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Zinc in PDB 3akq: Crystal Structure of Xylanase From Trichoderma Longibrachiatum

Enzymatic activity of Crystal Structure of Xylanase From Trichoderma Longibrachiatum

All present enzymatic activity of Crystal Structure of Xylanase From Trichoderma Longibrachiatum:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Xylanase From Trichoderma Longibrachiatum, PDB code: 3akq was solved by M.Sugahara, N.Kunishima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.14 / 0.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.921, 37.516, 84.300, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 20.4

Other elements in 3akq:

The structure of Crystal Structure of Xylanase From Trichoderma Longibrachiatum also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum (pdb code 3akq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum, PDB code: 3akq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3akq

Go back to Zinc Binding Sites List in 3akq
Zinc binding site 1 out of 5 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Xylanase From Trichoderma Longibrachiatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn191

b:11.9
occ:1.00
 CL A:CL196 1.5 21.1 1.0
O A:HOH343 1.9 23.9 1.0
O A:HOH344 1.9 16.1 1.0
O A:HOH347 2.0 14.5 1.0
O A:HOH349 2.2 16.3 1.0
ND1 A:HIS144 2.3 13.4 1.0
CG A:HIS144 3.2 11.5 1.0
CL A:CL197 3.2 20.7 1.0
ZN A:ZN195 3.2 19.3 1.0
CE1 A:HIS144 3.3 14.5 1.0
ZN A:ZN193 3.3 14.9 1.0
CB A:HIS144 3.4 8.9 1.0
ZN A:ZN194 3.4 16.0 1.0
O A:HOH350 3.6 24.9 1.0
O A:HOH348 3.7 21.6 1.0
O A:HOH346 3.8 14.3 1.0
ZN A:ZN192 3.9 16.0 1.0
O A:HOH416 3.9 14.0 1.0
O A:HOH337 4.0 21.6 1.0
OD1 A:ASN92 4.0 9.1 1.0
O A:HOH545 4.1 22.4 1.0
CD2 A:HIS144 4.3 12.7 1.0
NE2 A:HIS144 4.4 15.0 1.0
O A:HOH345 4.4 26.0 1.0
O A:PHE93 4.6 10.3 1.0
O A:HOH280 4.8 25.9 1.0
CA A:HIS144 4.8 8.3 1.0

Zinc binding site 2 out of 5 in 3akq

Go back to Zinc Binding Sites List in 3akq
Zinc binding site 2 out of 5 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Xylanase From Trichoderma Longibrachiatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn192

b:16.0
occ:1.00
 O A:HOH348 1.8 21.6 1.0
O A:HOH346 1.8 14.3 1.0
ZN A:ZN195 3.1 19.3 1.0
ZN A:ZN194 3.2 16.0 1.0
ZN A:ZN193 3.2 14.9 1.0
CL A:CL197 3.4 20.7 1.0
O A:HOH349 3.4 16.3 1.0
O A:HOH344 3.5 16.1 1.0
O A:HOH347 3.7 14.5 1.0
CL A:CL196 3.8 21.1 1.0
ZN A:ZN191 3.9 11.9 1.0
O A:HOH350 4.2 24.9 1.0
O A:HOH345 4.5 26.0 1.0
O A:HOH343 4.8 23.9 1.0

Zinc binding site 3 out of 5 in 3akq

Go back to Zinc Binding Sites List in 3akq
Zinc binding site 3 out of 5 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Xylanase From Trichoderma Longibrachiatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn193

b:14.9
occ:1.00
 O A:HOH348 1.7 21.6 1.0
O A:HOH345 1.7 26.0 1.0
O A:HOH347 1.7 14.5 1.0
O A:HOH349 1.8 16.3 1.0
CL A:CL196 3.1 21.1 1.0
ZN A:ZN192 3.2 16.0 1.0
ZN A:ZN191 3.3 11.9 1.0
O A:HOH343 3.9 23.9 1.0
O A:HOH545 4.0 22.4 1.0
O A:HOH346 4.1 14.3 1.0
CB A:HIS144 4.2 8.9 1.0
ZN A:ZN194 4.3 16.0 1.0
O A:HOH416 4.4 14.0 1.0
O A:HOH344 4.5 16.1 1.0
O A:HIS144 4.5 8.2 1.0
O A:HOH350 4.6 24.9 1.0
ZN A:ZN195 4.8 19.3 1.0
ND1 A:HIS144 4.9 13.4 1.0

Zinc binding site 4 out of 5 in 3akq

Go back to Zinc Binding Sites List in 3akq
Zinc binding site 4 out of 5 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Xylanase From Trichoderma Longibrachiatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn194

b:16.0
occ:1.00
 O A:HOH346 1.6 14.3 1.0
CL A:CL197 1.7 20.7 1.0
CL A:CL196 2.4 21.1 1.0
O A:HOH349 3.0 16.3 1.0
ZN A:ZN192 3.2 16.0 1.0
O A:HOH344 3.3 16.1 1.0
ZN A:ZN191 3.4 11.9 1.0
O A:HOH416 3.8 14.0 1.0
O A:HOH348 3.9 21.6 1.0
O A:HOH337 4.0 21.6 1.0
ZN A:ZN195 4.2 19.3 1.0
ZN A:ZN193 4.3 14.9 1.0
O A:HOH347 4.4 14.5 1.0
O A:HOH275 4.5 18.9 1.0
ND1 A:HIS144 4.6 13.4 1.0
O A:HOH277 4.9 23.4 1.0
O A:HOH358 5.0 25.7 1.0

Zinc binding site 5 out of 5 in 3akq

Go back to Zinc Binding Sites List in 3akq
Zinc binding site 5 out of 5 in the Crystal Structure of Xylanase From Trichoderma Longibrachiatum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Xylanase From Trichoderma Longibrachiatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn195

b:19.3
occ:1.00
 O A:HOH344 1.7 16.1 1.0
O A:HOH350 2.3 24.9 1.0
ZN A:ZN192 3.1 16.0 1.0
CL A:CL197 3.1 20.7 1.0
ZN A:ZN191 3.2 11.9 1.0
O A:HOH343 3.4 23.9 1.0
O A:HOH346 3.5 14.3 1.0
O A:HOH360 3.9 25.5 1.0
O A:HOH347 4.0 14.5 1.0
O A:HOH348 4.0 21.6 1.0
CL A:CL196 4.1 21.1 1.0
ZN A:ZN194 4.2 16.0 1.0
O A:HOH443 4.3 24.0 1.0
O A:HOH349 4.5 16.3 1.0
O A:HOH280 4.7 25.9 1.0
O A:HOH337 4.7 21.6 1.0
O A:HOH279 4.8 25.8 1.0
ZN A:ZN193 4.8 14.9 1.0

Reference:

M.Sugahara, Y.Kageyama-Morikawa, N.Kunishima. Packing Space Expansion of Protein Crystallization Screening with Synthetic Zeolite As A Heteroepitaxic Nucleant Cryst.Growth Des. V. 11 110 2011.
ISSN: ISSN 1528-7483
DOI: 10.1021/CG100987G
Page generated: Thu Oct 24 11:12:54 2024

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