Zinc in PDB 7bv5: Crystal Structure of the Yeast Heterodimeric ADAT2/3

All present enzymatic activity of Crystal Structure of the Yeast Heterodimeric ADAT2/3:
3.5.4.33;

The structure of Crystal Structure of the Yeast Heterodimeric ADAT2/3, PDB code: 7bv5 was solved by W.Xie, X.Liu, R.Chen, Y.Sun, R.Chen, J.Zhou, Q.Tian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	138.591, 118.543, 91.142, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.5

The binding sites of Zinc atom in the Crystal Structure of the Yeast Heterodimeric ADAT2/3 (pdb code 7bv5). 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 the Yeast Heterodimeric ADAT2/3, PDB code: 7bv5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Yeast Heterodimeric ADAT2/3


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 the Yeast Heterodimeric ADAT2/3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:34.3 occ:1.00 ND1 A:HIS54 1.9 29.0 1.0 O A:HOH416 2.0 25.1 1.0 SG A:CYS91 2.3 34.6 1.0 SG A:CYS88 2.3 30.7 1.0 CE1 A:HIS54 2.7 28.5 1.0 CG A:HIS54 2.9 31.6 1.0 CB A:CYS88 3.3 29.3 1.0 CB A:CYS91 3.4 33.4 1.0 CB A:HIS54 3.4 31.2 1.0 N A:CYS88 3.7 27.1 1.0 NE2 A:HIS54 3.8 28.9 1.0 CD2 A:HIS54 3.9 29.3 1.0 CA A:CYS88 4.1 29.7 1.0 N A:CYS91 4.2 32.2 1.0 CE A:MET90 4.3 32.2 1.0 CA A:CYS91 4.4 31.8 1.0 OE1 A:GLU56 4.4 45.0 1.0 OE2 A:GLU56 4.6 46.9 1.0 O A:CYS88 4.7 31.1 1.0 O A:HOH408 4.7 42.3 1.0 C A:CYS88 4.7 31.4 1.0 CD A:GLU56 4.8 42.8 1.0 C A:PRO87 4.9 26.7 1.0 NE2 C:HIS263 4.9 32.2 1.0 CA A:HIS54 4.9 30.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Yeast Heterodimeric ADAT2/3


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 the Yeast Heterodimeric ADAT2/3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:35.8 occ:1.00 ND1 B:HIS54 1.9 33.2 1.0 O B:HOH412 2.0 22.1 1.0 SG B:CYS88 2.2 25.9 1.0 SG B:CYS91 2.3 33.1 1.0 CE1 B:HIS54 2.8 30.6 1.0 CG B:HIS54 3.0 33.1 1.0 CB B:CYS88 3.4 29.9 1.0 CB B:CYS91 3.4 32.6 1.0 CB B:HIS54 3.4 31.6 1.0 N B:CYS88 3.9 32.9 1.0 NE2 B:HIS54 3.9 32.8 1.0 CD2 B:HIS54 4.0 33.0 1.0 OE1 B:GLU56 4.1 39.4 1.0 CA B:CYS88 4.2 31.1 1.0 N B:CYS91 4.3 31.6 1.0 CE B:MET90 4.3 29.5 1.0 CA B:CYS91 4.4 31.1 1.0 O B:HOH408 4.4 40.4 1.0 CD B:GLU56 4.8 38.1 1.0 C B:CYS88 4.8 30.1 1.0 O B:HOH402 4.9 46.2 1.0 O B:CYS88 4.9 31.1 1.0 OE2 B:GLU56 4.9 37.7 1.0 CA B:HIS54 4.9 31.2 1.0 CE1 D:HIS263 5.0 35.5 1.0 C B:PRO87 5.0 31.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Yeast Heterodimeric ADAT2/3


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 the Yeast Heterodimeric ADAT2/3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:35.2 occ:1.00 ND1 C:HIS216 2.1 35.4 1.0 SG C:CYS254 2.2 36.0 1.0 SG C:CYS322 2.3 43.0 1.0 SG C:CYS257 2.3 31.2 1.0 CE1 C:HIS216 3.0 35.7 1.0 CG C:HIS216 3.1 33.6 1.0 CB C:CYS257 3.4 35.6 1.0 CB C:HIS216 3.4 30.7 1.0 CB C:CYS254 3.5 34.2 1.0 CB C:CYS322 3.7 36.3 1.0 O C:HOH527 3.8 32.2 1.0 CE C:MET256 3.8 33.0 1.0 N C:CYS254 4.0 30.3 1.0 N C:CYS257 4.1 32.8 1.0 NE2 C:HIS216 4.1 41.0 1.0 CD2 C:HIS216 4.2 35.5 1.0 CA C:CYS254 4.3 31.6 1.0 CA C:CYS257 4.3 34.4 1.0 O C:CYS321 4.4 31.6 1.0 CA C:CYS322 4.6 36.5 1.0 C C:CYS321 4.6 33.7 1.0 N C:CYS322 4.7 35.8 1.0 C C:CYS254 4.8 28.0 1.0 O C:CYS254 4.8 24.1 1.0 CA C:HIS216 4.9 28.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Yeast Heterodimeric ADAT2/3


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 the Yeast Heterodimeric ADAT2/3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:36.5 occ:1.00 ND1 D:HIS216 2.1 37.2 1.0 SG D:CYS322 2.2 37.1 1.0 SG D:CYS257 2.3 38.7 1.0 SG D:CYS254 2.3 32.6 1.0 CE1 D:HIS216 3.0 33.9 1.0 CG D:HIS216 3.1 34.4 1.0 CB D:CYS257 3.3 35.5 1.0 CB D:HIS216 3.5 34.2 1.0 CB D:CYS254 3.5 34.5 1.0 CB D:CYS322 3.9 34.3 1.0 N D:CYS254 3.9 36.2 1.0 CE D:MET256 3.9 31.8 1.0 O D:HOH522 4.0 19.6 1.0 N D:CYS257 4.0 30.0 1.0 NE2 D:HIS216 4.1 34.5 1.0 CD2 D:HIS216 4.2 34.3 1.0 CA D:CYS254 4.2 34.6 1.0 CA D:CYS257 4.2 32.7 1.0 O D:CYS321 4.3 31.6 1.0 C D:CYS321 4.6 36.1 1.0 N D:CYS322 4.6 41.0 1.0 C D:CYS254 4.6 33.5 1.0 CA D:CYS322 4.7 36.7 1.0 O D:CYS254 4.7 34.0 1.0 O D:HOH512 4.7 65.2 1.0 CB D:MET256 4.8 32.3 1.0 C D:PRO253 5.0 36.1 1.0

W.Xie, X.Liu, R.Chen, Y.Sun, R.Chen, J.Zhou, Q.Tian. Crystal Structure of the Yeast Heterodimeric ADAT2/3 Bmc Biol. 2020.
ISSN: ESSN 1741-7007