Zinc in PDB 4dwx: Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds

All present enzymatic activity of Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds:
3.2.1.14;

The structure of Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds, PDB code: 4dwx 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)	45.78 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.914, 84.684, 108.815, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.4

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

Zinc binding site 1 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:17.2 occ:1.00 OD2 A:ASP12 2.0 16.8 1.0 O1 A:SO4302 2.0 20.7 1.0 NE2 A:HIS8 2.0 17.9 1.0 CG A:ASP12 2.9 16.1 1.0 CD2 A:HIS8 3.0 17.4 1.0 OD1 A:ASP12 3.0 16.3 1.0 CE1 A:HIS8 3.1 18.9 1.0 S A:SO4302 3.1 21.1 1.0 O2 A:SO4302 3.3 23.4 1.0 O3 A:SO4302 3.6 24.4 1.0 O A:HOH425 3.8 18.6 1.0 CG A:HIS8 4.1 17.3 1.0 ND1 A:HIS8 4.1 18.8 1.0 CB A:ASP12 4.3 14.7 1.0 O4 A:SO4302 4.3 22.8 1.0 O A:HOH608 4.4 39.8 1.0 NH2 A:ARG18 4.4 16.0 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:20.6 occ:1.00 OD1 A:ASP20 2.1 17.0 1.0 ND1 A:HIS17 2.1 15.7 1.0 O A:HOH590 2.2 20.8 1.0 OD2 A:ASP20 2.6 18.5 1.0 CG A:ASP20 2.6 17.2 1.0 CE1 A:HIS17 3.0 14.9 1.0 CG A:HIS17 3.1 16.0 1.0 CB A:HIS17 3.5 16.4 1.0 CA A:HIS17 3.6 15.9 1.0 O A:HOH582 3.8 36.7 1.0 O A:LEU16 4.1 15.2 1.0 CB A:ASP20 4.1 18.3 1.0 NE2 A:HIS17 4.2 18.0 1.0 CD2 A:HIS17 4.2 14.9 1.0 O A:HOH473 4.4 23.2 1.0 N A:HIS17 4.5 14.2 1.0 C A:HIS17 4.5 15.1 1.0 C A:LEU16 4.6 14.7 1.0 O A:HIS17 4.6 16.2 1.0 CA A:ASP20 4.8 20.4 1.0 N A:ASP20 5.0 18.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:12.1 occ:1.00 O A:HOH428 2.1 13.9 1.0 O A:HOH479 2.1 18.6 1.0 NE2 A:HIS121 2.2 9.9 1.0 O A:HOH501 2.5 17.4 1.0 CE1 A:HIS121 3.1 11.7 1.0 CD2 A:HIS121 3.2 10.2 1.0 O A:HOH557 3.9 28.4 1.0 O A:HOH658 4.2 43.2 1.0 ND1 A:HIS121 4.2 11.1 1.0 CD2 A:TYR96 4.3 13.9 1.0 CG A:HIS121 4.3 10.4 1.0 CE2 A:TYR96 4.8 13.5 1.0 CG2 A:THR98 4.8 12.8 1.0 OH A:TYR123 5.0 24.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn307 b:13.2 occ:1.00 O A:HOH532 2.1 14.5 1.0 ND1 A:HIS206 2.1 11.8 1.0 O A:HOH618 2.2 16.8 1.0 O A:HOH554 2.5 23.3 1.0 CE1 A:HIS206 3.0 11.2 1.0 CG A:HIS206 3.2 11.9 1.0 CB A:HIS206 3.5 10.4 1.0 O A:HOH452 4.2 23.8 1.0 NE2 A:HIS206 4.2 11.0 1.0 CD2 A:HIS206 4.3 11.4 1.0 O A:LEU202 4.4 15.0 1.0 O A:GLY201 4.5 14.3 1.0 O A:CYS204 4.5 12.6 1.0 O A:HOH620 4.5 34.6 1.0 CA A:HIS206 4.9 11.0 1.0 C A:LEU202 4.9 13.3 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of A Family Gh-19 Chitinase From Rye Seeds


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:24.3 occ:1.00 OD2 B:ASP12 2.1 19.8 1.0 NE2 B:HIS8 2.1 21.7 1.0 O3 B:SO4302 2.2 30.1 1.0 O B:HOH467 2.2 21.7 1.0 CG B:ASP12 2.8 19.4 1.0 OD1 B:ASP12 2.9 20.2 1.0 CD2 B:HIS8 3.0 20.6 1.0 S B:SO4302 3.1 27.9 1.0 CE1 B:HIS8 3.2 22.6 1.0 O1 B:SO4302 3.3 31.6 1.0 O4 B:SO4302 3.5 29.5 1.0 CG B:HIS8 4.2 20.8 1.0 ND1 B:HIS8 4.3 21.4 1.0 CB B:ASP12 4.3 17.4 1.0 O2 B:SO4302 4.4 31.1 1.0 NH2 B:ARG18 4.4 15.9 1.0 O B:HOH685 4.5 42.7 1.0

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