Iron in PDB 5k78: DBR1 in Complex with 16-Mer Branched Rna

The structure of DBR1 in Complex with 16-Mer Branched Rna, PDB code: 5k78 was solved by N.E.Clark, A.B.Taylor, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.34 / 2.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.893, 142.673, 215.131, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.6

The structure of DBR1 in Complex with 16-Mer Branched Rna also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Iron atom in the DBR1 in Complex with 16-Mer Branched Rna (pdb code 5k78). 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 16-Mer Branched Rna, PDB code: 5k78:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the DBR1 in Complex with 16-Mer Branched Rna


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 16-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:63.1 occ:1.00 OD1 A:ASN90 2.2 62.7 1.0 NE2 A:HIS180 2.3 56.0 1.0 ND1 A:HIS230 2.4 67.7 1.0 OD2 A:ASP45 2.5 74.0 1.0 CG A:ASP45 3.1 58.8 1.0 OD1 A:ASP45 3.2 78.0 1.0 CD2 A:HIS180 3.2 75.0 1.0 CE1 A:HIS180 3.3 77.2 1.0 CE1 A:HIS230 3.3 58.3 1.0 CG A:ASN90 3.3 57.6 1.0 ZN A:ZN402 3.3 95.9 1.0 CG A:HIS230 3.4 68.0 1.0 CA A:HIS230 3.5 71.5 1.0 CB A:HIS230 3.7 64.2 1.0 ND2 A:ASN90 3.8 72.3 1.0 O A:HIS230 4.0 69.3 1.0 C A:HIS230 4.3 82.9 1.0 ND1 A:HIS180 4.3 82.7 1.0 CG A:HIS180 4.4 72.2 1.0 CB A:ASP45 4.4 66.5 1.0 SG A:CYS14 4.4 85.6 1.0 NE2 A:HIS230 4.4 71.4 1.0 N A:ASN90 4.5 59.7 1.0 N A:HIS230 4.5 58.8 1.0 CD2 A:HIS230 4.5 80.1 1.0 CB A:ASN90 4.6 56.2 1.0 NE2 A:HIS16 4.9 53.7 1.0

Iron binding site 2 out of 5 in the DBR1 in Complex with 16-Mer Branched Rna


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 16-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:82.2 occ:1.00 NE2 B:HIS180 2.2 66.1 1.0 OD1 B:ASN90 2.3 79.4 1.0 ND1 B:HIS230 2.4 69.9 1.0 OD2 B:ASP45 2.4 94.4 1.0 CD2 B:HIS180 3.1 81.1 1.0 CG B:ASP45 3.1 69.9 1.0 CE1 B:HIS180 3.2 94.9 1.0 ZN B:ZN402 3.3 1.0 1.0 OD1 B:ASP45 3.3 78.8 1.0 CG B:ASN90 3.3 81.2 1.0 CE1 B:HIS230 3.3 70.7 1.0 CA B:HIS230 3.4 71.8 1.0 CG B:HIS230 3.4 70.6 1.0 CB B:HIS230 3.7 98.1 1.0 ND2 B:ASN90 3.8 69.6 1.0 O B:HIS230 3.9 89.3 1.0 C B:HIS230 4.1 0.0 1.0 SG B:CYS14 4.2 0.9 1.0 CG B:HIS180 4.3 77.2 1.0 ND1 B:HIS180 4.3 85.3 1.0 CB B:ASP45 4.3 77.3 1.0 N B:HIS230 4.4 81.8 1.0 NE2 B:HIS230 4.5 0.4 1.0 N B:ASN90 4.5 71.8 1.0 CD2 B:HIS230 4.5 74.1 1.0 CB B:ASN90 4.6 73.2 1.0 NE2 B:HIS16 4.9 73.2 1.0

Iron binding site 3 out of 5 in the DBR1 in Complex with 16-Mer Branched Rna


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 16-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:48.2 occ:1.00 OD1 C:ASN90 2.2 57.2 1.0 NE2 C:HIS180 2.3 53.5 1.0 ND1 C:HIS230 2.4 42.9 1.0 OD2 C:ASP45 2.4 66.6 1.0 OP2 x:G510 2.5 0.1 0.9 CG C:ASP45 3.0 37.8 1.0 OD1 C:ASP45 3.1 53.5 1.0 CD2 C:HIS180 3.1 36.3 1.0 CE1 C:HIS230 3.2 38.6 1.0 CG C:ASN90 3.2 38.5 1.0 CE1 C:HIS180 3.4 52.4 1.0 P x:G510 3.4 48.1 0.8 OP1 x:G510 3.4 81.0 0.8 ZN C:ZN402 3.5 78.5 1.0 CG C:HIS230 3.5 42.8 1.0 ND2 C:ASN90 3.7 44.3 1.0 CA C:HIS230 3.7 42.1 1.0 CB C:HIS230 3.9 55.9 1.0 O C:HIS230 4.1 58.0 1.0 O5' x:G510 4.3 0.2 0.9 CG C:HIS180 4.4 56.7 1.0 NE2 C:HIS230 4.4 54.4 1.0 N C:ASN90 4.4 46.2 1.0 CB C:ASP45 4.4 51.7 1.0 C C:HIS230 4.4 73.0 1.0 ND1 C:HIS180 4.5 62.1 1.0 CB C:ASN90 4.5 50.2 1.0 SG C:CYS14 4.5 68.0 1.0 CD2 C:HIS230 4.5 62.3 1.0 OP3 x:G510 4.7 0.8 0.9 C5' x:G510 4.8 46.0 0.8 N C:HIS230 4.8 70.5 1.0 NE2 C:HIS16 4.9 43.2 1.0 CA C:ASN90 5.0 37.6 1.0

Iron binding site 4 out of 5 in the DBR1 in Complex with 16-Mer Branched Rna


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 16-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:74.3 occ:1.00 OD1 D:ASN90 2.1 65.3 1.0 NE2 D:HIS180 2.1 84.4 1.0 OP2 y:G510 2.3 0.3 0.8 OD2 D:ASP45 2.4 95.2 1.0 ND1 D:HIS230 2.5 49.1 1.0 CG D:ASP45 3.0 43.9 1.0 CD2 D:HIS180 3.1 54.1 1.0 CG D:ASN90 3.1 57.2 1.0 CE1 D:HIS180 3.1 44.8 1.0 OD1 D:ASP45 3.1 59.0 1.0 CE1 D:HIS230 3.3 77.4 1.0 ZN D:ZN402 3.3 79.5 1.0 P y:G510 3.5 85.3 0.8 ND2 D:ASN90 3.5 71.2 1.0 CG D:HIS230 3.6 69.3 1.0 CA D:HIS230 3.7 99.1 1.0 OP1 y:G510 3.7 0.5 0.8 CB D:HIS230 3.9 72.9 1.0 O D:HIS230 4.2 0.8 1.0 ND1 D:HIS180 4.2 73.6 1.0 CG D:HIS180 4.2 43.4 1.0 CB D:ASP45 4.3 59.2 1.0 O5' y:G510 4.3 0.9 0.8 N D:ASN90 4.4 45.7 1.0 SG D:CYS14 4.4 0.2 1.0 CB D:ASN90 4.4 55.1 1.0 C D:HIS230 4.5 56.0 1.0 NE2 D:HIS230 4.5 55.0 1.0 OP3 y:G510 4.6 0.6 0.8 CD2 D:HIS230 4.6 63.6 1.0 N D:HIS230 4.7 49.0 1.0 NE2 D:HIS16 4.8 56.0 1.0 C5' y:G510 4.8 99.4 0.8 CA D:ASN90 4.9 42.7 1.0

Iron binding site 5 out of 5 in the DBR1 in Complex with 16-Mer Branched Rna


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 16-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:54.9 occ:1.00 NE2 E:HIS180 2.1 62.5 1.0 OD1 E:ASN90 2.3 45.0 1.0 ND1 E:HIS230 2.4 47.2 1.0 OD2 E:ASP45 2.4 59.1 1.0 CG E:ASP45 3.0 44.3 1.0 CE1 E:HIS180 3.1 56.9 1.0 CD2 E:HIS180 3.1 38.1 1.0 CE1 E:HIS230 3.2 40.2 1.0 OD1 E:ASP45 3.2 59.9 1.0 ZN E:ZN402 3.3 75.9 1.0 CG E:ASN90 3.4 46.3 1.0 CG E:HIS230 3.5 45.3 1.0 CA E:HIS230 3.6 40.8 1.0 CB E:HIS230 3.8 55.5 1.0 ND2 E:ASN90 3.8 50.7 1.0 O E:HIS230 4.0 60.1 1.0 ND1 E:HIS180 4.2 45.4 1.0 SG E:CYS14 4.2 67.0 1.0 CG E:HIS180 4.3 59.3 1.0 CB E:ASP45 4.3 55.4 1.0 C E:HIS230 4.4 44.6 1.0 NE2 E:HIS230 4.4 50.2 1.0 N E:ASN90 4.5 46.8 1.0 CD2 E:HIS230 4.5 56.8 1.0 N E:HIS230 4.6 54.1 1.0 CB E:ASN90 4.6 41.7 1.0 NE2 E:HIS16 4.7 44.4 1.0 NE2 E:HIS232 5.0 75.3 1.0

N.E.Clark, A.Katolik, K.Roberts, A.B.Taylor, S.P.Holloway, J.P.Schuermann, E.J.Montemayor, S.W.Stevens, P.F.Fitzpatrick, M.J.Damha, P.J.Hart. The Rna Lariat Debranching Enzyme DBR1: Metal Dependence and Branched Rna Co-Crystal Structures Proc.Natl.Acad.Sci.Usa 2016.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1612729114