Zinc in PDB 7k31: Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site

The structure of Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site, PDB code: 7k31 was solved by K.Shi, N.M.Moeller, S.Banerjee, L.Yin, K.Orellana, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.47 / 2.88
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	151.12, 151.12, 117.58, 90, 90, 120
R / Rfree (%)	18.2 / 23.8

The structure of Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site (pdb code 7k31). 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 Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site, PDB code: 7k31:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site


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 Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:82.2 occ:1.00 CB A:CYS271 2.1 101.6 1.0 SG A:CYS252 2.3 70.1 1.0 SG A:CYS271 2.3 96.0 1.0 SG A:CYS268 2.3 61.4 1.0 SG A:CYS249 2.3 105.0 1.0 CB A:CYS249 3.1 76.6 1.0 CB A:CYS268 3.1 78.4 1.0 CB A:CYS252 3.2 55.8 1.0 N A:CYS252 3.5 67.9 1.0 CA A:CYS271 3.6 87.0 1.0 CA A:CYS252 3.9 63.2 1.0 N A:CYS271 4.2 76.0 1.0 C A:CYS271 4.3 92.9 1.0 N A:GLY273 4.5 62.9 1.0 CA A:CYS249 4.6 62.4 1.0 CA A:CYS268 4.6 77.5 1.0 C A:CYS252 4.6 58.3 1.0 CB A:ARG251 4.7 62.4 1.0 C A:ARG251 4.7 71.6 1.0 N A:TYR253 4.7 68.3 1.0 N A:GLY272 4.7 85.6 1.0 OH A:TYR256 4.7 55.5 1.0 CA A:GLY273 4.8 76.1 1.0 N A:ARG251 4.9 51.7 1.0 OG1 A:THR254 4.9 60.0 1.0 CA A:ARG251 5.0 58.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site


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 Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:52.5 occ:1.00 OE2 A:GLU76 2.0 66.0 1.0 OE1 A:GLU76 2.1 68.5 1.0 NE2 A:HIS139 2.1 26.9 1.0 OP2 C:DI14 2.2 42.9 1.0 CD A:GLU76 2.2 54.3 1.0 ND1 A:HIS84 2.3 44.4 1.0 CE1 A:HIS139 3.0 18.9 1.0 OP1 C:DI14 3.0 45.9 1.0 CD2 A:HIS139 3.2 46.5 1.0 CE1 A:HIS84 3.2 55.8 1.0 ZN A:ZN404 3.2 8.7 0.5 P C:DI14 3.3 44.7 1.0 CG A:HIS84 3.4 34.2 1.0 OD1 A:ASN193 3.6 33.3 1.0 CG A:GLU76 3.7 19.2 1.0 CB A:HIS84 3.8 30.5 1.0 ND1 A:HIS139 4.1 18.8 1.0 CE1 A:HIS8 4.2 18.3 1.0 NE2 A:HIS8 4.2 53.0 1.0 CG A:HIS139 4.2 18.5 1.0 O3' C:DC13 4.3 38.4 1.0 O5' C:DI14 4.3 57.8 1.0 NE2 A:HIS10 4.3 41.4 1.0 C5' C:DI14 4.3 41.5 1.0 NE2 A:HIS84 4.4 41.4 1.0 NE A:ARG114 4.4 48.2 1.0 CG A:ASN193 4.5 45.1 1.0 CD2 A:HIS84 4.5 30.2 1.0 CD A:ARG114 4.6 31.0 1.0 ND2 A:ASN193 4.6 40.7 1.0 CB A:GLU76 4.8 19.3 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site


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 Endonuclease Q Complex with 27-Mer Duplex Substrate with Di at the Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn404 b:8.7 occ:0.52 OD1 A:ASN193 2.0 33.3 1.0 NE2 A:HIS10 2.0 41.4 1.0 OE1 A:GLU76 2.0 68.5 1.0 NE2 A:HIS8 2.1 53.0 1.0 OP1 C:DI14 2.3 45.9 1.0 CD2 A:HIS10 2.6 39.3 1.0 CE1 A:HIS8 3.0 18.3 1.0 CD2 A:HIS8 3.0 47.8 1.0 CG A:ASN193 3.1 45.1 1.0 CE1 A:HIS10 3.1 48.3 1.0 ZN A:ZN403 3.2 52.5 1.0 CD A:GLU76 3.2 54.3 1.0 P C:DI14 3.6 44.7 1.0 CG A:HIS10 3.8 34.6 1.0 OP2 C:DI14 3.8 42.9 1.0 ND2 A:ASN193 3.8 40.7 1.0 OE2 A:GLU76 3.9 66.0 1.0 ND1 A:HIS10 4.0 49.7 1.0 CB A:ASN193 4.1 19.5 1.0 ND1 A:HIS8 4.1 17.6 1.0 CG A:HIS8 4.2 40.5 1.0 CG A:GLU76 4.3 19.2 1.0 NE A:ARG114 4.3 48.2 1.0 NE2 A:HIS195 4.3 47.7 1.0 CA A:ASN193 4.3 19.3 1.0 CB A:GLU76 4.4 19.3 1.0 O5' C:DI14 4.5 57.8 1.0 NE2 A:HIS139 4.6 26.9 1.0 O3' C:DC13 4.8 38.4 1.0 NH2 A:ARG114 4.8 52.2 1.0 CD2 A:HIS139 4.8 46.5 1.0 C5' C:DI14 4.8 41.5 1.0

K.Shi, N.H.Moeller, S.Banerjee, J.L.Mccann, M.A.Carpenter, L.Yin, R.Moorthy, K.Orellana, D.A.Harki, R.S.Harris, H.Aihara. Structural Basis For Recognition of Distinct Deaminated Dna Lesions By Endonuclease Q. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33658373
DOI: 10.1073/PNAS.2021120118