Zinc in PDB 8efg: Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions

The structure of Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions, PDB code: 8efg was solved by J.Dorival, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.30 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.88, 76.51, 77.36, 90, 90, 90
R / Rfree (%)	16.3 / 18.9

The structure of Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions (pdb code 8efg). 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 Human TATDN1 Bound to Damp and Two Zinc Ions, PDB code: 8efg:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions


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 Human TATDN1 Bound to Damp and Two Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.7 occ:0.35 ZN A:ZN301 0.0 21.7 0.3 ZN A:ZN301 1.9 22.1 0.3 OD1 A:ASP222 2.0 20.6 1.0 OP1 A:DA308 2.1 25.1 1.0 O A:HOH457 2.4 41.2 1.0 O A:HOH409 2.5 39.0 1.0 CG A:ASP222 2.6 20.3 1.0 OD2 A:ASP222 2.6 21.5 1.0 OP2 A:DA308 2.6 26.5 1.0 P A:DA308 2.8 21.7 1.0 O A:HOH622 3.7 19.7 1.0 ND2 A:ASN12 3.7 20.9 1.0 OP3 A:DA308 3.7 21.3 1.0 OD1 A:ASN12 4.1 24.3 1.0 O5' A:DA308 4.1 26.3 1.0 CB A:ASP222 4.1 15.3 1.0 OE1 A:GLU112 4.1 21.6 1.0 CD1 A:TRP225 4.2 18.4 1.0 CG A:ASN12 4.3 21.7 1.0 C5' A:DA308 4.3 27.3 1.0 ZN A:ZN302 4.4 18.2 1.0 N9 A:ADE311 4.4 51.3 1.0 CE1 A:HIS174 4.4 15.4 1.0 O A:HOH567 4.7 28.9 1.0 O A:ASP222 4.7 16.6 1.0 NE1 A:TRP225 4.8 19.9 1.0 CA A:ASP222 4.8 15.0 1.0 NE2 A:HIS174 4.9 16.1 1.0 OE2 A:GLU112 5.0 18.8 1.0 O A:HOH450 5.0 19.2 1.0 CD A:GLU112 5.0 17.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions


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 Human TATDN1 Bound to Damp and Two Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.1 occ:0.35 ZN A:ZN301 0.0 22.1 0.3 ZN A:ZN301 1.9 21.7 0.3 O A:HOH409 2.3 39.0 1.0 O A:HOH622 2.3 19.7 1.0 OE1 A:GLU112 2.5 21.6 1.0 OP2 A:DA308 2.7 26.5 1.0 OD1 A:ASP222 2.8 20.6 1.0 CD A:GLU112 3.5 17.8 1.0 CE1 A:HIS174 3.5 15.4 1.0 ZN A:ZN302 3.6 18.2 1.0 CG A:ASP222 3.6 20.3 1.0 P A:DA308 3.6 21.7 1.0 OP1 A:DA308 3.6 25.1 1.0 O A:HOH457 3.7 41.2 1.0 OE2 A:GLU112 3.8 18.8 1.0 NE2 A:HIS174 3.8 16.1 1.0 OD2 A:ASP222 4.0 21.5 1.0 OD1 A:ASN12 4.1 24.3 1.0 O A:HOH730 4.3 33.2 1.0 CG2 A:THR50 4.3 18.6 1.0 OP3 A:DA308 4.3 21.3 1.0 O A:HOH450 4.3 19.2 1.0 ND2 A:ASN12 4.4 20.9 1.0 CE2 A:PHE147 4.5 18.6 1.0 ND1 A:HIS174 4.6 17.2 1.0 OG1 A:THR50 4.7 17.6 1.0 CG A:ASN12 4.7 21.7 1.0 CB A:THR50 4.7 18.9 1.0 CG A:GLU112 4.8 19.6 1.0 CB A:ASP222 4.8 15.3 1.0 CZ A:PHE147 4.9 18.6 1.0 CD2 A:HIS174 5.0 16.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human TATDN1 Bound to Damp and Two Zinc Ions


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 Human TATDN1 Bound to Damp and Two Zinc Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:18.2 occ:1.00 OE2 A:GLU112 1.8 18.8 1.0 NE2 A:HIS174 2.0 16.1 1.0 ND1 A:HIS149 2.0 19.1 1.0 OP2 A:DA308 2.0 26.5 1.0 CD A:GLU112 2.8 17.8 1.0 CE1 A:HIS149 2.9 20.4 1.0 CE1 A:HIS174 2.9 15.4 1.0 CD2 A:HIS174 3.1 16.1 1.0 CG A:HIS149 3.1 18.5 1.0 P A:DA308 3.2 21.7 1.0 OE1 A:GLU112 3.2 21.6 1.0 OP3 A:DA308 3.4 21.3 1.0 CB A:HIS149 3.5 17.9 1.0 ZN A:ZN301 3.6 22.1 0.3 O5' A:DA308 3.8 26.3 1.0 CG A:GLU112 4.0 19.6 1.0 ND1 A:HIS174 4.1 17.2 1.0 NE2 A:HIS149 4.1 21.5 1.0 NE2 A:HIS77 4.1 18.1 1.0 CD2 A:HIS149 4.2 20.2 1.0 CG A:HIS174 4.2 16.1 1.0 ZN A:ZN301 4.4 21.7 0.3 C5' A:DA308 4.4 27.3 1.0 OP1 A:DA308 4.4 25.1 1.0 CA A:HIS149 4.4 18.2 1.0 CD2 A:HIS77 4.7 19.6 1.0 CB A:SER175 4.8 18.8 1.0 C3' A:DA308 4.9 30.0 0.9 O A:HOH453 5.0 29.4 1.0

J.Dorival, B.F.Eichman. Human Tatd Enzymes Contain Apurinic/Apyrimidinic (Ap) Endonuclease Activity To Be Published.