Zinc in PDB 5uki: MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1

The structure of MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1, PDB code: 5uki was solved by M.R.Macbeth, L.Ransey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.88 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.341, 70.920, 109.266, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21

The structure of MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Zinc atom in the MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1 (pdb code 5uki). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1, PDB code: 5uki:

Zinc binding site 1 out of 1 in the MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MN2+ and ZN2+ Requirements For the Lariat Debranching Enzyme, DBR1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn400 b:27.4 occ:1.00 O A:HOH545 1.9 18.4 1.0 NE2 A:HIS16 2.1 21.9 1.0 NE2 A:HIS232 2.1 25.5 1.0 SG A:CYS14 2.3 20.9 1.0 OD2 A:ASP45 2.9 21.8 1.0 CD2 A:HIS232 3.0 22.8 1.0 CE1 A:HIS16 3.1 21.5 1.0 CD2 A:HIS16 3.1 21.7 1.0 CB A:CYS14 3.1 22.7 1.0 CE1 A:HIS232 3.2 26.3 1.0 MN A:MN401 3.4 22.1 1.0 O A:HIS230 3.8 22.7 1.0 O A:HOH643 3.9 29.6 1.0 CG A:ASP45 4.0 24.3 1.0 CA A:HIS230 4.1 20.0 1.0 ND1 A:HIS16 4.2 21.3 1.0 CG A:HIS232 4.2 25.9 1.0 CG A:HIS16 4.2 20.8 1.0 ND1 A:HIS232 4.2 25.7 1.0 C A:HIS230 4.3 21.5 1.0 O A:HOH579 4.5 18.9 1.0 CB A:ASP45 4.5 20.9 1.0 CA A:CYS14 4.5 20.9 1.0 N A:HIS230 4.7 18.9 1.0 CE1 A:HIS180 4.7 18.9 1.0 O A:HOH659 4.8 35.8 1.0 NE2 A:HIS180 4.8 17.9 1.0 CB A:LYS249 4.8 27.3 1.0 ND1 A:HIS230 4.8 21.3 1.0

E.Ransey, E.Paredes, S.K.Dey, S.R.Das, A.Heroux, M.R.Macbeth. Crystal Structure of the Entamoeba Histolytica Rna Lariat Debranching Enzyme EHDBR1 Reveals A Catalytic ZN2+/MN2+Heterobinucleation. Febs Lett. V. 591 2003 2017.
ISSN: ISSN 1873-3468
PubMed: 28504306
DOI: 10.1002/1873-3468.12677