Zinc 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:

Iron

(Fe)

5 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the As-Isolated DBR1 with Fe(II) and Zn(II), PDB code: 5k73:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:49.5 occ:1.00 O A:OH406 2.1 53.0 1.0 NE2 A:HIS16 2.3 53.6 1.0 NE2 A:HIS232 2.3 53.1 1.0 SG A:CYS14 2.4 40.0 1.0 OD2 A:ASP45 2.6 39.6 1.0 CB A:CYS14 3.1 40.7 1.0 CD2 A:HIS232 3.1 49.9 1.0 CE1 A:HIS16 3.1 49.9 1.0 CD2 A:HIS16 3.3 51.6 1.0 FE A:FE2401 3.3 47.4 1.0 CE1 A:HIS232 3.4 58.0 1.0 CG A:ASP45 3.8 39.2 1.0 O A:HIS230 3.8 38.1 1.0 O A:HOH501 3.9 44.3 1.0 CA A:HIS230 4.2 39.7 1.0 ND1 A:HIS16 4.3 57.9 1.0 CG A:HIS232 4.3 48.7 1.0 CB A:ASP45 4.3 40.8 1.0 C A:HIS230 4.4 45.1 1.0 CG A:HIS16 4.4 55.5 1.0 ND1 A:HIS232 4.5 49.9 1.0 CA A:CYS14 4.5 38.2 1.0 NE2 A:HIS180 4.6 36.0 1.0 O A:HOH542 4.6 40.0 1.0 N A:HIS230 4.6 41.3 1.0 CE1 A:HIS180 4.6 34.2 1.0 OD1 A:ASP45 4.8 36.8 1.0 CB A:LYS249 4.9 42.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:49.2 occ:1.00 NE2 B:HIS232 2.2 44.5 1.0 O B:OH406 2.2 57.2 1.0 NE2 B:HIS16 2.3 39.1 1.0 SG B:CYS14 2.4 41.0 1.0 OD2 B:ASP45 2.6 33.3 1.0 CB B:CYS14 3.0 38.8 1.0 CD2 B:HIS232 3.0 46.7 1.0 CD2 B:HIS16 3.2 41.5 1.0 CE1 B:HIS16 3.3 45.0 1.0 CE1 B:HIS232 3.3 54.0 1.0 FE B:FE2401 3.4 47.0 1.0 CG B:ASP45 3.8 37.4 1.0 O B:HOH501 3.9 43.7 1.0 O B:HIS230 4.0 37.0 1.0 CA B:HIS230 4.2 30.7 1.0 CG B:HIS232 4.2 46.0 1.0 ND1 B:HIS232 4.3 47.2 1.0 CB B:ASP45 4.3 40.4 1.0 ND1 B:HIS16 4.3 47.8 1.0 CG B:HIS16 4.4 40.9 1.0 C B:HIS230 4.4 41.0 1.0 CA B:CYS14 4.5 40.1 1.0 O B:HOH559 4.5 34.9 1.0 NE2 B:HIS180 4.6 37.4 1.0 N B:HIS230 4.7 34.3 1.0 CE1 B:HIS180 4.7 42.8 1.0 CB B:LYS249 4.8 50.1 1.0 OD1 B:ASP45 4.8 40.3 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn403 b:53.1 occ:1.00 O C:OH406 2.1 74.8 1.0 NE2 C:HIS232 2.2 54.6 1.0 NE2 C:HIS16 2.3 49.0 1.0 SG C:CYS14 2.5 47.0 1.0 OD2 C:ASP45 2.7 50.8 1.0 CD2 C:HIS232 3.0 48.7 1.0 CB C:CYS14 3.1 45.0 1.0 CE1 C:HIS16 3.1 43.5 1.0 FE C:FE2402 3.3 49.1 1.0 CD2 C:HIS16 3.3 50.4 1.0 CE1 C:HIS232 3.3 53.1 1.0 CG C:ASP45 3.8 43.2 1.0 O C:HIS230 3.9 45.4 1.0 O C:HOH501 4.0 49.6 1.0 CG C:HIS232 4.2 51.7 1.0 CA C:HIS230 4.2 45.4 1.0 ND1 C:HIS16 4.2 49.5 1.0 CB C:ASP45 4.3 44.8 1.0 ND1 C:HIS232 4.4 55.1 1.0 CG C:HIS16 4.4 50.6 1.0 C C:HIS230 4.4 43.7 1.0 O C:HOH558 4.5 40.2 1.0 CA C:CYS14 4.5 43.6 1.0 NE2 C:HIS180 4.6 49.7 1.0 CE1 C:HIS180 4.7 48.8 1.0 N C:HIS230 4.7 48.0 1.0 CB C:LYS249 4.8 56.3 1.0 OD1 C:ASP45 4.9 36.9 1.0 ND1 C:HIS230 5.0 43.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:59.0 occ:1.00 O D:OH407 2.1 47.6 1.0 SG D:CYS14 2.3 53.8 1.0 NE2 D:HIS16 2.4 58.4 1.0 NE2 D:HIS232 2.5 70.6 1.0 OD2 D:ASP45 2.7 49.2 1.0 CB D:CYS14 2.9 54.0 1.0 CD2 D:HIS232 3.1 73.9 1.0 CD2 D:HIS16 3.3 64.0 1.0 CE1 D:HIS16 3.4 61.7 1.0 FE D:FE2401 3.4 59.1 1.0 CE1 D:HIS232 3.7 71.2 1.0 CG D:ASP45 3.8 42.2 1.0 O D:HIS230 4.2 65.0 1.0 CB D:ASP45 4.3 42.8 1.0 CA D:HIS230 4.3 53.3 1.0 O D:HOH501 4.3 49.5 1.0 CA D:CYS14 4.4 50.2 1.0 CG D:HIS232 4.4 73.6 1.0 O D:HOH569 4.4 52.9 1.0 ND1 D:HIS16 4.4 66.7 1.0 CG D:HIS16 4.4 62.1 1.0 C D:HIS230 4.5 57.8 1.0 ND1 D:HIS232 4.7 72.0 1.0 CE1 D:HIS180 4.7 52.5 1.0 N D:HIS230 4.7 46.0 1.0 NE2 D:HIS180 4.7 49.0 1.0 CB D:LYS249 4.8 60.0 1.0 OD1 D:ASP45 4.9 44.6 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:45.5 occ:1.00 O E:OH404 2.1 50.0 1.0 NE2 E:HIS232 2.3 44.2 1.0 NE2 E:HIS16 2.3 46.1 1.0 SG E:CYS14 2.3 41.7 1.0 OD2 E:ASP45 2.7 32.4 1.0 CB E:CYS14 2.9 35.9 1.0 CD2 E:HIS232 3.0 39.2 1.0 CE1 E:HIS16 3.2 46.2 1.0 CD2 E:HIS16 3.2 46.6 1.0 FE E:FE2401 3.3 43.1 1.0 CE1 E:HIS232 3.4 50.2 1.0 CG E:ASP45 3.8 39.0 1.0 O E:HIS230 3.9 44.2 1.0 O E:HOH501 4.0 40.8 1.0 CA E:HIS230 4.3 38.8 1.0 CG E:HIS232 4.3 44.6 1.0 ND1 E:HIS16 4.3 46.5 1.0 CB E:ASP45 4.3 38.0 1.0 CG E:HIS16 4.3 45.0 1.0 CA E:CYS14 4.4 38.3 1.0 ND1 E:HIS232 4.4 50.6 1.0 O E:HOH548 4.5 39.8 1.0 C E:HIS230 4.5 41.5 1.0 CE1 E:HIS180 4.7 34.7 1.0 NE2 E:HIS180 4.7 33.3 1.0 CB E:LYS249 4.7 46.4 1.0 N E:HIS230 4.7 45.1 1.0 OD1 E:ASP45 4.9 34.0 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