Zinc in PDB 5ylg: Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A

The structure of Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A, PDB code: 5ylg was solved by T.Ohnuma, Y.Kitaoku, N.Umemoto, T.Numata, T.Fukamizo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.18 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.839, 50.125, 92.362, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22

The binding sites of Zinc atom in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A (pdb code 5ylg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A, PDB code: 5ylg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A


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 Lysm Domain From Pteris Ryukyuensis Chitinase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:10.8 occ:1.00 OD2 A:ASP26 1.9 11.5 1.0 OE1 C:GLU28 2.0 11.1 1.0 CD C:GLU28 2.6 11.3 1.0 OE2 C:GLU28 2.7 11.7 1.0 CG A:ASP26 2.8 10.0 1.0 OD1 A:ASP26 3.0 11.7 1.0 O A:HOH213 3.8 15.8 1.0 OG A:SER23 4.0 10.2 1.0 CG C:GLU28 4.1 10.8 1.0 CB A:ASP26 4.2 10.9 1.0 O C:HOH204 4.3 17.0 1.0 OG C:SER25 4.4 19.6 0.8 CB C:GLU28 4.7 10.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A


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 Lysm Domain From Pteris Ryukyuensis Chitinase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:11.3 occ:1.00 OD1 A:ASN37 1.8 9.8 1.0 OD1 B:ASP26 2.0 10.7 1.0 OD2 A:ASP35 2.1 11.6 1.0 OE1 D:GLU28 2.1 9.9 1.0 CG B:ASP26 2.6 11.4 1.0 CD D:GLU28 2.7 11.0 1.0 OD2 B:ASP26 2.7 12.0 1.0 CG A:ASP35 2.7 9.9 1.0 OE2 D:GLU28 2.8 11.3 1.0 OD1 A:ASP35 2.8 11.6 1.0 CG A:ASN37 2.9 12.0 1.0 ND2 A:ASN37 3.2 14.2 1.0 O B:HOH119 4.0 24.3 1.0 CB A:ASP35 4.1 9.9 1.0 CB B:ASP26 4.1 10.7 1.0 CB A:ASN38 4.1 11.8 1.0 CG D:GLU28 4.2 10.5 1.0 CB A:ASN37 4.2 10.5 1.0 O A:HOH203 4.3 16.6 1.0 OG B:SER23 4.5 10.9 1.0 C A:ASN37 4.5 10.3 1.0 N A:ASN38 4.6 9.4 1.0 CA A:ASN37 4.7 9.4 1.0 CD2 D:LEU24 4.7 12.4 1.0 N A:ASN37 4.7 9.0 1.0 CA D:SER25 4.7 11.6 1.0 CB D:SER25 4.7 12.8 1.0 CG D:LEU24 4.8 10.7 1.0 O B:HOH107 4.8 15.4 1.0 CB D:GLU28 4.8 11.7 1.0 O A:ASN37 4.9 9.6 1.0 CA B:ASP26 5.0 10.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A


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 Lysm Domain From Pteris Ryukyuensis Chitinase A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:10.6 occ:1.00 OE1 A:GLU28 1.8 8.2 1.0 OD2 C:ASP35 2.0 8.6 1.0 OD2 D:ASP26 2.0 11.9 1.0 OD1 C:ASN37 2.2 10.0 1.0 CD A:GLU28 2.4 11.7 1.0 OE2 A:GLU28 2.5 12.4 1.0 CG C:ASP35 2.6 9.3 1.0 OD1 C:ASP35 2.7 9.8 1.0 CG D:ASP26 2.9 13.1 1.0 CG C:ASN37 3.0 9.8 1.0 OD1 D:ASP26 3.2 14.3 1.0 ND2 C:ASN37 3.3 10.5 1.0 CG A:GLU28 4.0 10.2 1.0 OG D:SER23 4.0 14.6 0.5 CB C:ASN38 4.1 10.7 1.0 N D:SER23 4.1 11.7 1.0 CB C:ASP35 4.1 9.4 1.0 CB D:ASP26 4.2 11.2 1.0 O A:HOH206 4.3 16.1 1.0 O C:HOH216 4.4 13.4 1.0 CB C:ASN37 4.4 10.6 1.0 N C:ASN38 4.4 9.9 1.0 CA D:ILE22 4.4 15.9 1.0 CB D:ILE22 4.5 16.1 1.0 C C:ASN37 4.6 11.4 1.0 CB D:SER23 4.6 11.8 0.5 CB A:GLU28 4.7 9.5 1.0 CB D:SER23 4.7 13.5 0.5 CG2 D:ILE22 4.8 17.6 1.0 C D:ILE22 4.8 13.7 1.0 CA C:ASN37 4.9 10.3 1.0 N C:ASN37 4.9 10.0 1.0 CA D:SER23 5.0 11.4 0.5 CA C:ASN38 5.0 9.5 1.0 O C:ASN37 5.0 11.6 1.0

Y.Kitaoku, N.Umemoto, T.Taira, T.Fukamizo, T.Numata, T.Ohnuma. Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A To Be Published.