 4.7 16.7 1.0
O A:HOH569 4.7 28.9 1.0
C A:ASP308 4.8 24.4 1.0
C A:SER311 4.8 13.0 1.0
OG A:SER307 5.0 23.7 1.0
O A:ASN26 5.0 18.0 1.0
CG A:PHE28 5.0 16.9 1.0

Reference:

R.D.Dann, H.V.Solomon, S.Lansky, A.Ben-David, N.Lavid, R.Salama, Y.Shoham, G.Shoham. Xylanase T6 (XT6) From Geobacillus Stearothermophilus in Complex with Xylohexaose To Be Published.
Page generated: Wed Dec 16 05:41:27 2020

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