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Zinc in PDB 4dyg: Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4

Enzymatic activity of Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4

All present enzymatic activity of Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4:
3.2.1.14;

Protein crystallography data

The structure of Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4, PDB code: 4dyg was solved by T.Numata, N.Umemoto, T.Ohnuma, T.Fukamizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.69 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.695, 85.387, 108.364, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 (pdb code 4dyg). 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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4, PDB code: 4dyg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 4dyg

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Zinc binding site 1 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4


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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:18.2
occ:1.00
 OD2 A:ASP12 2.0 19.3 1.0
O1 A:SO4306 2.0 20.1 1.0
NE2 A:HIS8 2.1 20.4 1.0
CG A:ASP12 2.8 17.7 1.0
CD2 A:HIS8 3.0 20.5 1.0
OD1 A:ASP12 3.1 18.3 1.0
S A:SO4306 3.1 19.9 1.0
CE1 A:HIS8 3.1 22.5 1.0
O2 A:SO4306 3.3 22.0 1.0
O3 A:SO4306 3.6 23.3 1.0
O A:HOH432 3.7 19.5 1.0
CG A:HIS8 4.1 20.6 1.0
ND1 A:HIS8 4.2 21.7 1.0
CB A:ASP12 4.3 16.8 1.0
O4 A:SO4306 4.3 20.4 1.0
NH2 A:ARG18 4.5 15.7 1.0
O A:HIS8 5.0 18.6 1.0

Zinc binding site 2 out of 5 in 4dyg

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Zinc binding site 2 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4


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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:19.5
occ:1.00
 ND1 A:HIS17 2.0 16.0 1.0
OD1 A:ASP20 2.1 19.4 1.0
O A:HOH600 2.2 21.2 1.0
OD2 A:ASP20 2.6 20.2 1.0
CG A:ASP20 2.6 19.1 1.0
CE1 A:HIS17 2.9 14.4 1.0
CG A:HIS17 3.1 14.8 1.0
CB A:HIS17 3.6 16.1 1.0
CA A:HIS17 3.6 15.7 1.0
O A:HOH625 3.7 33.9 1.0
NE2 A:HIS17 4.1 17.0 1.0
CB A:ASP20 4.1 20.4 1.0
O A:LEU16 4.1 15.1 1.0
CD2 A:HIS17 4.2 15.3 1.0
O A:HOH438 4.4 24.2 1.0
N A:HIS17 4.5 15.6 1.0
C A:HIS17 4.6 15.8 1.0
O A:HIS17 4.6 16.1 1.0
C A:LEU16 4.7 15.5 1.0
CA A:ASP20 4.8 21.4 1.0
N A:ASP20 5.0 20.4 1.0

Zinc binding site 3 out of 5 in 4dyg

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Zinc binding site 3 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4


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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn310

b:14.0
occ:1.00
 O A:HOH506 2.1 16.4 1.0
NE2 A:HIS121 2.1 12.4 1.0
O A:HOH516 2.2 17.7 1.0
O A:HOH598 2.5 19.2 1.0
CE1 A:HIS121 3.0 13.7 1.0
CD2 A:HIS121 3.2 11.8 1.0
O A:HOH667 4.0 34.4 1.0
ND1 A:HIS121 4.2 14.1 1.0
CD2 A:TYR96 4.3 16.1 1.0
CG A:HIS121 4.3 11.1 1.0
CE2 A:TYR96 4.7 16.8 1.0
OH A:TYR123 4.9 25.5 1.0
CG2 A:THR98 4.9 14.2 1.0

Zinc binding site 4 out of 5 in 4dyg

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Zinc binding site 4 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4


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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:15.1
occ:1.00
 O A:HOH541 2.1 16.7 1.0
ND1 A:HIS206 2.1 14.6 1.0
O A:HOH581 2.2 17.2 1.0
O A:HOH492 2.5 23.2 1.0
CE1 A:HIS206 3.0 14.2 1.0
CG A:HIS206 3.2 14.9 1.0
CB A:HIS206 3.6 12.6 1.0
O A:HOH570 3.9 30.0 1.0
O A:HOH450 4.1 28.1 1.0
NE2 A:HIS206 4.2 14.1 1.0
CD2 A:HIS206 4.3 13.9 1.0
O A:LEU202 4.3 16.9 1.0
O A:GLY201 4.4 18.1 1.0
O A:CYS204 4.5 13.9 1.0
O A:HOH702 4.6 47.6 1.0
C A:LEU202 4.8 16.4 1.0
CA A:HIS206 4.9 13.6 1.0

Zinc binding site 5 out of 5 in 4dyg

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Zinc binding site 5 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4


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 A Family Gh-19 Chitinase From Rye Seeds in Complex with (Glcnac)4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:25.1
occ:1.00
 OD2 B:ASP12 2.1 24.2 1.0
NE2 B:HIS8 2.1 23.8 1.0
O B:HOH618 2.2 22.1 1.0
O3 B:SO4306 2.2 36.8 1.0
CG B:ASP12 2.9 23.5 1.0
OD1 B:ASP12 3.0 22.8 1.0
S B:SO4306 3.0 34.7 1.0
CD2 B:HIS8 3.1 22.1 1.0
CE1 B:HIS8 3.1 23.7 1.0
O1 B:SO4306 3.2 38.6 1.0
O4 B:SO4306 3.3 35.6 1.0
O B:HOH541 3.9 39.2 1.0
O B:HOH656 4.1 37.9 1.0
ND1 B:HIS8 4.2 23.0 1.0
CG B:HIS8 4.2 21.8 1.0
CB B:ASP12 4.3 20.6 1.0
NH2 B:ARG18 4.3 19.8 1.0
O2 B:SO4306 4.4 38.6 1.0

Reference:

T.Ohnuma, T.Numata, T.Osawa, H.Inanaga, Y.Okazaki, S.Shinya, K.Kondo, T.Fukuda, T.Fukamizo. Crystal Structure and Chitin Oligosaccharide-Binding Mode of A 'Loopful' Family GH19 Chitinase From Rye, Secale Cereale, Seeds Febs J. V. 279 3639 2012.
ISSN: ISSN 1742-464X
PubMed: 22831795
DOI: 10.1111/J.1742-4658.2012.08723.X
Page generated: Sat Oct 26 21:43:26 2024

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