Zinc in PDB 1fsj: Crystal Structure of the E9 Dnase Domain

All present enzymatic activity of Crystal Structure of the E9 Dnase Domain:
3.1.21.1;

The structure of Crystal Structure of the E9 Dnase Domain, PDB code: 1fsj was solved by U.C.Kuhlmann, A.J.Pommer, G.R.Moore, R.James, C.Kleanthous, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.120, 82.960, 113.660, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.2

The binding sites of Zinc atom in the Crystal Structure of the E9 Dnase Domain (pdb code 1fsj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the E9 Dnase Domain, PDB code: 1fsj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the E9 Dnase Domain


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 E9 Dnase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:8.1 occ:1.00 O3 B:PO4801 1.9 12.3 1.0 NE2 B:HIS131 2.1 7.8 1.0 NE2 B:HIS127 2.1 4.7 1.0 ND1 B:HIS102 2.1 6.3 1.0 O B:HOH932 3.0 16.4 1.0 CE1 B:HIS102 3.0 5.9 1.0 CD2 B:HIS127 3.0 5.5 1.0 CD2 B:HIS131 3.1 9.2 1.0 CE1 B:HIS131 3.1 11.3 1.0 CE1 B:HIS127 3.1 6.4 1.0 CG B:HIS102 3.1 5.5 1.0 P B:PO4801 3.2 16.3 1.0 O4 B:PO4801 3.4 20.9 1.0 CB B:HIS102 3.6 6.5 1.0 CA B:HIS102 3.8 5.7 1.0 O1 B:PO4801 3.8 23.5 1.0 N B:HIS103 4.0 7.4 1.0 NE2 B:HIS102 4.1 6.0 1.0 ND1 B:HIS131 4.2 7.5 1.0 CG B:HIS127 4.2 3.3 1.0 ND1 B:HIS127 4.2 6.8 1.0 CG B:HIS131 4.2 7.6 1.0 CD2 B:HIS102 4.2 7.7 1.0 O2 B:PO4801 4.3 20.7 1.0 C B:HIS102 4.4 6.9 1.0 O B:HIS103 4.4 6.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the E9 Dnase Domain


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 E9 Dnase Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn902 b:8.5 occ:1.00 O3 C:PO4802 2.0 8.9 1.0 ND1 C:HIS302 2.1 7.6 1.0 NE2 C:HIS331 2.1 6.0 1.0 NE2 C:HIS327 2.1 6.8 1.0 O C:HOH911 2.9 14.1 1.0 CE1 C:HIS302 3.0 7.8 1.0 CD2 C:HIS327 3.1 5.8 1.0 CE1 C:HIS331 3.1 9.8 1.0 CD2 C:HIS331 3.1 7.2 1.0 CE1 C:HIS327 3.1 5.3 1.0 P C:PO4802 3.1 11.5 1.0 CG C:HIS302 3.1 4.8 1.0 O4 C:PO4802 3.3 17.9 1.0 CB C:HIS302 3.6 6.0 1.0 O1 C:PO4802 3.8 19.8 1.0 CA C:HIS302 3.8 5.5 1.0 N C:HIS303 3.9 5.0 1.0 NE2 C:HIS302 4.1 8.5 1.0 ND1 C:HIS331 4.2 7.4 1.0 ND1 C:HIS327 4.2 6.3 1.0 CG C:HIS327 4.2 6.5 1.0 CG C:HIS331 4.2 6.5 1.0 CD2 C:HIS302 4.2 8.4 1.0 C C:HIS302 4.3 5.4 1.0 O2 C:PO4802 4.3 17.4 1.0 O C:HIS303 4.4 5.8 1.0 CG2 C:ILE330 4.9 8.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the E9 Dnase Domain


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 E9 Dnase Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn903 b:8.9 occ:1.00 O3 D:PO4803 2.0 16.8 1.0 NE2 D:HIS531 2.1 7.2 1.0 ND1 D:HIS502 2.1 6.3 1.0 NE2 D:HIS527 2.2 5.0 1.0 O D:HOH28 2.8 13.7 1.0 CE1 D:HIS502 2.9 5.6 1.0 CD2 D:HIS531 3.1 7.6 1.0 CE1 D:HIS531 3.1 10.9 1.0 P D:PO4803 3.1 16.2 1.0 CD2 D:HIS527 3.1 3.1 1.0 CE1 D:HIS527 3.2 7.0 1.0 CG D:HIS502 3.2 6.8 1.0 O4 D:PO4803 3.2 22.2 1.0 CB D:HIS502 3.6 4.6 1.0 CA D:HIS502 3.8 6.1 1.0 O1 D:PO4803 3.9 23.0 1.0 N D:HIS503 4.0 6.8 1.0 NE2 D:HIS502 4.1 5.6 1.0 ND1 D:HIS531 4.2 8.3 1.0 O2 D:PO4803 4.2 19.6 1.0 CG D:HIS531 4.2 7.6 1.0 CD2 D:HIS502 4.2 7.4 1.0 ND1 D:HIS527 4.3 6.9 1.0 CG D:HIS527 4.3 4.8 1.0 C D:HIS502 4.3 6.6 1.0 O D:HIS503 4.4 7.3 1.0 CE B:LYS134 4.6 18.2 1.0 CG2 D:ILE530 5.0 8.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the E9 Dnase Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the E9 Dnase Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn904 b:10.0 occ:1.00 O3 E:PO4804 2.0 14.3 1.0 NE2 E:HIS731 2.1 9.8 1.0 ND1 E:HIS702 2.1 6.0 1.0 NE2 E:HIS727 2.1 9.1 1.0 O E:HOH31 3.0 16.1 1.0 CE1 E:HIS702 3.0 6.6 1.0 CD2 E:HIS731 3.0 8.9 1.0 CE1 E:HIS731 3.1 10.2 1.0 CD2 E:HIS727 3.1 9.2 1.0 P E:PO4804 3.1 17.6 1.0 CG E:HIS702 3.2 6.3 1.0 CE1 E:HIS727 3.2 10.8 1.0 O4 E:PO4804 3.3 22.8 1.0 CB E:HIS702 3.5 5.2 1.0 CA E:HIS702 3.8 7.7 1.0 O1 E:PO4804 3.8 24.7 1.0 N E:HIS703 4.0 10.0 1.0 NE2 E:HIS702 4.2 6.2 1.0 ND1 E:HIS731 4.2 9.9 1.0 CG E:HIS731 4.2 8.9 1.0 CG E:HIS727 4.2 7.2 1.0 CD2 E:HIS702 4.2 7.3 1.0 ND1 E:HIS727 4.3 9.4 1.0 O2 E:PO4804 4.3 21.1 1.0 C E:HIS702 4.3 9.2 1.0 O E:HIS703 4.4 9.3 1.0 CG2 E:ILE730 5.0 11.4 1.0

U.C.Kuhlmann, A.J.Pommer, G.R.Moore, R.James, C.Kleanthous, A.M.Hemmings. Structure of the E9 Dnase Domain in Comparison with the Inhibited Structure of the E9 Dnase/IM9 Complex To Be Published.