Zinc in PDB 8yt1: Crystal Structure of Acmsd in Complex with Malonate

The structure of Crystal Structure of Acmsd in Complex with Malonate, PDB code: 8yt1 was solved by Y.Yang, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.05 / 2.22
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	104.278, 152.024, 153.858, 90, 90, 90
R / Rfree (%)	20.8 / 25.9

The binding sites of Zinc atom in the Crystal Structure of Acmsd in Complex with Malonate (pdb code 8yt1). 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 Acmsd in Complex with Malonate, PDB code: 8yt1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Acmsd in Complex with Malonate


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 Acmsd in Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.9 occ:1.00 NE2 A:HIS9 2.2 36.9 1.0 NE2 A:HIS11 2.2 45.5 1.0 O A:HOH532 2.3 46.6 1.0 OD1 A:ASP294 2.3 46.0 1.0 NE2 A:HIS177 2.4 39.2 1.0 CD2 A:HIS177 3.0 35.9 1.0 CG A:ASP294 3.0 45.7 1.0 CE1 A:HIS9 3.1 38.3 1.0 CD2 A:HIS11 3.1 43.7 1.0 OD2 A:ASP294 3.1 48.1 1.0 CD2 A:HIS9 3.3 35.8 1.0 CE1 A:HIS11 3.3 45.8 1.0 CE1 A:HIS177 3.6 41.1 1.0 NE2 A:HIS228 4.1 44.9 1.0 CE1 A:HIS228 4.2 46.5 1.0 ND1 A:HIS9 4.3 37.1 1.0 CG A:HIS177 4.3 37.6 1.0 CG A:HIS11 4.3 48.0 1.0 CB A:ASP294 4.3 45.3 1.0 ND1 A:HIS11 4.4 46.8 1.0 CG A:HIS9 4.4 43.4 1.0 ND1 A:HIS177 4.5 38.5 1.0 CA A:ASP294 4.6 40.5 1.0 O A:HOH568 4.6 59.6 1.0 C2 A:MLA402 4.7 54.2 0.8 O1A A:MLA402 4.9 52.9 0.8

Zinc binding site 2 out of 3 in the Crystal Structure of Acmsd in Complex with Malonate


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 Acmsd in Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:46.2 occ:1.00 NE2 B:HIS11 2.2 52.5 1.0 NE2 B:HIS177 2.3 46.7 1.0 NE2 B:HIS9 2.4 42.8 1.0 O B:HOH550 2.4 53.2 1.0 OD1 B:ASP294 2.5 45.2 1.0 CD2 B:HIS177 3.0 40.4 1.0 CD2 B:HIS11 3.1 46.7 1.0 CG B:ASP294 3.1 44.9 1.0 OD2 B:ASP294 3.2 48.1 1.0 CE1 B:HIS11 3.2 48.2 1.0 CD2 B:HIS9 3.3 44.8 1.0 CE1 B:HIS9 3.3 45.7 1.0 CE1 B:HIS177 3.5 46.9 1.0 NE2 B:HIS228 4.1 46.4 1.0 CG B:HIS11 4.2 50.0 1.0 ND1 B:HIS11 4.3 52.6 1.0 CG B:HIS177 4.3 49.3 1.0 CE1 B:HIS228 4.4 46.2 1.0 ND1 B:HIS9 4.4 47.5 1.0 CB B:ASP294 4.5 46.8 1.0 CG B:HIS9 4.5 44.4 1.0 ND1 B:HIS177 4.5 49.0 1.0 CA B:ASP294 4.7 43.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Acmsd in Complex with Malonate


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 Acmsd in Complex with Malonate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:53.4 occ:1.00 OD1 C:ASP294 2.2 54.7 1.0 NE2 C:HIS177 2.3 51.9 1.0 NE2 C:HIS11 2.4 56.6 1.0 NE2 C:HIS9 2.5 56.3 1.0 O C:HOH520 2.7 62.0 1.0 CG C:ASP294 2.9 52.3 1.0 CD2 C:HIS11 3.0 53.1 1.0 OD2 C:ASP294 3.0 58.9 1.0 CD2 C:HIS177 3.1 51.3 1.0 CE1 C:HIS9 3.3 53.4 1.0 CD2 C:HIS9 3.4 57.9 1.0 CE1 C:HIS177 3.5 55.6 1.0 CE1 C:HIS11 3.6 59.3 1.0 NE2 C:HIS228 4.1 52.5 1.0 CG C:HIS11 4.2 58.0 1.0 CB C:ASP294 4.3 52.4 1.0 CG C:HIS177 4.4 54.3 1.0 CE1 C:HIS228 4.4 54.3 1.0 O C:HOH560 4.4 64.8 1.0 ND1 C:HIS9 4.4 54.5 1.0 CG C:HIS9 4.5 55.8 1.0 ND1 C:HIS177 4.5 51.6 1.0 ND1 C:HIS11 4.5 59.6 1.0 CA C:ASP294 4.7 55.5 1.0

Y.Yang, A.Liu. Crystal Structure of Acmsd in Complex with Oxaloacetic Acid To Be Published.