Zinc in PDB 5zhz: Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis

All present enzymatic activity of Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis:
3.1.21.2;

The structure of Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis, PDB code: 5zhz was solved by W.Zhang, Y.Xu, M.Yan, S.Li, H.Wang, H.Yang, W.Zhou, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.52 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.638, 55.269, 102.939, 90.00, 90.00, 90.00
R / Rfree (%)	13.9 / 15.9

The binding sites of Zinc atom in the Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis (pdb code 5zhz). 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 the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis, PDB code: 5zhz:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis


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 Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:12.7 occ:1.00 NE2 A:HIS96 1.9 13.6 1.0 O A:HOH411 2.0 16.8 1.0 OE1 A:GLU129 2.0 11.0 1.0 NE2 A:HIS56 2.1 11.1 1.0 O3 A:SO4303 2.1 16.0 1.0 CD2 A:HIS96 2.6 14.0 1.0 CD A:GLU129 2.8 10.4 1.0 OE2 A:GLU129 3.0 11.4 1.0 CE1 A:HIS56 3.1 11.2 1.0 CD2 A:HIS56 3.1 10.6 1.0 CE1 A:HIS96 3.1 13.0 1.0 S A:SO4303 3.2 14.1 1.0 ZN A:ZN305 3.3 12.4 1.0 O2 A:SO4303 3.5 14.9 1.0 O1 A:SO4303 3.8 17.4 1.0 CG A:HIS96 4.0 13.1 1.0 ND1 A:HIS96 4.1 13.1 1.0 CE1 A:HIS191 4.2 9.9 1.0 ND1 A:HIS56 4.2 10.9 1.0 CG A:GLU129 4.2 11.1 1.0 CG A:HIS56 4.2 10.4 1.0 CE1 A:TYR59 4.2 17.4 1.0 ND1 A:HIS191 4.3 10.1 1.0 OE2 A:GLU233 4.4 13.3 1.0 O4 A:SO4303 4.4 14.9 1.0 CE1 A:HIS165 4.5 10.6 1.0 CB A:GLU129 4.6 11.0 1.0 CG2 A:ILE94 4.8 13.9 1.0 OE1 A:GLU233 4.8 10.8 1.0 CD1 A:TYR59 5.0 17.4 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis


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 Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:12.4 occ:1.00 OD2 A:ASP162 2.1 10.3 1.0 OE2 A:GLU129 2.1 11.4 1.0 O A:HOH411 2.1 16.8 1.0 OE1 A:GLU233 2.1 10.8 1.0 O2 A:SO4303 2.2 14.9 1.0 ND1 A:HIS191 2.2 10.1 1.0 CD A:GLU233 3.0 11.4 1.0 CD A:GLU129 3.0 10.4 1.0 CE1 A:HIS191 3.1 9.9 1.0 OE2 A:GLU233 3.2 13.3 1.0 CG A:ASP162 3.2 10.4 1.0 CG A:HIS191 3.2 10.0 1.0 S A:SO4303 3.3 14.1 1.0 ZN A:ZN304 3.3 12.7 1.0 OE1 A:GLU129 3.4 11.0 1.0 CB A:HIS191 3.6 10.3 1.0 O3 A:SO4303 3.6 16.0 1.0 CB A:ASP162 3.7 10.6 1.0 CE1 A:HIS165 3.8 10.6 1.0 O1 A:SO4303 4.0 17.4 1.0 ND2 A:ASN193 4.1 11.4 1.0 NE2 A:HIS191 4.2 10.5 1.0 OD1 A:ASP162 4.3 11.2 1.0 CD2 A:HIS191 4.3 10.9 1.0 CG A:GLU129 4.3 11.1 1.0 NE2 A:HIS165 4.3 10.7 1.0 CG A:GLU233 4.4 12.2 1.0 O4 A:SO4303 4.4 14.9 1.0 CE1 A:HIS206 4.5 11.9 1.0 ND1 A:HIS165 4.5 10.5 1.0 ZN A:ZN306 4.6 12.1 1.0 NE2 A:HIS96 4.8 13.6 1.0 NE2 A:HIS206 4.9 11.5 1.0 CA A:ASP162 4.9 10.1 1.0 NE2 A:HIS56 4.9 11.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis


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 Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:12.1 occ:1.00 NE2 A:HIS206 2.0 11.5 1.0 O4 A:SO4303 2.0 14.9 1.0 NE2 A:HIS165 2.0 10.7 1.0 OD2 A:ASP204 2.0 15.0 1.0 OD1 A:ASP204 2.5 15.1 1.0 CG A:ASP204 2.6 14.1 1.0 O2 A:SO4303 2.7 14.9 1.0 CE1 A:HIS206 2.9 11.9 1.0 S A:SO4303 3.0 14.1 1.0 CE1 A:HIS165 3.0 10.6 1.0 CD2 A:HIS165 3.0 10.6 1.0 CD2 A:HIS206 3.0 12.1 1.0 O A:HOH653 3.8 39.9 1.0 O3 A:SO4303 3.9 16.0 1.0 O1 A:SO4303 3.9 17.4 1.0 O A:HOH647 4.0 35.4 1.0 ND1 A:HIS206 4.1 12.4 1.0 ND1 A:HIS165 4.1 10.5 1.0 CB A:ASP204 4.1 13.5 1.0 CG A:HIS165 4.2 10.4 1.0 CG A:HIS206 4.2 12.0 1.0 OD2 A:ASP162 4.2 10.3 1.0 O A:HOH484 4.3 44.3 1.0 ZN A:ZN305 4.6 12.4 1.0 CG A:ASP162 4.8 10.4 1.0 OD1 A:ASP162 4.8 11.2 1.0 O A:HOH601 4.9 17.2 1.0 CA A:ASP204 4.9 13.1 1.0

W.Zhang, Y.Xu, M.Yan, S.Li, H.Wang, H.Yang, W.Zhou, Z.Rao. Crystal Structure of the Apurinic/Apyrimidinic Endonuclease IV From Mycobacterium Tuberculosis. Biochem. Biophys. Res. V. 498 111 2018COMMUN..
ISSN: ESSN 1090-2104
PubMed: 29496453
DOI: 10.1016/J.BBRC.2018.02.181