Zinc in PDB 6yn4: Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.

Enzymatic activity of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.

All present enzymatic activity of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.:
3.2.1.14;

Protein crystallography data

The structure of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose., PDB code: 6yn4 was solved by 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) 48.38 / 1.82
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.352, 68.352, 177.757, 90, 90, 90
R / Rfree (%) 18 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. (pdb code 6yn4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose., PDB code: 6yn4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6yn4

Go back to Zinc Binding Sites List in 6yn4
Zinc binding site 1 out of 5 in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn508

b:20.0
occ:0.80
 NE2 A:HIS92 1.9 19.0 1.0
O A:ACT507 2.1 21.4 1.0
O A:HOH840 2.2 28.4 1.0
OXT A:ACT504 2.6 43.5 1.0
O A:ACT504 2.7 44.0 1.0
C A:ACT507 2.8 22.5 1.0
OXT A:ACT507 2.8 23.5 1.0
CE1 A:HIS92 2.9 18.6 1.0
CD2 A:HIS92 2.9 16.9 1.0
C A:ACT504 3.0 42.8 1.0
ND1 A:HIS92 4.0 16.7 1.0
CG A:HIS92 4.0 15.0 1.0
CH3 A:ACT507 4.2 22.9 1.0
O A:GLU90 4.3 10.8 1.0
CH3 A:ACT504 4.5 41.9 1.0
CE3 A:TRP98 4.6 22.1 0.5
CD2 A:TYR106 4.7 17.1 1.0
CE2 A:TYR106 4.7 18.4 1.0
CZ3 A:TRP98 4.8 22.1 0.5

Zinc binding site 2 out of 5 in 6yn4

Go back to Zinc Binding Sites List in 6yn4
Zinc binding site 2 out of 5 in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:12.4
occ:0.80
 OD1 A:ASP51 2.1 11.4 1.0
O A:HOH850 2.1 20.9 1.0
O A:ACT505 2.5 38.3 1.0
OXT A:ACT505 2.6 43.3 1.0
OD2 A:ASP51 2.6 12.7 1.0
CG A:ASP51 2.7 11.2 1.0
C A:ACT505 2.8 40.6 1.0
O3 B:NAG4 4.0 19.8 1.0
CB A:ASP51 4.1 11.0 1.0
O A:HOH861 4.3 32.2 1.0
CH3 A:ACT505 4.4 38.6 1.0
CA A:ASP51 4.8 10.5 1.0
O A:HOH732 4.9 29.2 1.0
C3 B:NAG4 5.0 21.8 1.0

Zinc binding site 3 out of 5 in 6yn4

Go back to Zinc Binding Sites List in 6yn4
Zinc binding site 3 out of 5 in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:26.8
occ:0.75
 O A:HOH613 2.0 36.7 1.0
NE2 A:HIS395 2.1 23.1 1.0
O A:HOH899 2.1 32.4 1.0
O A:HOH926 2.3 29.5 1.0
O A:HOH868 2.8 47.8 1.0
CE1 A:HIS395 3.0 22.9 1.0
CD2 A:HIS395 3.2 22.1 1.0
O A:GLY399 4.0 28.0 1.0
ND1 A:HIS395 4.1 21.3 1.0
CG A:HIS395 4.3 20.1 1.0
CG A:LEU401 4.7 19.5 1.0
CD1 A:LEU401 4.7 20.4 1.0

Zinc binding site 4 out of 5 in 6yn4

Go back to Zinc Binding Sites List in 6yn4
Zinc binding site 4 out of 5 in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn511

b:28.0
occ:0.75
 NE2 A:HIS205 1.9 16.6 1.0
OD1 A:ASP232 1.9 14.3 1.0
O A:HOH918 2.3 35.3 1.0
CE1 A:HIS205 2.7 15.8 1.0
CG A:ASP232 2.8 11.9 1.0
CD2 A:HIS205 3.0 15.9 1.0
OD2 A:ASP232 3.2 11.4 1.0
ND1 A:HIS205 3.8 16.3 1.0
O A:HOH626 3.9 14.4 1.0
CG A:HIS205 3.9 14.6 1.0
CB A:ASP232 4.2 10.9 1.0
NH1 A:ARG190 4.3 10.4 1.0
CA A:ASP232 4.5 10.1 1.0
ZN A:ZN512 4.7 38.1 0.7
O A:HOH901 4.8 41.5 1.0
N A:ASP232 4.9 9.9 1.0

Zinc binding site 5 out of 5 in 6yn4

Go back to Zinc Binding Sites List in 6yn4
Zinc binding site 5 out of 5 in the Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of D169A/E171A Double Mutant of Chitinase CHIT42 From Trichoderma Harzianum Complexed with Chitintetraose. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn512

b:38.1
occ:0.70
 O A:HOH876 2.2 36.4 1.0
ND1 A:HIS205 2.2 16.3 1.0
O A:HOH887 2.7 40.3 1.0
CE1 A:HIS205 2.7 15.8 1.0
O A:HOH785 2.7 38.4 1.0
CG A:HIS205 3.3 14.6 1.0
NE2 A:HIS205 3.8 16.6 1.0
CB A:HIS205 4.0 13.7 1.0
CD2 A:HIS205 4.1 15.9 1.0
OD1 A:ASP194 4.6 19.3 1.0
CA A:HIS205 4.7 12.1 1.0
ZN A:ZN511 4.7 28.0 0.8

Reference:

E.Jimenez-Ortega, P.E.Kidibule, M.Fernandez-Lobato, J.Sanz-Aparicio. Structural Inspection and Protein Motions Modelling of A Fungal Glycoside Hydrolase Family 18 Chitinase By Crystallography Depicts A Dynamic Enzymatic Mechanism Comput Struct Biotechnol J V. 19 5466 2021.
ISSN: ESSN 2001-0370
DOI: 10.1016/J.CSBJ.2021.09.027
Page generated: Fri Nov 5 16:43:13 2021

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