Chlorine in PDB 5zki: Human Exog-H140A in Complex with Duplex Dna

The structure of Human Exog-H140A in Complex with Duplex Dna, PDB code: 5zki was solved by C.C.Wu, J.L.J.Lin, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 2.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.497, 91.123, 129.451, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.8

The structure of Human Exog-H140A in Complex with Duplex Dna also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Chlorine atom in the Human Exog-H140A in Complex with Duplex Dna (pdb code 5zki). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Human Exog-H140A in Complex with Duplex Dna, PDB code: 5zki:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Human Exog-H140A in Complex with Duplex Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Exog-H140A in Complex with Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:59.2 occ:1.00 H A:TYR174 2.4 56.5 1.0 H A:ILE256 2.5 57.3 1.0 HA A:ASN170 2.9 58.7 1.0 HB2 A:TYR174 2.9 63.8 1.0 H A:GLY257 3.0 68.0 1.0 HA3 A:GLY173 3.2 48.0 1.0 N A:TYR174 3.3 47.1 1.0 HA A:ALA255 3.3 68.4 1.0 O A:ASP169 3.3 53.4 1.0 HB A:ILE256 3.3 67.5 1.0 N A:ILE256 3.4 47.7 1.0 HB3 A:ASP169 3.6 58.7 1.0 C A:ASP169 3.7 49.2 1.0 CB A:TYR174 3.7 53.2 1.0 N A:GLY257 3.8 56.7 1.0 HH21 A:ARG177 3.8 56.7 0.5 CA A:ASN170 3.8 48.9 1.0 HH22 A:ARG177 3.8 56.7 0.5 HB3 A:TYR174 3.9 63.8 1.0 N A:ASN170 3.9 49.2 1.0 NH2 A:ARG177 4.0 47.2 0.5 CA A:GLY173 4.0 40.0 1.0 CA A:TYR174 4.1 48.3 1.0 CB A:ILE256 4.1 56.2 1.0 CA A:ALA255 4.1 57.0 1.0 C A:GLY173 4.1 49.3 1.0 CA A:ILE256 4.2 55.8 1.0 C A:ALA255 4.3 56.8 1.0 H A:GLY173 4.3 61.0 1.0 HB1 A:ALA255 4.3 60.7 1.0 CB A:ASP169 4.4 48.9 1.0 HG13 A:ILE256 4.4 63.1 1.0 H A:ASN170 4.4 59.0 1.0 HA2 A:GLY257 4.4 69.1 1.0 C A:ILE256 4.4 62.4 1.0 HB2 A:ASP169 4.5 58.7 1.0 HA A:TYR174 4.6 58.0 1.0 CA A:ASP169 4.6 43.2 1.0 O A:ASN170 4.6 45.0 1.0 C A:ASN170 4.6 53.2 1.0 N A:GLY173 4.7 50.8 1.0 HB2 A:ASN170 4.7 61.5 1.0 CA A:GLY257 4.7 57.6 1.0 HA2 A:GLY173 4.7 48.0 1.0 O A:GLU254 4.7 41.7 1.0 HD22 A:ASN170 4.8 51.9 1.0 CB A:ALA255 4.8 50.6 1.0 CB A:ASN170 4.8 51.2 1.0 HD12 A:ILE256 4.8 67.6 1.0 CG1 A:ILE256 4.8 52.6 1.0 HD1 A:TYR174 4.8 66.1 1.0 H A:TRP175 4.8 51.5 1.0 HA A:ASP169 4.9 51.8 1.0 CG A:TYR174 5.0 48.0 1.0

Chlorine binding site 2 out of 2 in the Human Exog-H140A in Complex with Duplex Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Exog-H140A in Complex with Duplex Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:60.9 occ:1.00 H B:TYR174 2.2 42.8 1.0 H B:ILE256 2.5 59.2 0.6 O B:ILE256 2.8 48.9 0.6 OD1 B:ASP169 2.8 54.1 0.3 HB2 B:TYR174 2.9 54.0 1.0 HA B:ASN170 2.9 46.3 1.0 HA3 B:GLY173 2.9 40.8 1.0 H B:ILE256 3.0 58.9 0.5 N B:TYR174 3.1 35.6 1.0 O B:ASP169 3.2 41.5 0.3 O B:ASP169 3.2 41.5 0.7 N B:ILE256 3.3 49.4 0.6 H B:GLY257 3.3 58.8 0.5 HA B:ALA255 3.3 60.1 0.5 HA B:ALA255 3.4 60.1 0.6 C B:ASP169 3.6 45.1 0.3 C B:ASP169 3.6 46.4 0.7 C B:ILE256 3.7 47.4 0.6 CB B:TYR174 3.7 45.0 1.0 N B:ILE256 3.7 49.1 0.5 HB3 B:ASP169 3.7 56.2 0.7 CA B:GLY173 3.7 34.0 1.0 CA B:ASN170 3.8 38.6 1.0 HB B:ILE256 3.8 49.2 0.5 CG B:ASP169 3.8 49.4 0.3 O B:HOH516 3.8 59.1 1.0 HB3 B:TYR174 3.9 54.0 1.0 N B:ASN170 3.9 41.5 1.0 C B:GLY173 3.9 35.0 1.0 HB B:ILE256 3.9 50.1 0.6 CA B:TYR174 4.0 40.5 1.0 CA B:ILE256 4.0 45.1 0.6 H B:GLY173 4.1 47.6 1.0 N B:GLY257 4.1 49.0 0.5 CA B:ALA255 4.1 50.1 0.6 C B:ALA255 4.2 45.6 0.6 CA B:ALA255 4.2 50.1 0.5 HB3 B:ASP169 4.2 55.4 0.3 HB1 B:ALA255 4.4 51.3 0.6 HB1 B:ALA255 4.4 51.5 0.5 N B:GLY173 4.4 39.6 1.0 CB B:ASP169 4.4 46.8 0.7 CB B:ASP169 4.4 46.2 0.3 HA B:TYR174 4.4 48.6 1.0 HA2 B:GLY173 4.4 40.8 1.0 C B:ALA255 4.5 45.6 0.5 CB B:ILE256 4.5 41.8 0.6 HB2 B:ASP169 4.5 56.2 0.7 H B:ASN170 4.5 49.8 0.7 H B:ASN170 4.5 49.8 0.3 O B:ASN170 4.5 40.0 1.0 CB B:ILE256 4.5 41.0 0.5 C B:ASN170 4.5 41.6 1.0 CA B:ILE256 4.6 47.4 0.5 HG13 B:ILE256 4.6 57.2 0.5 OD2 B:ASP169 4.6 53.5 0.3 CA B:ASP169 4.6 44.2 0.3 CA B:ASP169 4.6 43.6 0.7 H B:TRP175 4.7 48.0 1.0 HB2 B:ASN170 4.7 60.1 1.0 HA2 B:GLY257 4.8 55.9 0.6 HD1 B:TYR174 4.8 45.0 1.0 CB B:ALA255 4.8 42.9 0.5 HA2 B:GLY257 4.8 53.4 0.5 CB B:ALA255 4.8 42.8 0.6 O B:GLU254 4.8 41.2 1.0 N B:GLY257 4.8 51.0 0.6 CB B:ASN170 4.8 50.1 1.0 HA B:ILE256 4.9 54.1 0.6 HD22 B:ASN170 4.9 52.0 1.0 HA B:ASP169 4.9 53.1 0.3 HG13 B:ILE256 4.9 55.5 0.6 HA B:ASP169 4.9 52.4 0.7 C B:ILE256 4.9 48.3 0.5 HD12 B:ILE256 4.9 53.9 0.5 HB2 B:ALA255 4.9 51.5 0.5 CG B:TYR174 4.9 46.9 1.0

C.C.Wu, J.L.J.Lin, H.F.Yang-Yen, H.S.Yuan. A Unique Exonuclease Exog Cleaves Between Rna and Dna in Mitochondrial Dna Replication. Nucleic Acids Res. V. 47 5405 2019.
ISSN: ESSN 1362-4962
PubMed: 30949702
DOI: 10.1093/NAR/GKZ241