Zinc in PDB 4pxv: 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: 4pxv was solved by T.Ohnuma, 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)	46.15 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.686, 50.229, 92.292, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 22.9

The binding sites of Zinc atom in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A (pdb code 4pxv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A, PDB code: 4pxv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 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:12.9 occ:1.00 OD1 A:ASN37 2.0 8.6 1.0 OD1 C:ASP26 2.0 8.9 1.0 OD2 A:ASP35 2.0 9.4 1.0 OE1 B:GLU28 2.0 8.6 1.0 OE2 B:GLU28 2.6 8.6 1.0 CD B:GLU28 2.7 8.7 1.0 OD1 A:ASP35 2.7 9.6 1.0 CG A:ASP35 2.7 9.4 1.0 CG C:ASP26 2.7 8.9 1.0 OD2 C:ASP26 2.8 9.0 1.0 CG A:ASN37 2.9 9.3 1.0 ND2 A:ASN37 3.3 9.3 1.0 CG B:GLU28 4.1 8.8 1.0 CB A:ASP35 4.1 9.6 1.0 CB A:ASN38 4.2 10.6 1.0 O C:HOH114 4.2 21.7 1.0 CB C:ASP26 4.2 9.0 1.0 O A:HOH211 4.3 13.0 1.0 CB A:ASN37 4.3 9.2 1.0 OG C:SER23 4.4 9.5 1.0 C A:ASN37 4.6 9.5 1.0 N A:ASN38 4.6 9.8 1.0 CA B:SER25 4.7 9.7 1.0 CD2 B:LEU24 4.7 10.6 1.0 CG B:LEU24 4.7 10.4 1.0 CA A:ASN37 4.8 9.3 1.0 CB B:GLU28 4.8 9.0 1.0 CB B:SER25 4.8 10.1 1.0 O C:HOH116 4.8 15.0 1.0 N A:ASN37 4.8 9.3 1.0 N B:SER25 4.9 9.5 1.0 CA C:ASP26 4.9 9.0 1.0 O A:ASN37 4.9 9.3 1.0

Zinc binding site 2 out of 4 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:13.8 occ:1.00 OD2 A:ASP26 1.9 9.3 1.0 OE1 D:GLU28 2.0 11.0 1.0 CD D:GLU28 2.6 11.1 1.0 OE2 D:GLU28 2.7 11.1 1.0 CG A:ASP26 2.8 8.8 1.0 OD1 A:ASP26 2.9 9.6 1.0 O A:HOH208 3.7 18.1 1.0 CG D:GLU28 4.1 10.9 1.0 OG A:SER23 4.1 9.4 1.0 CB A:ASP26 4.2 8.6 1.0 O A:HOH207 4.3 15.3 1.0 O A:HOH221 4.3 18.3 1.0 OG D:SER25 4.5 15.2 1.0 CB D:GLU28 4.7 11.0 1.0

Zinc binding site 3 out of 4 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 B:Zn101 b:34.1 occ:1.00 OD2 B:ASP35 2.1 11.4 1.0 OE2 C:GLU28 2.2 14.3 1.0 OE1 C:GLU28 2.6 15.0 1.0 CD C:GLU28 2.7 13.7 1.0 CG B:ASP35 2.9 10.6 1.0 OD1 B:ASP35 3.0 10.3 1.0 CG C:GLU28 4.2 13.0 1.0 CB B:ASP35 4.3 10.1 1.0 O B:HOH220 4.4 28.8 1.0 CD2 C:LEU24 4.5 10.2 1.0 ND2 B:ASN37 4.6 15.8 1.0 CG C:LEU24 4.6 9.9 1.0 CB B:ASN37 4.7 14.3 1.0

Zinc binding site 4 out of 4 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 4 of Crystal Structure of Lysm Domain From Pteris Ryukyuensis Chitinase A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:12.2 occ:1.00 OD2 D:ASP35 1.9 8.6 1.0 OD2 B:ASP26 1.9 10.2 1.0 OE1 A:GLU28 2.0 8.9 1.0 OD1 D:ASN37 2.1 9.1 1.0 OE2 A:GLU28 2.5 9.6 1.0 CG D:ASP35 2.6 8.9 1.0 CD A:GLU28 2.6 8.9 1.0 OD1 D:ASP35 2.7 8.9 1.0 CG B:ASP26 2.9 9.7 1.0 CG D:ASN37 3.0 9.4 1.0 OD1 B:ASP26 3.2 10.0 1.0 ND2 D:ASN37 3.3 9.5 1.0 CB D:ASN38 4.0 11.0 1.0 CB D:ASP35 4.1 8.8 1.0 CG A:GLU28 4.1 8.8 1.0 N B:SER23 4.2 11.6 1.0 CB B:ASP26 4.2 9.5 1.0 O A:HOH213 4.2 20.0 1.0 O D:HOH212 4.3 13.2 1.0 CB D:ASN37 4.4 9.7 1.0 N D:ASN38 4.4 10.3 1.0 C D:ASN37 4.5 10.1 1.0 CA B:ILE22 4.6 13.0 1.0 CB B:ILE22 4.6 13.0 1.0 CB B:SER23 4.7 12.1 1.0 CB A:GLU28 4.7 8.7 1.0 CA D:ASN37 4.8 9.8 1.0 CG2 B:ILE22 4.9 13.4 1.0 CA D:ASN38 4.9 10.6 1.0 C B:ILE22 4.9 12.2 1.0 O D:ASN37 4.9 10.1 1.0 N D:ASN37 4.9 9.8 1.0

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