Zinc in PDB 8dzk: DBR1 in Complex with 5-Mer Cleavage Product

The structure of DBR1 in Complex with 5-Mer Cleavage Product, PDB code: 8dzk was solved by N.E.Clark, A.B.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.12 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.272, 143.341, 214.006, 90, 90, 90
R / Rfree (%)	17.8 / 20.9

The structure of DBR1 in Complex with 5-Mer Cleavage Product also contains other interesting chemical elements:

Iron

(Fe)

5 atoms

The binding sites of Zinc atom in the DBR1 in Complex with 5-Mer Cleavage Product (pdb code 8dzk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the DBR1 in Complex with 5-Mer Cleavage Product, PDB code: 8dzk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:63.8 occ:1.00 NE2 A:HIS16 2.2 60.7 1.0 SG A:CYS14 2.3 55.3 1.0 NE2 A:HIS232 2.3 62.5 1.0 O1P F:G46511 2.3 54.9 0.8 OD2 A:ASP45 2.7 43.8 1.0 CE1 A:HIS16 2.9 55.8 1.0 CB A:CYS14 3.0 48.6 1.0 CD2 A:HIS232 3.2 55.0 1.0 CE1 A:HIS232 3.3 64.6 1.0 P F:G46511 3.4 48.8 0.8 CD2 A:HIS16 3.4 57.1 1.0 S2P F:G46511 3.4 65.4 0.8 CG A:ASP45 3.7 45.4 1.0 FE A:FE2401 3.7 39.9 1.0 CB A:ASP45 4.1 41.5 1.0 ND1 A:HIS16 4.1 59.0 1.0 O3P F:G46511 4.3 53.5 0.8 CG A:HIS16 4.4 57.9 1.0 CG A:HIS232 4.4 61.0 1.0 ND1 A:HIS232 4.4 61.9 1.0 CA A:CYS14 4.4 46.2 1.0 CA A:HIS230 4.4 46.9 1.0 O5' F:G46511 4.5 58.2 0.8 CE1 A:HIS180 4.5 40.5 1.0 O A:HOH541 4.6 49.2 1.0 NE2 A:HIS180 4.7 39.8 1.0 O A:HIS230 4.7 54.0 1.0 CB A:LYS249 4.8 57.9 1.0 N A:HIS230 4.8 45.6 1.0 C A:HIS230 4.8 50.2 1.0 OD1 A:ASP45 4.8 44.6 1.0

Zinc binding site 2 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:63.1 occ:1.00 NE2 B:HIS16 2.3 60.1 1.0 SG B:CYS14 2.3 51.9 1.0 NE2 B:HIS232 2.3 58.7 1.0 O3P G:G46511 2.4 55.0 0.8 OD2 B:ASP45 2.8 44.5 1.0 CB B:CYS14 3.0 50.4 1.0 CE1 B:HIS16 3.1 59.6 1.0 CD2 B:HIS232 3.2 57.1 1.0 S2P G:G46511 3.2 72.8 0.8 P G:G46511 3.3 51.8 0.8 CD2 B:HIS16 3.3 54.5 1.0 CE1 B:HIS232 3.4 64.1 1.0 FE B:FE2401 3.7 41.8 1.0 CG B:ASP45 3.8 44.1 1.0 O1P G:G46511 4.2 62.2 0.8 CB B:ASP45 4.3 44.0 1.0 ND1 B:HIS16 4.3 61.9 1.0 CA B:HIS230 4.4 44.7 1.0 CG B:HIS232 4.4 60.6 1.0 CG B:HIS16 4.4 57.2 1.0 CA B:CYS14 4.4 48.3 1.0 ND1 B:HIS232 4.4 62.3 1.0 O B:HIS230 4.5 52.4 1.0 O5' G:G46511 4.5 68.2 0.8 O B:HOH551 4.6 47.7 1.0 C5' G:G46511 4.6 69.8 0.8 CE1 B:HIS180 4.7 39.5 1.0 C B:HIS230 4.8 49.4 1.0 NE2 B:HIS180 4.8 39.3 1.0 N B:HIS230 4.9 39.6 1.0 CB B:LYS249 4.9 55.5 1.0 OD1 B:ASP45 4.9 44.6 1.0

Zinc binding site 3 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:70.0 occ:1.00 O3P N:G46511 2.0 60.1 0.8 NE2 C:HIS16 2.3 64.8 1.0 SG C:CYS14 2.3 55.6 1.0 NE2 C:HIS232 2.4 62.8 1.0 OD2 C:ASP45 2.8 49.2 1.0 CB C:CYS14 3.0 54.9 1.0 CE1 C:HIS16 3.1 61.0 1.0 P N:G46511 3.2 53.5 0.8 CD2 C:HIS232 3.3 59.1 1.0 CD2 C:HIS16 3.3 61.2 1.0 CE1 C:HIS232 3.4 69.7 1.0 S2P N:G46511 3.5 79.5 0.8 FE C:FE2401 3.7 45.6 1.0 CG C:ASP45 3.8 50.2 1.0 CB C:ASP45 4.1 47.1 1.0 O5' N:G46511 4.1 63.9 0.8 O1P N:G46511 4.1 59.2 0.8 ND1 C:HIS16 4.2 66.7 1.0 CG C:HIS16 4.4 62.3 1.0 CA C:CYS14 4.4 51.1 1.0 CA C:HIS230 4.4 51.4 1.0 CG C:HIS232 4.5 61.8 1.0 ND1 C:HIS232 4.5 64.8 1.0 CE1 C:HIS180 4.5 47.1 1.0 O C:HIS230 4.5 52.2 1.0 NE2 C:HIS180 4.6 47.3 1.0 C C:HIS230 4.7 53.8 1.0 O C:HOH520 4.8 48.3 1.0 N C:HIS230 4.8 48.0 1.0 CE C:LYS249 4.9 72.6 1.0 CB C:LYS249 4.9 55.5 1.0 OD1 C:ASP45 5.0 46.1 1.0

Zinc binding site 4 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:77.3 occ:1.00 SG D:CYS14 2.2 64.9 1.0 NE2 D:HIS16 2.3 72.6 1.0 NE2 D:HIS232 2.3 80.5 1.0 O1P O:G46511 2.5 66.7 0.9 OD2 D:ASP45 2.8 59.1 1.0 CB D:CYS14 2.9 70.6 1.0 CD2 D:HIS16 3.1 71.3 1.0 CD2 D:HIS232 3.2 74.8 1.0 CE1 D:HIS232 3.3 86.5 1.0 CE1 D:HIS16 3.3 74.8 1.0 P O:G46511 3.6 70.7 0.9 FE D:FE2401 3.7 54.4 1.0 S2P O:G46511 3.8 98.6 0.9 CG D:ASP45 3.9 54.3 1.0 CB D:ASP45 4.3 55.8 1.0 CA D:CYS14 4.3 64.1 1.0 CG D:HIS16 4.3 71.2 1.0 CG D:HIS232 4.3 78.6 1.0 ND1 D:HIS232 4.3 84.0 1.0 ND1 D:HIS16 4.3 74.3 1.0 CA D:HIS230 4.4 59.0 1.0 O3P O:G46511 4.5 77.2 0.9 NE2 D:HIS180 4.6 48.5 1.0 CE1 D:HIS180 4.7 51.7 1.0 O D:HIS230 4.7 69.6 1.0 O D:HOH519 4.8 64.6 1.0 C D:HIS230 4.8 67.7 1.0 N D:HIS230 4.8 57.4 1.0 O5' O:G46511 4.8 86.9 0.9 C5' O:G46511 4.9 87.0 0.9 OD1 D:ASP45 5.0 53.1 1.0 N D:CYS14 5.0 62.4 1.0

Zinc binding site 5 out of 5 in the DBR1 in Complex with 5-Mer Cleavage Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of DBR1 in Complex with 5-Mer Cleavage Product within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:55.9 occ:1.00 SG E:CYS14 2.3 50.4 1.0 NE2 E:HIS16 2.3 57.2 1.0 NE2 E:HIS232 2.3 59.2 1.0 O3P P:G46511 2.3 54.9 0.7 OD2 E:ASP45 2.8 47.0 1.0 CB E:CYS14 3.0 49.9 1.0 CD2 E:HIS232 3.1 53.6 1.0 CE1 E:HIS16 3.2 59.9 1.0 CD2 E:HIS16 3.3 56.2 1.0 CE1 E:HIS232 3.3 66.5 1.0 P P:G46511 3.4 58.4 0.7 S2P P:G46511 3.5 81.2 0.7 FE E:FE2401 3.6 45.7 1.0 CG E:ASP45 3.8 44.2 1.0 O1P P:G46511 4.1 64.2 0.7 O E:HIS230 4.2 50.9 1.0 ND1 E:HIS16 4.3 61.4 1.0 CB E:ASP45 4.3 42.5 1.0 CA E:HIS230 4.3 46.1 1.0 CG E:HIS232 4.3 57.0 1.0 CG E:HIS16 4.4 55.2 1.0 ND1 E:HIS232 4.4 61.8 1.0 CA E:CYS14 4.4 49.6 1.0 CE1 E:HIS180 4.6 39.6 1.0 O5' P:G46511 4.6 71.6 0.7 C5' P:G46511 4.6 70.2 0.7 C E:HIS230 4.6 48.9 1.0 NE2 E:HIS180 4.7 40.8 1.0 O E:HOH515 4.8 44.1 1.0 N E:HIS230 4.8 45.4 1.0 CB E:LYS249 4.9 58.0 1.0 OD1 E:ASP45 4.9 43.2 1.0 ND1 E:HIS230 5.0 45.5 1.0

N.E.Clark, A.B.Taylor. DBR1 in Complex with 5-Mer Cleavage Product To Be Published.