Iron 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:

Zinc

(Zn)

5 atoms

The binding sites of Iron 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 Iron atom.
In total 5 binding sites of Iron where determined in the DBR1 in Complex with 5-Mer Cleavage Product, PDB code: 8dzk:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron 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 Iron with other atoms in the Fe 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:Fe401 b:39.9 occ:1.00 OD1 A:ASN90 2.0 42.0 1.0 NE2 A:HIS180 2.0 39.8 1.0 OD2 A:ASP45 2.2 43.8 1.0 ND1 A:HIS230 2.3 43.7 1.0 O1P F:G46511 2.5 54.9 0.8 O3P F:G46511 2.5 53.5 0.8 CE1 A:HIS180 3.0 40.5 1.0 P F:G46511 3.0 48.8 0.8 CG A:ASP45 3.0 45.4 1.0 CD2 A:HIS180 3.0 36.0 1.0 CE1 A:HIS230 3.1 46.2 1.0 CG A:ASN90 3.1 44.3 1.0 OD1 A:ASP45 3.1 44.6 1.0 CG A:HIS230 3.4 44.3 1.0 ND2 A:ASN90 3.6 44.1 1.0 ZN A:ZN402 3.7 63.8 1.0 CA A:HIS230 3.8 46.9 1.0 CB A:HIS230 3.8 42.8 1.0 ND1 A:HIS180 4.1 37.7 1.0 CG A:HIS180 4.2 39.3 1.0 O5' F:G46511 4.2 58.2 0.8 N A:ASN90 4.3 40.2 1.0 NE2 A:HIS230 4.3 46.0 1.0 O A:HIS230 4.4 54.0 1.0 CB A:ASN90 4.4 39.8 1.0 CB A:ASP45 4.4 41.5 1.0 CD2 A:HIS230 4.4 47.9 1.0 SG A:CYS14 4.5 55.3 1.0 C5' F:G46511 4.5 57.3 0.8 S2P F:G46511 4.5 65.4 0.8 C A:HIS230 4.7 50.2 1.0 N A:HIS230 4.8 45.6 1.0 CD2 A:HIS91 4.9 51.0 1.0 CA A:ASN90 4.9 39.3 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe401 b:41.8 occ:1.00 OD1 B:ASN90 2.0 46.1 1.0 O3P G:G46511 2.1 55.0 0.8 NE2 B:HIS180 2.1 39.3 1.0 OD2 B:ASP45 2.3 44.5 1.0 ND1 B:HIS230 2.3 49.4 1.0 O1P G:G46511 2.7 62.2 0.8 P G:G46511 2.9 51.8 0.8 CG B:ASP45 3.1 44.1 1.0 CE1 B:HIS180 3.1 39.5 1.0 CD2 B:HIS180 3.1 36.8 1.0 CG B:ASN90 3.1 47.9 1.0 CE1 B:HIS230 3.1 56.5 1.0 OD1 B:ASP45 3.2 44.6 1.0 CG B:HIS230 3.4 46.7 1.0 ND2 B:ASN90 3.6 51.3 1.0 ZN B:ZN402 3.7 63.1 1.0 CB B:HIS230 3.7 41.4 1.0 CA B:HIS230 3.8 44.7 1.0 O5' G:G46511 3.9 68.2 0.8 ND1 B:HIS180 4.2 39.6 1.0 CG B:HIS180 4.2 39.2 1.0 N B:ASN90 4.3 40.8 1.0 NE2 B:HIS230 4.3 54.5 1.0 O B:HIS230 4.4 52.4 1.0 CB B:ASN90 4.4 43.9 1.0 CD2 B:HIS230 4.4 51.6 1.0 CB B:ASP45 4.5 44.0 1.0 SG B:CYS14 4.5 51.9 1.0 S2P G:G46511 4.6 72.8 0.8 C B:HIS230 4.7 49.4 1.0 C5' G:G46511 4.8 69.8 0.8 N B:HIS230 4.9 39.6 1.0 CA B:ASN90 4.9 47.6 1.0 CD2 B:HIS91 4.9 60.1 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe401 b:45.6 occ:1.00 OD1 C:ASN90 1.9 46.5 1.0 NE2 C:HIS180 2.1 47.3 1.0 OD2 C:ASP45 2.2 49.2 1.0 ND1 C:HIS230 2.3 49.2 1.0 O3P N:G46511 2.5 60.1 0.8 O1P N:G46511 2.7 59.2 0.8 CD2 C:HIS180 3.0 44.8 1.0 CG C:ASP45 3.0 50.2 1.0 CG C:ASN90 3.1 47.3 1.0 CE1 C:HIS230 3.1 54.1 1.0 CE1 C:HIS180 3.1 47.1 1.0 P N:G46511 3.2 53.5 0.8 OD1 C:ASP45 3.3 46.1 1.0 CG C:HIS230 3.4 49.5 1.0 ND2 C:ASN90 3.6 53.5 1.0 ZN C:ZN402 3.7 70.0 1.0 CA C:HIS230 3.8 51.4 1.0 CB C:HIS230 3.8 44.0 1.0 O5' N:G46511 4.1 63.9 0.8 CG C:HIS180 4.2 46.9 1.0 ND1 C:HIS180 4.2 41.9 1.0 N C:ASN90 4.2 43.4 1.0 NE2 C:HIS230 4.3 54.0 1.0 O C:HIS230 4.3 52.2 1.0 CB C:ASN90 4.3 44.5 1.0 CB C:ASP45 4.4 47.1 1.0 CD2 C:HIS230 4.4 49.9 1.0 SG C:CYS14 4.5 55.6 1.0 C C:HIS230 4.6 53.8 1.0 C5' N:G46511 4.7 68.3 0.8 N C:HIS230 4.8 48.0 1.0 S2P N:G46511 4.8 79.5 0.8 CA C:ASN90 4.8 47.5 1.0 CG2 C:ILE132 5.0 44.2 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe401 b:54.4 occ:1.00 OD1 D:ASN90 2.0 54.5 1.0 NE2 D:HIS180 2.1 48.5 1.0 O1P O:G46511 2.2 66.7 0.9 OD2 D:ASP45 2.2 59.1 1.0 ND1 D:HIS230 2.3 56.1 1.0 O3P O:G46511 3.0 77.2 0.9 CD2 D:HIS180 3.0 46.7 1.0 CG D:ASP45 3.0 54.3 1.0 OD1 D:ASP45 3.1 53.1 1.0 CE1 D:HIS230 3.2 62.9 1.0 CG D:ASN90 3.2 59.5 1.0 P O:G46511 3.2 70.7 0.9 CE1 D:HIS180 3.2 51.7 1.0 CG D:HIS230 3.4 57.4 1.0 ZN D:ZN402 3.7 77.3 1.0 CB D:HIS230 3.7 53.7 1.0 ND2 D:ASN90 3.8 63.5 1.0 CA D:HIS230 3.8 59.0 1.0 O5' O:G46511 4.0 86.9 0.9 CG D:HIS180 4.2 48.0 1.0 ND1 D:HIS180 4.2 51.4 1.0 N D:ASN90 4.3 44.7 1.0 NE2 D:HIS230 4.3 65.0 1.0 CB D:ASN90 4.3 52.7 1.0 CB D:ASP45 4.4 55.8 1.0 SG D:CYS14 4.4 64.9 1.0 CD2 D:HIS230 4.4 58.6 1.0 O D:HIS230 4.5 69.6 1.0 C D:HIS230 4.7 67.7 1.0 C5' O:G46511 4.7 87.0 0.9 N D:HIS230 4.8 57.4 1.0 CA D:ASN90 4.9 50.3 1.0 S2P O:G46511 4.9 98.6 0.9 CG2 D:ILE132 5.0 49.9 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe401 b:45.7 occ:1.00 NE2 E:HIS180 2.0 40.8 1.0 OD1 E:ASN90 2.0 41.6 1.0 OD2 E:ASP45 2.2 47.0 1.0 O3P P:G46511 2.2 54.9 0.7 ND1 E:HIS230 2.4 45.5 1.0 CE1 E:HIS180 2.8 39.6 1.0 O1P P:G46511 2.8 64.2 0.7 CG E:ASP45 3.0 44.2 1.0 CD2 E:HIS180 3.1 38.0 1.0 P P:G46511 3.1 58.4 0.7 CG E:ASN90 3.1 48.9 1.0 OD1 E:ASP45 3.1 43.2 1.0 CE1 E:HIS230 3.3 51.2 1.0 CG E:HIS230 3.4 45.0 1.0 ZN E:ZN402 3.6 55.9 1.0 ND2 E:ASN90 3.6 52.2 1.0 CB E:HIS230 3.8 43.7 1.0 CA E:HIS230 3.8 46.1 1.0 O5' P:G46511 3.9 71.6 0.7 ND1 E:HIS180 4.0 39.2 1.0 CG E:HIS180 4.1 40.0 1.0 N E:ASN90 4.2 36.9 1.0 SG E:CYS14 4.3 50.4 1.0 O E:HIS230 4.3 50.9 1.0 CB E:ASN90 4.4 40.0 1.0 CB E:ASP45 4.4 42.5 1.0 NE2 E:HIS230 4.4 49.1 1.0 C5' P:G46511 4.5 70.2 0.7 CD2 E:HIS230 4.5 49.9 1.0 C E:HIS230 4.6 48.9 1.0 N E:HIS230 4.8 45.4 1.0 S2P P:G46511 4.8 81.2 0.7 CA E:ASN90 4.9 43.3 1.0

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