Zinc in PDB 5k77: DBR1 in Complex with 7-Mer Branched Rna

The structure of DBR1 in Complex with 7-Mer Branched Rna, PDB code: 5k77 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)	118.01 / 2.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.151, 141.892, 212.511, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.3

The structure of DBR1 in Complex with 7-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 7-Mer Branched Rna (pdb code 5k77). 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 7-Mer Branched Rna, PDB code: 5k77:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the DBR1 in Complex with 7-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 7-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:44.9 occ:1.00 O A:OH408 2.0 31.0 1.0 NE2 A:HIS232 2.2 49.5 1.0 NE2 A:HIS16 2.2 40.5 1.0 SG A:CYS14 2.6 47.1 1.0 OP1 v:G510 2.8 48.2 1.0 OD2 A:ASP45 2.9 34.0 1.0 CD2 A:HIS232 3.0 41.7 1.0 CE1 A:HIS232 3.2 45.5 1.0 CB A:CYS14 3.2 39.6 1.0 CD2 A:HIS16 3.2 45.5 1.0 CE1 A:HIS16 3.2 37.0 1.0 FE A:FE2402 3.5 34.8 1.0 P v:G510 3.9 51.3 1.0 CG A:ASP45 3.9 36.8 1.0 O A:HIS230 4.0 34.5 1.0 OP2 v:G510 4.1 54.8 1.0 CG A:HIS232 4.2 46.7 1.0 ND1 A:HIS232 4.2 44.1 1.0 CB A:ASP45 4.3 30.4 1.0 ND1 A:HIS16 4.3 40.6 1.0 CG A:HIS16 4.3 47.4 1.0 CA A:HIS230 4.4 38.5 1.0 C A:HIS230 4.5 41.3 1.0 CA A:CYS14 4.7 37.9 1.0 O A:HOH526 4.7 39.5 1.0 C5' v:G510 4.7 49.1 1.0 CE1 A:HIS180 4.7 33.5 1.0 NE2 A:HIS180 4.8 35.1 1.0 CB A:LYS249 4.8 43.2 1.0 O5' v:G510 4.8 58.2 1.0 N A:HIS230 4.9 40.7 1.0 ND1 A:HIS230 5.0 31.4 1.0

Zinc binding site 2 out of 5 in the DBR1 in Complex with 7-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 7-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:44.0 occ:1.00 O B:OH407 2.0 31.4 1.0 NE2 B:HIS232 2.2 38.2 1.0 NE2 B:HIS16 2.3 38.4 1.0 SG B:CYS14 2.5 47.9 1.0 OP1 w:G510 2.6 55.6 1.0 OD2 B:ASP45 2.9 36.0 1.0 CD2 B:HIS232 3.1 42.6 1.0 CB B:CYS14 3.1 47.0 1.0 CD2 B:HIS16 3.2 36.0 1.0 CE1 B:HIS16 3.2 41.2 1.0 CE1 B:HIS232 3.2 43.2 1.0 FE B:FE2401 3.5 37.5 1.0 P w:G510 3.8 56.2 1.0 CG B:ASP45 3.9 37.9 1.0 OP2 w:G510 4.1 51.2 1.0 O B:HIS230 4.1 41.0 1.0 CG B:HIS232 4.3 43.9 1.0 CB B:ASP45 4.3 32.9 1.0 ND1 B:HIS232 4.3 39.2 1.0 ND1 B:HIS16 4.3 40.4 1.0 CG B:HIS16 4.3 39.4 1.0 C5' w:G510 4.4 66.2 1.0 CA B:HIS230 4.5 43.6 1.0 O5' w:G510 4.6 64.8 1.0 CA B:CYS14 4.6 40.0 1.0 CE1 B:HIS180 4.6 35.7 1.0 C B:HIS230 4.6 42.6 1.0 O B:HOH566 4.7 31.5 1.0 NE2 B:HIS180 4.7 33.6 1.0 N B:HIS230 4.9 36.4 1.0

Zinc binding site 3 out of 5 in the DBR1 in Complex with 7-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 7-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:46.0 occ:1.00 O C:OH410 2.0 34.5 1.0 NE2 C:HIS16 2.1 38.9 1.0 NE2 C:HIS232 2.2 38.6 1.0 SG C:CYS14 2.5 41.4 1.0 OP1 x:G510 2.8 43.1 1.0 OD2 C:ASP45 2.8 38.6 1.0 CE1 C:HIS16 3.0 33.9 1.0 CD2 C:HIS232 3.1 35.1 1.0 CB C:CYS14 3.2 38.3 1.0 CD2 C:HIS16 3.2 38.0 1.0 CE1 C:HIS232 3.2 39.4 1.0 FE C:FE2402 3.6 35.1 1.0 CG C:ASP45 3.9 39.0 1.0 P x:G510 3.9 52.7 1.0 OP2 x:G510 4.1 58.1 1.0 O C:HIS230 4.2 33.4 1.0 ND1 C:HIS16 4.2 42.5 1.0 CB C:ASP45 4.2 33.2 1.0 CG C:HIS232 4.2 36.8 1.0 ND1 C:HIS232 4.3 43.0 1.0 CG C:HIS16 4.3 44.3 1.0 C5' x:G510 4.5 57.4 1.0 CA C:HIS230 4.5 35.4 1.0 CE1 C:HIS180 4.5 29.9 1.0 CA C:CYS14 4.6 36.0 1.0 NE2 C:HIS180 4.6 34.5 1.0 O5' x:G510 4.7 56.9 1.0 C C:HIS230 4.7 35.9 1.0 O C:HOH558 4.8 34.2 1.0 N C:HIS230 5.0 31.1 1.0 OD1 C:ASP45 5.0 35.0 1.0

Zinc binding site 4 out of 5 in the DBR1 in Complex with 7-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 7-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:50.6 occ:1.00 O D:OH408 2.0 45.4 1.0 NE2 D:HIS16 2.2 39.5 1.0 NE2 D:HIS232 2.2 48.8 1.0 SG D:CYS14 2.4 43.9 1.0 OP1 y:G510 2.8 60.1 1.0 OD2 D:ASP45 2.8 38.1 1.0 CD2 D:HIS232 3.1 48.2 1.0 CD2 D:HIS16 3.1 36.9 1.0 CB D:CYS14 3.2 37.0 1.0 CE1 D:HIS16 3.2 42.8 1.0 CE1 D:HIS232 3.3 53.3 1.0 FE D:FE2401 3.6 39.1 1.0 CG D:ASP45 3.9 38.6 1.0 P y:G510 4.0 63.5 1.0 O D:HIS230 4.1 50.7 1.0 CB D:ASP45 4.2 30.8 1.0 OP2 y:G510 4.2 57.3 1.0 CG D:HIS232 4.3 47.6 1.0 ND1 D:HIS16 4.3 38.5 1.0 CG D:HIS16 4.3 42.4 1.0 ND1 D:HIS232 4.4 52.1 1.0 CA D:HIS230 4.4 42.5 1.0 C D:HIS230 4.5 44.4 1.0 CE1 D:HIS180 4.6 35.9 1.0 CA D:CYS14 4.6 42.7 1.0 C5' y:G510 4.6 59.6 1.0 NE2 D:HIS180 4.7 36.5 1.0 O D:HOH544 4.8 42.8 1.0 O5' y:G510 4.8 63.0 1.0 N D:HIS230 4.9 44.2 1.0 OD1 D:ASP45 5.0 45.6 1.0

Zinc binding site 5 out of 5 in the DBR1 in Complex with 7-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 7-Mer Branched Rna within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn402 b:41.2 occ:1.00 O E:OH407 1.9 32.1 1.0 NE2 E:HIS232 2.2 38.2 1.0 NE2 E:HIS16 2.2 39.0 1.0 SG E:CYS14 2.4 42.0 1.0 OP1 z:G510 2.7 44.5 1.0 OD2 E:ASP45 2.8 35.4 1.0 CD2 E:HIS232 3.0 34.7 1.0 CB E:CYS14 3.1 33.4 1.0 CD2 E:HIS16 3.1 35.5 1.0 CE1 E:HIS16 3.2 30.8 1.0 CE1 E:HIS232 3.2 40.6 1.0 FE E:FE2401 3.5 35.5 1.0 P z:G510 3.8 53.9 1.0 CG E:ASP45 3.9 36.8 1.0 OP2 z:G510 4.0 55.0 1.0 O E:HIS230 4.0 38.8 1.0 CB E:ASP45 4.2 36.9 1.0 CG E:HIS232 4.2 42.2 1.0 ND1 E:HIS232 4.3 42.4 1.0 ND1 E:HIS16 4.3 37.7 1.0 CG E:HIS16 4.3 39.5 1.0 CA E:HIS230 4.4 35.1 1.0 C5' z:G510 4.4 50.9 1.0 CA E:CYS14 4.6 29.7 1.0 C E:HIS230 4.6 35.5 1.0 CE1 E:HIS180 4.6 26.8 1.0 O5' z:G510 4.6 54.7 1.0 NE2 E:HIS180 4.7 34.9 1.0 O E:HOH538 4.8 33.7 1.0 N E:HIS230 4.9 36.2 1.0 OD1 E:ASP45 5.0 37.6 1.0

N.E.Clark, A.Katolik, K.M.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. Metal Dependence and Branched Rna Cocrystal Structures of the Rna Lariat Debranching Enzyme DBR1. Proc. Natl. Acad. Sci. V. 113 14727 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27930312
DOI: 10.1073/PNAS.1612729114