Zinc in PDB 6epb: Structure of Chitinase 42 From Trichoderma Harzianum

Enzymatic activity of Structure of Chitinase 42 From Trichoderma Harzianum

All present enzymatic activity of Structure of Chitinase 42 From Trichoderma Harzianum:
3.2.1.14;

Protein crystallography data

The structure of Structure of Chitinase 42 From Trichoderma Harzianum, PDB code: 6epb was solved by M.Ramirez-Escudero, E.Jimenez-Ortega, J.Sanz-Aparicio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.82 / 1.75
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.353, 68.353, 178.279, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Chitinase 42 From Trichoderma Harzianum (pdb code 6epb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of Chitinase 42 From Trichoderma Harzianum, PDB code: 6epb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6epb

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Zinc binding site 1 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:88.3
occ:1.00
 O A:ACT528 2.0 34.6 1.0
OE1 A:GLU171 2.3 25.3 1.0
O A:HOH844 2.3 40.1 1.0
O A:HOH601 2.8 24.2 1.0
OE2 A:GLU171 2.8 24.0 1.0
O A:HOH723 2.8 39.5 1.0
CD A:GLU171 2.9 22.7 1.0
C A:ACT528 3.1 33.9 1.0
O A:HOH623 3.2 38.9 1.0
OXT A:ACT528 3.6 28.6 1.0
OD2 A:ASP169 3.7 15.9 0.5
N A:TRP131 3.8 23.2 0.8
CB A:TRP131 4.1 31.2 0.8
CA A:GLY130 4.3 19.4 1.0
CH3 A:ACT528 4.4 33.2 1.0
CG A:GLU171 4.4 20.3 1.0
CA A:TRP131 4.4 27.4 0.8
C A:GLY130 4.4 21.5 1.0
SD A:MET237 4.5 26.8 1.0
CG A:ASP169 4.5 14.5 0.5
OD1 A:ASP169 4.6 15.0 0.5
CZ A:PHE71 4.8 14.3 1.0

Zinc binding site 2 out of 7 in 6epb

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Zinc binding site 2 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:18.5
occ:0.80
 O A:HOH862 2.0 29.4 1.0
OD1 A:ASP51 2.1 16.1 1.0
OD2 A:ASP51 2.6 16.6 1.0
CG A:ASP51 2.6 16.1 1.0
CB A:ASP51 4.1 15.3 1.0
O A:HOH833 4.3 14.0 1.0
O2 A:EDO527 4.4 35.4 1.0
CA A:ASP51 4.8 14.4 1.0
C2 A:EDO527 4.9 39.6 1.0

Zinc binding site 3 out of 7 in 6epb

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Zinc binding site 3 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:27.4
occ:0.70
 OD1 A:ASP232 1.9 15.8 1.0
NE2 A:HIS205 1.9 19.1 1.0
O A:ACT530 2.1 45.5 1.0
O A:HOH853 2.1 37.9 1.0
CE1 A:HIS205 2.7 18.9 1.0
CG A:ASP232 2.8 14.3 1.0
CD2 A:HIS205 3.0 19.2 1.0
C A:ACT530 3.1 46.5 1.0
OD2 A:ASP232 3.1 14.4 1.0
CH3 A:ACT530 3.5 46.7 1.0
ND1 A:HIS205 3.8 19.2 1.0
O A:HOH652 3.9 19.2 1.0
CG A:HIS205 3.9 17.6 1.0
CB A:ASP232 4.1 13.4 1.0
OXT A:ACT530 4.2 44.9 1.0
NH1 A:ARG190 4.3 14.4 1.0
CA A:ASP232 4.5 12.9 1.0
ZN A:ZN506 4.9 37.8 0.7
N A:ASP232 4.9 13.0 1.0

Zinc binding site 4 out of 7 in 6epb

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Zinc binding site 4 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:28.1
occ:1.00
 O A:HOH611 2.1 27.2 1.0
O A:HOH859 2.2 31.8 1.0
NE2 A:HIS395 2.2 21.4 1.0
O A:HOH865 2.2 23.0 1.0
O A:HOH861 2.2 27.6 1.0
CE1 A:HIS395 3.1 21.1 1.0
CD2 A:HIS395 3.2 20.6 1.0
O A:GLY399 3.8 27.6 1.0
ND1 A:HIS395 4.2 20.8 1.0
CG A:HIS395 4.3 20.1 1.0
CG A:LEU401 4.6 21.7 1.0
CD1 A:LEU401 4.8 22.3 1.0
C A:GLY399 4.9 23.8 1.0

Zinc binding site 5 out of 7 in 6epb

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Zinc binding site 5 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:26.3
occ:0.80
 O A:HOH830 2.0 26.9 1.0
NE2 A:HIS92 2.0 22.4 1.0
O1 A:EDO517 2.1 42.2 1.0
O A:HOH856 2.4 35.8 1.0
O2 A:EDO517 2.7 50.3 1.0
CD2 A:HIS92 2.9 20.6 1.0
CE1 A:HIS92 3.0 22.3 1.0
C1 A:EDO517 3.0 46.3 1.0
C2 A:EDO517 3.4 48.3 1.0
CG A:HIS92 4.1 18.5 1.0
ND1 A:HIS92 4.1 20.5 1.0
O A:GLU90 4.3 14.2 1.0
O A:HOH854 4.5 44.3 1.0
CD2 A:TYR106 4.6 19.2 1.0
CE2 A:TYR106 4.7 19.8 1.0

Zinc binding site 6 out of 7 in 6epb

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Zinc binding site 6 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:37.8
occ:0.70
 ND1 A:HIS205 1.9 19.2 1.0
O A:HOH840 2.1 32.9 1.0
CE1 A:HIS205 2.6 18.9 1.0
O A:HOH860 2.7 46.7 1.0
CG A:HIS205 3.1 17.6 1.0
CB A:HIS205 3.7 17.0 1.0
NE2 A:HIS205 3.7 19.1 1.0
CD2 A:HIS205 4.0 19.2 1.0
OD1 A:ASP194 4.0 21.2 1.0
CA A:HIS205 4.2 15.6 1.0
O A:HOH819 4.6 16.2 1.0
CH3 A:ACT530 4.6 46.7 1.0
NH2 A:ARG190 4.6 15.1 1.0
CG A:ASP194 4.7 19.4 1.0
ZN A:ZN503 4.9 27.4 0.7
OD2 A:ASP194 4.9 21.9 1.0
CZ A:ARG190 4.9 14.8 1.0

Zinc binding site 7 out of 7 in 6epb

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Zinc binding site 7 out of 7 in the Structure of Chitinase 42 From Trichoderma Harzianum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Chitinase 42 From Trichoderma Harzianum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn507

b:35.2
occ:0.80
 OXT A:ACT531 2.1 34.7 1.0
O A:HOH831 2.2 43.4 1.0
OE2 A:GLU316 2.4 38.7 1.0
N1 A:IMD532 2.8 45.8 0.9
C5 A:IMD532 2.9 45.2 0.9
C A:ACT531 3.0 35.7 1.0
CD A:GLU316 3.1 37.9 1.0
CH3 A:ACT531 3.2 36.2 1.0
OE1 A:GLU316 3.2 39.0 1.0
O A:HOH641 3.5 38.6 1.0
O A:HOH677 4.0 38.6 1.0
C2 A:IMD532 4.1 44.6 0.9
NH2 A:ARG52 4.1 18.4 1.0
O A:ACT531 4.2 38.4 1.0
C4 A:IMD532 4.3 44.8 0.9
O A:HOH842 4.3 45.1 1.0
NE1 A:TRP47 4.5 16.8 1.0
CG A:GLU316 4.5 35.0 1.0
CZ2 A:TRP378 4.6 16.6 1.0
CZ2 A:TRP47 4.6 16.5 1.0
NE1 A:TRP378 4.7 17.6 1.0
N3 A:IMD532 4.8 44.9 0.9
O A:HOH881 4.9 45.0 1.0
CE2 A:TRP47 4.9 16.5 1.0

Reference:

P.E.Kidibule, P.Santos-Moriano, E.Jimenez-Ortega, M.Ramirez-Escudero, M.C.Limon, M.Remacha, F.J.Plou, J.Sanz-Aparicio, M.Fernandez-Lobato. Use of Chitin and Chitosan to Produce New Chitooligosaccharides By Chitinase CHIT42: Enzymatic Activity and Structural Basis of Protein Specificity. Microb. Cell Fact. V. 17 47 2018.
ISSN: ISSN 1475-2859
PubMed: 29566690
DOI: 10.1186/S12934-018-0895-X
Page generated: Wed Dec 16 11:43:47 2020

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