Zinc 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:

Iron

(Fe)

5 atoms

The binding sites of Zinc 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 Zinc atom.
In total 5 binding sites of Zinc where determined in the DBR1 in Complex with 16-Mer Branched Rna, PDB code: 5k78:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:95.9 occ:1.00 NE2 A:HIS232 2.2 0.4 1.0 NE2 A:HIS16 2.3 53.7 1.0 SG A:CYS14 2.6 85.6 1.0 OD2 A:ASP45 2.7 74.0 1.0 CD2 A:HIS232 3.0 71.0 1.0 CE1 A:HIS16 3.2 95.9 1.0 CB A:CYS14 3.2 72.3 1.0 CE1 A:HIS232 3.3 63.4 1.0 FE A:FE2401 3.3 63.1 1.0 CD2 A:HIS16 3.3 63.2 1.0 CG A:ASP45 3.7 58.8 1.0 O A:HIS230 4.0 69.3 1.0 CB A:ASP45 4.2 66.5 1.0 CG A:HIS232 4.2 76.0 1.0 CA A:HIS230 4.3 71.5 1.0 ND1 A:HIS232 4.3 97.8 1.0 ND1 A:HIS16 4.4 60.6 1.0 C A:HIS230 4.4 82.9 1.0 CG A:HIS16 4.4 70.8 1.0 NE2 A:HIS180 4.7 56.0 1.0 CA A:CYS14 4.7 90.8 1.0 OD1 A:ASP45 4.7 78.0 1.0 N A:HIS230 4.7 58.8 1.0 CE1 A:HIS180 4.8 77.2 1.0 ND1 A:HIS230 4.9 67.7 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:1.0 occ:1.00 NE2 B:HIS232 2.3 0.8 1.0 NE2 B:HIS16 2.5 73.2 1.0 SG B:CYS14 2.5 0.9 1.0 CD2 B:HIS232 2.9 82.8 1.0 OD2 B:ASP45 2.9 94.4 1.0 CB B:CYS14 3.2 88.5 1.0 FE B:FE2401 3.3 82.2 1.0 CD2 B:HIS16 3.3 77.8 1.0 CE1 B:HIS232 3.4 0.4 1.0 CE1 B:HIS16 3.5 77.4 1.0 O B:HIS230 3.9 89.3 1.0 CG B:ASP45 3.9 69.9 1.0 CG B:HIS232 4.2 89.3 1.0 CA B:HIS230 4.2 71.8 1.0 CB B:ASP45 4.2 77.3 1.0 C B:HIS230 4.3 0.0 1.0 ND1 B:HIS232 4.4 0.5 1.0 CG B:HIS16 4.5 72.9 1.0 ND1 B:HIS16 4.6 83.7 1.0 NE2 B:HIS180 4.6 66.1 1.0 CA B:CYS14 4.6 0.6 1.0 N B:HIS230 4.7 81.8 1.0 CE1 B:HIS180 4.7 94.9 1.0 OD1 B:ASP45 5.0 78.8 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:78.5 occ:1.00 NE2 C:HIS232 2.2 82.3 1.0 OP1 x:G510 2.2 81.0 0.8 NE2 C:HIS16 2.4 43.2 1.0 SG C:CYS14 2.6 68.0 1.0 OD2 C:ASP45 2.7 66.6 1.0 CD2 C:HIS232 3.0 54.1 1.0 CE1 C:HIS232 3.2 56.2 1.0 CD2 C:HIS16 3.3 45.1 1.0 CB C:CYS14 3.3 38.7 1.0 CE1 C:HIS16 3.4 61.3 1.0 FE C:FE2401 3.5 48.2 1.0 P x:G510 3.5 48.1 0.8 CG C:ASP45 3.8 37.8 1.0 O5' x:G510 3.9 0.2 0.9 O C:HIS230 4.0 58.0 1.0 OP2 x:G510 4.0 0.1 0.9 CB C:ASP45 4.2 51.7 1.0 CG C:HIS232 4.2 86.5 1.0 ND1 C:HIS232 4.2 48.8 1.0 CA C:HIS230 4.3 42.1 1.0 C C:HIS230 4.5 73.0 1.0 ND1 C:HIS16 4.5 41.5 1.0 CG C:HIS16 4.5 54.0 1.0 NE2 C:HIS180 4.6 53.5 1.0 O C:HOH507 4.7 29.9 1.0 OP3 x:G510 4.7 0.8 0.9 CE1 C:HIS180 4.7 52.4 1.0 CA C:CYS14 4.8 40.0 1.0 OD1 C:ASP45 4.8 53.5 1.0 N C:HIS230 4.8 70.5 1.0 ND1 C:HIS230 5.0 42.9 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:79.5 occ:1.00 NE2 D:HIS232 2.4 64.6 1.0 NE2 D:HIS16 2.4 56.0 1.0 SG D:CYS14 2.6 0.2 1.0 OP1 y:G510 2.6 0.5 0.8 OD2 D:ASP45 2.9 95.2 1.0 CD2 D:HIS232 3.1 94.3 1.0 CB D:CYS14 3.2 47.9 1.0 CD2 D:HIS16 3.3 72.7 1.0 FE D:FE2401 3.3 74.3 1.0 CE1 D:HIS16 3.4 47.5 1.0 CE1 D:HIS232 3.5 0.2 1.0 P y:G510 3.6 85.3 0.8 CG D:ASP45 3.8 43.9 1.0 OP2 y:G510 3.8 0.3 0.8 O D:HIS230 4.0 0.8 1.0 CB D:ASP45 4.1 59.2 1.0 CA D:HIS230 4.2 99.1 1.0 O5' y:G510 4.3 0.9 0.8 CG D:HIS232 4.4 67.1 1.0 NE2 D:HIS180 4.5 84.4 1.0 C D:HIS230 4.5 56.0 1.0 CE1 D:HIS180 4.5 44.8 1.0 CG D:HIS16 4.5 92.0 1.0 ND1 D:HIS232 4.5 0.1 1.0 ND1 D:HIS16 4.5 0.3 1.0 CA D:CYS14 4.6 88.1 1.0 N D:HIS230 4.7 49.0 1.0 OD1 D:ASP45 4.8 59.0 1.0 ND1 D:HIS230 5.0 49.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn402 b:75.9 occ:1.00 NE2 E:HIS232 2.1 75.3 1.0 NE2 E:HIS16 2.4 44.4 1.0 SG E:CYS14 2.6 67.0 1.0 OD2 E:ASP45 2.8 59.1 1.0 CD2 E:HIS232 3.0 49.0 1.0 CE1 E:HIS232 3.1 47.6 1.0 FE E:FE2401 3.3 54.9 1.0 CD2 E:HIS16 3.3 60.7 1.0 CB E:CYS14 3.3 52.0 1.0 CE1 E:HIS16 3.4 43.1 1.0 CG E:ASP45 3.8 44.3 1.0 O E:HIS230 4.0 60.1 1.0 CG E:HIS232 4.2 53.1 1.0 ND1 E:HIS232 4.2 63.4 1.0 CB E:ASP45 4.2 55.4 1.0 CA E:HIS230 4.4 40.8 1.0 CG E:HIS16 4.4 49.4 1.0 ND1 E:HIS16 4.5 61.6 1.0 C E:HIS230 4.5 44.6 1.0 NE2 E:HIS180 4.6 62.5 1.0 CE1 E:HIS180 4.7 56.9 1.0 CA E:CYS14 4.7 63.0 1.0 OD1 E:ASP45 4.9 59.9 1.0 ND1 E:HIS230 4.9 47.2 1.0 N E:HIS230 5.0 54.1 1.0 O E:HOH504 5.0 28.0 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