Zinc in PDB 9ay8: Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii

The structure of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii, PDB code: 9ay8 was solved by L.J.Worrall, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.44 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	102.685, 164.568, 131.645, 90, 90.3, 90
R / Rfree (%)	16.8 / 19.3

The structure of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii also contains other interesting chemical elements:

Manganese	(Mn)	5 atoms
Cobalt	(Co)	5 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Zinc atom in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii (pdb code 9ay8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii, PDB code: 9ay8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:31.2 occ:1.00 NE2 A:HIS478 2.0 28.1 1.0 ND1 A:HIS476 2.1 33.9 1.0 SG A:CYS471 2.3 31.5 1.0 SG A:CYS434 2.3 31.0 1.0 CE1 A:HIS478 2.9 29.4 1.0 CE1 A:HIS476 3.1 35.7 1.0 CD2 A:HIS478 3.1 31.0 1.0 CB A:CYS471 3.1 30.4 1.0 CG A:HIS476 3.1 36.1 1.0 CB A:CYS434 3.3 30.5 1.0 CB A:HIS476 3.5 37.3 1.0 O A:HOH1359 3.6 42.3 1.0 ND1 A:HIS478 4.1 29.9 1.0 CG A:HIS478 4.2 31.3 1.0 NE2 A:HIS476 4.2 37.0 1.0 CD2 A:HIS476 4.3 36.2 1.0 CA A:CYS471 4.5 30.9 1.0 CA A:CYS434 4.6 30.8 1.0 O A:PHE407 4.7 30.5 1.0 CB A:ASN473 4.8 34.4 1.0 CA A:VAL408 4.9 26.6 1.0 C A:CYS471 4.9 33.0 1.0 CB A:SER484 5.0 28.0 1.0

Zinc binding site 2 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:28.5 occ:1.00 NE2 B:HIS478 2.0 27.0 1.0 ND1 B:HIS476 2.0 30.3 1.0 SG B:CYS434 2.3 30.4 1.0 SG B:CYS471 2.3 30.0 1.0 CE1 B:HIS478 3.0 28.1 1.0 CE1 B:HIS476 3.0 31.5 1.0 CG B:HIS476 3.0 33.3 1.0 CD2 B:HIS478 3.1 29.1 1.0 CB B:CYS471 3.2 27.7 1.0 CB B:CYS434 3.3 30.1 1.0 CB B:HIS476 3.4 33.6 1.0 O B:HOH1413 3.8 37.3 1.0 NE2 B:HIS476 4.1 33.8 1.0 ND1 B:HIS478 4.1 26.4 1.0 CD2 B:HIS476 4.2 32.3 1.0 CG B:HIS478 4.2 29.2 1.0 CA B:CYS471 4.6 29.5 1.0 CA B:CYS434 4.6 27.2 1.0 O B:PHE407 4.7 27.9 1.0 CB B:ASN473 4.7 36.0 1.0 CA B:VAL408 4.9 29.2 1.0 CA B:HIS476 5.0 33.7 1.0 C B:CYS471 5.0 30.9 1.0

Zinc binding site 3 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn701 b:32.7 occ:1.00 NE2 C:HIS478 2.0 31.2 1.0 ND1 C:HIS476 2.1 38.5 1.0 SG C:CYS471 2.3 33.0 1.0 SG C:CYS434 2.3 30.8 1.0 CE1 C:HIS478 2.9 35.2 1.0 CE1 C:HIS476 3.0 38.1 1.0 CD2 C:HIS478 3.1 35.3 1.0 CG C:HIS476 3.1 34.9 1.0 CB C:CYS471 3.1 34.9 1.0 CB C:CYS434 3.2 33.2 1.0 CB C:HIS476 3.4 36.7 1.0 O C:HOH1196 3.8 47.6 1.0 ND1 C:HIS478 4.1 32.4 1.0 NE2 C:HIS476 4.1 35.8 1.0 CG C:HIS478 4.2 35.5 1.0 CD2 C:HIS476 4.2 37.5 1.0 CA C:CYS471 4.6 34.7 1.0 CA C:CYS434 4.6 29.4 1.0 O C:PHE407 4.7 30.2 1.0 CB C:ASN473 4.8 37.0 1.0 CA C:VAL408 4.9 32.7 1.0 CB C:SER484 5.0 28.3 1.0 C C:CYS471 5.0 38.1 1.0 CA C:HIS476 5.0 37.6 1.0

Zinc binding site 4 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn701 b:31.3 occ:1.00 NE2 D:HIS478 1.9 30.2 1.0 ND1 D:HIS476 2.1 38.2 1.0 SG D:CYS434 2.3 31.2 1.0 SG D:CYS471 2.3 31.2 1.0 CE1 D:HIS478 2.9 31.4 1.0 CD2 D:HIS478 3.0 33.1 1.0 CB D:CYS471 3.1 30.1 1.0 CE1 D:HIS476 3.1 43.3 1.0 CG D:HIS476 3.1 46.4 1.0 CB D:CYS434 3.3 31.3 1.0 CB D:HIS476 3.5 41.8 1.0 ND1 D:HIS478 4.1 30.1 1.0 CG D:HIS478 4.1 33.0 1.0 NE2 D:HIS476 4.2 45.4 1.0 CD2 D:HIS476 4.2 45.3 1.0 CA D:CYS471 4.5 32.5 1.0 CA D:CYS434 4.6 29.9 1.0 O D:PHE407 4.8 32.0 1.0 CB D:ASN473 4.8 41.0 1.0 CB D:SER484 4.9 28.7 1.0 C D:CYS471 4.9 34.4 1.0 CA D:VAL408 4.9 30.3 1.0

Zinc binding site 5 out of 5 in the Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the A Type Blood Alpha-D-Galactosamine Galactosaminidase From Flavonifractor Plautii within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn701 b:33.8 occ:1.00 NE2 E:HIS478 1.9 31.1 1.0 ND1 E:HIS476 2.1 36.5 1.0 SG E:CYS471 2.3 36.7 1.0 SG E:CYS434 2.4 31.4 1.0 CE1 E:HIS478 2.9 35.9 1.0 CD2 E:HIS478 3.0 35.7 1.0 CE1 E:HIS476 3.1 36.8 1.0 CB E:CYS471 3.1 35.0 1.0 CG E:HIS476 3.1 38.7 1.0 CB E:CYS434 3.3 31.4 1.0 CB E:HIS476 3.5 40.7 1.0 O E:HOH1316 3.8 45.4 1.0 ND1 E:HIS478 4.0 34.1 1.0 CG E:HIS478 4.1 36.5 1.0 NE2 E:HIS476 4.2 38.8 1.0 CD2 E:HIS476 4.2 39.4 1.0 CA E:CYS471 4.5 35.3 1.0 CA E:CYS434 4.7 30.9 1.0 O E:PHE407 4.7 33.7 1.0 CB E:ASN473 4.8 41.8 1.0 C E:CYS471 4.9 35.5 1.0 CA E:VAL408 4.9 34.7 1.0 CB E:SER484 4.9 31.8 1.0

Y.Tian, L.J.Worrall, L.Sim, F.Liu, S.A.Nasseri, P.Rahfeld, W.Mu, J.N.Kizhakkedathu, N.C.J.Strynadka, S.G.Withers. Cobalt As A Cofactor For Alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens Acs Catalysis 2024.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.4C03643