Zinc in PDB 5dk5: Crystal Structure of Crn-4-Mes Complex

The structure of Crystal Structure of Crn-4-Mes Complex, PDB code: 5dk5 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.259, 67.624, 178.002, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.7

The structure of Crystal Structure of Crn-4-Mes Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Crn-4-Mes Complex (pdb code 5dk5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Crn-4-Mes Complex, PDB code: 5dk5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Crn-4-Mes Complex


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 Crn-4-Mes Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.3 occ:1.00 SG A:CYS270 2.3 25.1 1.0 SG A:CYS263 2.3 32.9 1.0 SG A:CYS260 2.3 24.4 1.0 SG A:CYS210 2.3 22.4 1.0 HB3 A:CYS210 2.8 21.6 1.0 HB3 A:CYS260 2.9 32.3 1.0 CB A:CYS260 2.9 26.9 1.0 HB2 A:CYS260 2.9 32.3 1.0 HB2 A:CYS270 3.0 43.5 1.0 CB A:CYS210 3.2 18.0 1.0 H A:CYS263 3.2 38.8 1.0 CB A:CYS270 3.3 36.2 1.0 HB3 A:CYS263 3.4 41.3 1.0 H A:CYS210 3.4 24.4 1.0 HH22 A:ARG136 3.5 25.5 1.0 CB A:CYS263 3.5 34.4 1.0 HB3 A:CYS270 3.7 43.5 1.0 HB2 A:CYS210 3.8 21.6 1.0 HB3 A:TYR262 3.9 39.0 1.0 N A:CYS263 3.9 32.3 1.0 N A:CYS210 4.0 20.3 1.0 HB2 A:CYS263 4.2 41.3 1.0 CA A:CYS210 4.2 19.9 1.0 NH2 A:ARG136 4.3 21.3 1.0 CA A:CYS263 4.3 34.6 1.0 HD2 A:TYR262 4.4 47.7 1.0 CA A:CYS260 4.4 30.2 1.0 HA A:CYS270 4.5 42.0 1.0 H A:TYR262 4.5 39.6 1.0 CA A:CYS270 4.5 35.0 1.0 HH21 A:ARG136 4.6 25.5 1.0 HB2 A:LYS265 4.6 46.6 1.0 H A:LYS265 4.6 43.9 1.0 HG23 A:THR209 4.6 36.0 1.0 HH12 A:ARG136 4.7 29.8 1.0 H A:ARG264 4.8 44.2 1.0 HA A:CYS260 4.8 36.2 1.0 CB A:TYR262 4.8 32.5 1.0 HA A:CYS210 4.8 23.9 1.0 HA A:THR209 4.8 26.6 1.0 O A:HOH567 5.0 31.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Crn-4-Mes Complex


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 Crn-4-Mes Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:42.7 occ:1.00 SG B:CYS260 2.3 41.1 1.0 SG B:CYS270 2.3 40.1 1.0 SG B:CYS210 2.4 49.1 1.0 SG B:CYS263 2.4 43.9 1.0 HB3 B:CYS210 2.7 44.3 1.0 H B:CYS263 3.0 62.4 1.0 HB3 B:CYS260 3.0 48.1 1.0 CB B:CYS210 3.1 36.9 1.0 CB B:CYS260 3.1 40.1 1.0 H B:CYS210 3.1 43.3 1.0 HB3 B:CYS263 3.1 64.6 1.0 HB2 B:CYS260 3.2 48.1 1.0 HH22 B:ARG136 3.3 55.8 1.0 CB B:CYS263 3.3 53.9 1.0 HB2 B:CYS270 3.4 71.3 1.0 CB B:CYS270 3.5 59.5 1.0 HB3 B:TYR262 3.6 48.4 1.0 N B:CYS210 3.8 36.1 1.0 N B:CYS263 3.8 52.0 1.0 HB2 B:CYS210 3.8 44.3 1.0 O B:HOH561 3.8 57.3 1.0 HB3 B:CYS270 4.0 71.3 1.0 CA B:CYS210 4.0 36.8 1.0 NH2 B:ARG136 4.1 46.5 1.0 HB2 B:CYS263 4.1 64.6 1.0 CA B:CYS263 4.2 54.7 1.0 HH21 B:ARG136 4.3 55.8 1.0 H B:TYR262 4.4 45.6 1.0 HA B:THR209 4.5 44.9 1.0 CA B:CYS260 4.5 41.6 1.0 CB B:TYR262 4.6 40.3 1.0 HD1 B:TYR262 4.6 50.9 1.0 HH12 B:ARG136 4.6 54.5 1.0 HA B:CYS210 4.6 44.2 1.0 HB B:THR209 4.7 49.7 1.0 HA B:CYS270 4.7 70.2 1.0 H B:LYS265 4.8 67.0 1.0 CA B:CYS270 4.8 58.5 1.0 H B:ARG264 4.8 67.9 1.0 C B:THR209 4.8 33.6 1.0 C B:TYR262 4.9 43.3 1.0 HA B:CYS260 4.9 49.9 1.0 HA B:CYS263 4.9 65.6 1.0 HB2 B:TYR262 5.0 48.4 1.0 C B:CYS263 5.0 55.1 1.0

K.-W.Huang, K.-C.Hsu, L.-Y.Chu, J.-M.Yang, H.S.Yuan, Y.-Y.Hsiao. Identification of Inhibitors For the Deddh Family of Exonucleases and A Unique Inhibition Mechanism By Crystal Structure Analysis of Crn-4 Bound with 2-Morpholin-4-Ylethanesulfonate (Mes) J.Med.Chem. V. 59 8019 2016.
ISSN: ISSN 0022-2623
PubMed: 27529560
DOI: 10.1021/ACS.JMEDCHEM.6B00794