Zinc in PDB 3spd: Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna

The structure of Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna, PDB code: 3spd was solved by Y.Gong, D.Zhu, J.Ding, C.Dou, X.Ren, T.Jiang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.50 / 1.91
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	220.409, 220.409, 135.031, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 21.1

The binding sites of Zinc atom in the Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna (pdb code 3spd). 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 Aprataxin Ortholog HNT3 in Complex with Dna, PDB code: 3spd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna


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 Aprataxin Ortholog HNT3 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:25.9 occ:1.00 OE2 A:GLU221 2.0 24.6 1.0 NE2 A:HIS217 2.1 25.5 1.0 SG A:CYS200 2.3 20.1 1.0 SG A:CYS203 2.4 27.2 1.0 CD A:GLU221 3.0 25.8 1.0 CD2 A:HIS217 3.1 23.0 1.0 CE1 A:HIS217 3.1 29.9 1.0 CB A:CYS203 3.1 26.0 1.0 CB A:CYS200 3.1 22.9 1.0 CG A:GLU221 3.2 21.3 1.0 N A:CYS203 3.6 27.3 1.0 CA A:CYS203 3.9 25.5 1.0 OE1 A:GLU221 4.1 25.8 1.0 ND1 A:HIS217 4.2 28.8 1.0 CG A:HIS217 4.2 25.6 1.0 C A:CYS203 4.5 28.9 1.0 C A:ARG202 4.6 30.8 1.0 CA A:CYS200 4.6 22.4 1.0 N A:GLY204 4.6 27.1 1.0 CB A:ARG202 4.6 25.8 1.0 CB A:GLU205 4.6 29.6 1.0 CB A:GLU221 4.7 24.3 1.0 N A:ARG202 4.9 25.3 1.0 N A:GLU205 4.9 31.4 1.0 CA A:ARG202 4.9 25.2 1.0 OE1 A:GLU205 4.9 32.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna


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 Aprataxin Ortholog HNT3 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:26.5 occ:1.00 OE2 B:GLU221 2.0 24.9 1.0 NE2 B:HIS217 2.1 25.9 1.0 SG B:CYS200 2.3 22.3 1.0 SG B:CYS203 2.4 27.8 1.0 CD B:GLU221 2.9 25.0 1.0 CD2 B:HIS217 3.1 24.8 1.0 CB B:CYS203 3.1 26.6 1.0 CE1 B:HIS217 3.1 31.1 1.0 CB B:CYS200 3.1 22.4 1.0 CG B:GLU221 3.2 22.2 1.0 N B:CYS203 3.6 25.7 1.0 CA B:CYS203 3.9 25.0 1.0 OE1 B:GLU221 4.1 26.4 1.0 ND1 B:HIS217 4.2 28.2 1.0 CG B:HIS217 4.2 25.3 1.0 C B:CYS203 4.5 29.2 1.0 C B:ARG202 4.6 29.9 1.0 CA B:CYS200 4.6 24.0 1.0 N B:GLY204 4.6 28.6 1.0 CB B:ARG202 4.6 25.8 1.0 CB B:GLU221 4.7 24.2 1.0 CB B:GLU205 4.7 30.8 1.0 O B:HOH901 4.8 36.8 1.0 N B:GLU205 4.9 29.7 1.0 N B:ARG202 4.9 24.6 1.0 CA B:ARG202 4.9 25.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna


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 Aprataxin Ortholog HNT3 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn601 b:26.5 occ:1.00 OE2 C:GLU221 2.0 25.2 1.0 NE2 C:HIS217 2.1 27.1 1.0 SG C:CYS200 2.3 20.7 1.0 SG C:CYS203 2.4 27.6 1.0 CD C:GLU221 2.9 26.6 1.0 CD2 C:HIS217 3.1 26.1 1.0 CE1 C:HIS217 3.1 31.1 1.0 CB C:CYS203 3.1 28.4 1.0 CB C:CYS200 3.2 24.2 1.0 CG C:GLU221 3.2 21.9 1.0 N C:CYS203 3.6 27.1 1.0 CA C:CYS203 3.9 23.6 1.0 OE1 C:GLU221 4.1 24.7 1.0 ND1 C:HIS217 4.2 31.2 1.0 CG C:HIS217 4.2 26.8 1.0 C C:CYS203 4.5 29.7 1.0 C C:ARG202 4.6 30.0 1.0 CA C:CYS200 4.6 24.5 1.0 N C:GLY204 4.6 29.3 1.0 CB C:ARG202 4.7 25.6 1.0 CB C:GLU221 4.7 22.4 1.0 CB C:GLU205 4.7 31.7 1.0 N C:GLU205 4.9 29.8 1.0 N C:ARG202 4.9 26.5 1.0 CA C:ARG202 4.9 25.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Aprataxin Ortholog HNT3 in Complex with Dna


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 Aprataxin Ortholog HNT3 in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn601 b:25.4 occ:1.00 OE2 D:GLU221 2.0 24.9 1.0 NE2 D:HIS217 2.1 25.7 1.0 SG D:CYS200 2.3 21.2 1.0 SG D:CYS203 2.4 28.0 1.0 CD D:GLU221 3.0 25.5 1.0 CD2 D:HIS217 3.1 26.0 1.0 CB D:CYS203 3.1 27.9 1.0 CE1 D:HIS217 3.1 30.0 1.0 CB D:CYS200 3.1 22.9 1.0 CG D:GLU221 3.2 22.6 1.0 N D:CYS203 3.6 25.9 1.0 CA D:CYS203 3.9 25.6 1.0 OE1 D:GLU221 4.1 24.1 1.0 ND1 D:HIS217 4.2 31.0 1.0 CG D:HIS217 4.2 26.0 1.0 C D:CYS203 4.5 30.3 1.0 CA D:CYS200 4.6 23.2 1.0 C D:ARG202 4.6 29.4 1.0 N D:GLY204 4.6 27.7 1.0 CB D:ARG202 4.6 24.7 1.0 CB D:GLU221 4.7 23.4 1.0 CB D:GLU205 4.7 29.5 1.0 O D:HOH578 4.7 36.4 1.0 N D:ARG202 4.9 24.6 1.0 N D:GLU205 4.9 31.1 1.0 CA D:ARG202 4.9 24.0 1.0 OE1 D:GLU205 4.9 35.1 1.0

Y.Gong, D.Zhu, J.Ding, C.Dou, X.Ren, L.Gu, T.Jiang, D.Wang. Crystal Structures of Aprataxin Ortholog HNT3 Reveal the Mechanism For Reversal of 5'-Adenylated Dna Nat.Struct.Mol.Biol. V. 18 1297 2011.
ISSN: ISSN 1545-9993
PubMed: 21984208
DOI: 10.1038/NSMB.2145