Iron in PDB 5k73: As-Isolated DBR1 with Fe(II) and Zn(II)

The structure of As-Isolated DBR1 with Fe(II) and Zn(II), PDB code: 5k73 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)	69.22 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.161, 141.705, 213.777, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.3

The structure of As-Isolated DBR1 with Fe(II) and Zn(II) also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Iron atom in the As-Isolated DBR1 with Fe(II) and Zn(II) (pdb code 5k73). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the As-Isolated DBR1 with Fe(II) and Zn(II), PDB code: 5k73:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:47.4 occ:1.00 NE2 A:HIS180 2.2 36.0 1.0 OD1 A:ASN90 2.2 45.5 1.0 OD2 A:ASP45 2.4 39.6 1.0 ND1 A:HIS230 2.5 40.1 1.0 O A:OH406 2.7 53.0 1.0 CD2 A:HIS180 3.1 33.9 1.0 CE1 A:HIS180 3.2 34.2 1.0 CG A:ASP45 3.2 39.2 1.0 CG A:ASN90 3.3 41.8 1.0 OD1 A:ASP45 3.3 36.8 1.0 ZN A:ZN402 3.3 49.5 1.0 CE1 A:HIS230 3.3 39.2 1.0 CG A:HIS230 3.5 39.7 1.0 CA A:HIS230 3.6 39.7 1.0 O A:HOH501 3.6 44.3 1.0 ND2 A:ASN90 3.8 43.8 1.0 CB A:HIS230 3.8 42.7 1.0 O A:HIS230 4.2 38.1 1.0 SG A:CYS14 4.2 40.0 1.0 ND1 A:HIS180 4.3 32.3 1.0 CG A:HIS180 4.3 35.5 1.0 N A:ASN90 4.4 36.8 1.0 C A:HIS230 4.4 45.1 1.0 NE2 A:HIS230 4.5 42.4 1.0 N A:HIS230 4.5 41.3 1.0 CB A:ASN90 4.6 42.3 1.0 CB A:ASP45 4.6 40.8 1.0 CD2 A:HIS230 4.6 39.0 1.0 CE1 A:HIS16 4.9 49.9 1.0 NE2 A:HIS16 4.9 53.6 1.0

Iron binding site 2 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:47.0 occ:1.00 OD1 B:ASN90 2.2 41.3 1.0 NE2 B:HIS180 2.2 37.4 1.0 OD2 B:ASP45 2.3 33.3 1.0 ND1 B:HIS230 2.6 41.0 1.0 O B:OH406 2.7 57.2 1.0 CG B:ASP45 3.1 37.4 1.0 CD2 B:HIS180 3.2 32.0 1.0 OD1 B:ASP45 3.2 40.3 1.0 CE1 B:HIS180 3.2 42.8 1.0 O B:HOH501 3.3 43.7 1.0 CG B:ASN90 3.3 41.7 1.0 ZN B:ZN402 3.4 49.2 1.0 CE1 B:HIS230 3.5 39.8 1.0 CG B:HIS230 3.6 36.3 1.0 CA B:HIS230 3.6 30.7 1.0 CB B:HIS230 3.8 35.6 1.0 ND2 B:ASN90 3.9 45.7 1.0 O B:HIS230 4.1 37.0 1.0 SG B:CYS14 4.1 41.0 1.0 ND1 B:HIS180 4.3 39.1 1.0 CG B:HIS180 4.3 33.9 1.0 N B:ASN90 4.4 38.1 1.0 C B:HIS230 4.4 41.0 1.0 CB B:ASP45 4.5 40.4 1.0 CB B:ASN90 4.6 44.2 1.0 N B:HIS230 4.6 34.3 1.0 NE2 B:HIS230 4.6 44.4 1.0 CD2 B:HIS230 4.7 45.4 1.0 NE2 B:HIS16 4.8 39.1 1.0 CE1 B:HIS16 4.9 45.0 1.0

Iron binding site 3 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:49.1 occ:1.00 OD2 C:ASP45 2.2 50.8 1.0 OD1 C:ASN90 2.2 45.6 1.0 NE2 C:HIS180 2.3 49.7 1.0 ND1 C:HIS230 2.6 43.6 1.0 O C:OH406 2.7 74.8 1.0 CG C:ASP45 3.0 43.2 1.0 CE1 C:HIS180 3.2 48.8 1.0 CG C:ASN90 3.2 46.2 1.0 OD1 C:ASP45 3.2 36.9 1.0 CD2 C:HIS180 3.3 48.6 1.0 ZN C:ZN403 3.3 53.1 1.0 O C:HOH501 3.3 49.6 1.0 CE1 C:HIS230 3.4 41.5 1.0 ND2 C:ASN90 3.6 45.1 1.0 CG C:HIS230 3.6 46.6 1.0 CA C:HIS230 3.7 45.4 1.0 CB C:HIS230 3.9 45.6 1.0 O C:HIS230 4.2 45.4 1.0 SG C:CYS14 4.2 47.0 1.0 ND1 C:HIS180 4.3 39.8 1.0 CG C:HIS180 4.4 45.9 1.0 CB C:ASP45 4.4 44.8 1.0 C C:HIS230 4.4 43.7 1.0 N C:ASN90 4.5 39.3 1.0 CB C:ASN90 4.6 40.2 1.0 NE2 C:HIS230 4.6 43.8 1.0 N C:HIS230 4.6 48.0 1.0 CD2 C:HIS230 4.7 44.7 1.0 CE1 C:HIS16 4.7 43.5 1.0 NE2 C:HIS16 4.8 49.0 1.0 NE2 C:HIS232 4.9 54.6 1.0

Iron binding site 4 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:59.1 occ:1.00 OD1 D:ASN90 2.2 52.1 1.0 NE2 D:HIS180 2.3 49.0 1.0 OD2 D:ASP45 2.4 49.2 1.0 ND1 D:HIS230 2.6 48.1 1.0 O D:OH407 2.7 47.6 1.0 CE1 D:HIS180 3.2 52.5 1.0 CG D:ASN90 3.3 45.2 1.0 CD2 D:HIS180 3.3 36.9 1.0 CG D:ASP45 3.3 42.2 1.0 O D:HOH501 3.3 49.5 1.0 OD1 D:ASP45 3.4 44.6 1.0 ZN D:ZN402 3.4 59.0 1.0 CE1 D:HIS230 3.5 50.4 1.0 CG D:HIS230 3.6 50.7 1.0 CA D:HIS230 3.6 53.3 1.0 ND2 D:ASN90 3.7 55.1 1.0 CB D:HIS230 3.8 50.0 1.0 O D:HIS230 4.0 65.0 1.0 ND1 D:HIS180 4.3 45.1 1.0 SG D:CYS14 4.3 53.8 1.0 C D:HIS230 4.3 57.8 1.0 CG D:HIS180 4.4 44.3 1.0 N D:ASN90 4.5 43.6 1.0 CB D:ASN90 4.6 36.3 1.0 N D:HIS230 4.6 46.0 1.0 NE2 D:HIS230 4.6 51.3 1.0 CB D:ASP45 4.7 42.8 1.0 CD2 D:HIS230 4.7 53.1 1.0 NE2 D:HIS16 4.9 58.4 1.0 CE1 D:HIS16 5.0 61.7 1.0

Iron binding site 5 out of 5 in the As-Isolated DBR1 with Fe(II) and Zn(II)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of As-Isolated DBR1 with Fe(II) and Zn(II) within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe401 b:43.1 occ:1.00 NE2 E:HIS180 2.2 33.3 1.0 OD2 E:ASP45 2.2 32.4 1.0 OD1 E:ASN90 2.2 39.3 1.0 ND1 E:HIS230 2.5 39.5 1.0 O E:OH404 2.7 50.0 1.0 CG E:ASP45 3.1 39.0 1.0 CE1 E:HIS180 3.1 34.7 1.0 CD2 E:HIS180 3.2 26.6 1.0 OD1 E:ASP45 3.3 34.0 1.0 CG E:ASN90 3.3 39.6 1.0 ZN E:ZN402 3.3 45.5 1.0 CE1 E:HIS230 3.4 33.4 1.0 O E:HOH501 3.4 40.8 1.0 CG E:HIS230 3.6 36.5 1.0 CA E:HIS230 3.6 38.8 1.0 ND2 E:ASN90 3.7 32.3 1.0 CB E:HIS230 3.9 38.0 1.0 SG E:CYS14 4.1 41.7 1.0 O E:HIS230 4.2 44.2 1.0 ND1 E:HIS180 4.2 27.6 1.0 CG E:HIS180 4.3 28.2 1.0 C E:HIS230 4.4 41.5 1.0 CB E:ASP45 4.4 38.0 1.0 N E:ASN90 4.5 35.9 1.0 NE2 E:HIS230 4.6 41.1 1.0 N E:HIS230 4.6 45.1 1.0 CB E:ASN90 4.6 30.6 1.0 CD2 E:HIS230 4.7 42.7 1.0 NE2 E:HIS16 4.8 46.1 1.0 CE1 E:HIS16 4.8 46.2 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