Zinc in PDB 5zru: Crystal Structure of Agl-Ka Catalytic Domain

The structure of Crystal Structure of Agl-Ka Catalytic Domain, PDB code: 5zru was solved by S.Yano, K.Makabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.247, 126.423, 80.540, 90.00, 97.83, 90.00
R / Rfree (%)	14.1 / 17.1

The structure of Crystal Structure of Agl-Ka Catalytic Domain also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Zinc atom in the Crystal Structure of Agl-Ka Catalytic Domain (pdb code 5zru). 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 Agl-Ka Catalytic Domain, PDB code: 5zru:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Agl-Ka Catalytic Domain


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 Agl-Ka Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:13.9 occ:1.00 OD2 A:ASP275 2.0 14.0 1.0 NE2 A:HIS0 2.1 15.6 1.0 NE2 A:HIS309 2.1 10.0 1.0 O A:HOH1121 2.1 14.6 1.0 CE1 A:HIS0 2.6 25.7 1.0 OD1 A:ASP275 2.6 14.7 1.0 CG A:ASP275 2.6 13.9 1.0 CE1 A:HIS309 3.0 9.7 1.0 CD2 A:HIS309 3.1 9.7 1.0 CD2 A:HIS0 3.3 22.4 1.0 O A:HOH798 3.9 11.6 1.0 ND1 A:HIS0 3.9 26.7 1.0 O A:HOH1175 3.9 21.4 1.0 OG A:SER277 4.0 9.2 1.0 CB A:ASP275 4.1 9.7 1.0 ND1 A:HIS309 4.2 10.8 1.0 CG A:HIS309 4.2 10.5 1.0 CG A:HIS0 4.2 24.4 1.0 CB A:SER277 4.3 10.3 1.0 OD1 A:ASN2 4.3 14.1 1.0 ND2 A:ASN2 4.5 15.5 1.0 CG A:ASN2 4.8 16.6 1.0 O A:HOH1106 4.9 30.6 1.0 O A:HOH1216 4.9 31.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Agl-Ka Catalytic Domain


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 Agl-Ka Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:19.6 occ:1.00 OE2 A:GLU291 2.0 21.5 1.0 NE2 A:HIS120 2.1 13.5 1.0 O A:HOH1166 2.4 27.3 1.0 CD A:GLU291 2.8 27.4 1.0 OE1 A:GLU291 2.9 33.0 1.0 CD2 A:HIS120 3.0 15.0 1.0 CE1 A:HIS120 3.1 14.0 1.0 ND1 A:HIS120 4.2 11.8 1.0 CG A:HIS120 4.2 11.3 1.0 O A:HOH1171 4.2 36.6 1.0 CG A:GLU291 4.3 24.5 1.0 O A:GLY290 4.8 30.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Agl-Ka Catalytic Domain


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 Agl-Ka Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn604 b:16.0 occ:1.00 OD2 C:ASP275 2.0 16.0 1.0 NE2 C:HIS309 2.1 12.6 1.0 NE2 C:HIS0 2.1 21.6 1.0 O C:HOH1097 2.1 19.3 1.0 CG C:ASP275 2.7 15.9 1.0 OD1 C:ASP275 2.7 19.8 1.0 CE1 C:HIS0 2.8 30.7 1.0 CE1 C:HIS309 3.0 12.5 1.0 CD2 C:HIS309 3.1 12.1 1.0 CD2 C:HIS0 3.3 27.5 1.0 O C:HOH812 3.8 12.4 1.0 O C:HOH1214 3.9 21.3 1.0 OG C:SER277 4.0 11.7 1.0 ND1 C:HIS0 4.0 33.8 1.0 ND1 C:HIS309 4.1 13.4 1.0 CB C:ASP275 4.2 10.1 1.0 CG C:HIS309 4.2 10.7 1.0 CB C:SER277 4.3 10.8 1.0 OD1 C:ASN2 4.3 18.1 1.0 CG C:HIS0 4.3 27.6 1.0 ND2 C:ASN2 4.5 15.3 1.0 O C:HOH1223 4.5 36.0 1.0 CG C:ASN2 4.8 17.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Agl-Ka Catalytic Domain


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 Agl-Ka Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn605 b:19.3 occ:1.00 OE1 C:GLU291 2.0 23.4 1.0 NE2 C:HIS120 2.1 13.5 1.0 O C:HOH1181 2.3 25.1 1.0 CD C:GLU291 2.9 31.2 1.0 CD2 C:HIS120 3.0 13.4 1.0 CE1 C:HIS120 3.1 13.7 1.0 OE2 C:GLU291 3.1 37.4 1.0 ND1 C:HIS120 4.2 12.1 1.0 CG C:HIS120 4.2 12.7 1.0 CG C:GLU291 4.3 26.7 1.0 O C:GLY290 4.8 35.9 1.0

S.Yano, K.Makabe. Crystal Structure of Alpha-1,3-Glucanase To Be Published.