Zinc in PDB 6i1d: Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae

The structure of Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae, PDB code: 6i1d was solved by C.H.Hill, V.Boreikaite, A.Kumar, A.Casanal, P.Kubik, G.Degliesposti, S.Maslen, A.Mariani, O.Von Loeffelholz, M.Girbig, M.Skehel, L.A.Passmore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.14 / 2.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.380, 124.270, 63.450, 90.00, 103.21, 90.00
R / Rfree (%)	17.3 / 22.2

The binding sites of Zinc atom in the Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae (pdb code 6i1d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae, PDB code: 6i1d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:55.7 occ:1.00 O A:HOH646 2.0 54.3 1.0 OD2 A:ASP184 2.1 51.5 1.0 NE2 A:HIS430 2.1 53.8 1.0 NE2 A:HIS73 2.3 42.2 1.0 OD2 A:ASP72 2.3 46.3 1.0 CD2 A:HIS73 3.0 36.0 1.0 CD2 A:HIS430 3.0 42.1 1.0 CE1 A:HIS430 3.0 43.3 1.0 CG A:ASP184 3.1 45.2 1.0 CG A:ASP72 3.3 54.6 1.0 OD1 A:ASP184 3.3 45.9 1.0 O A:HOH743 3.4 65.8 1.0 ZN A:ZN502 3.4 82.8 0.8 CE1 A:HIS73 3.5 45.1 1.0 OD1 A:ASP72 3.7 61.7 1.0 O A:HOH629 4.0 41.9 1.0 ND1 A:HIS430 4.1 43.9 1.0 CG A:HIS430 4.1 38.0 1.0 CG A:HIS73 4.3 43.7 1.0 NE2 A:HIS68 4.4 42.9 1.0 CB A:ASP184 4.4 43.3 1.0 ND1 A:HIS73 4.5 46.7 1.0 CE1 A:HIS408 4.5 49.0 1.0 CB A:ASP72 4.6 49.4 1.0 O A:HOH735 4.6 72.2 1.0 CE1 A:HIS68 4.6 42.1 1.0 CG1 A:VAL20 4.8 35.3 1.0 NE2 A:HIS408 4.9 51.7 1.0

Zinc binding site 2 out of 2 in the Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the YSH1-MPE1 Nuclease Complex From S.Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:82.8 occ:0.82 NE2 A:HIS163 2.3 54.7 1.0 ND1 A:HIS70 2.4 54.1 1.0 O A:HOH646 2.4 54.3 1.0 OD2 A:ASP184 2.6 51.5 1.0 NE2 A:HIS68 2.6 42.9 1.0 CD2 A:HIS163 3.1 48.6 1.0 CE1 A:HIS163 3.2 50.5 1.0 CE1 A:HIS70 3.3 53.4 1.0 CD2 A:HIS68 3.4 39.5 1.0 ZN A:ZN501 3.4 55.7 1.0 O A:HOH735 3.4 72.2 1.0 CG A:HIS70 3.4 45.0 1.0 CG A:ASP184 3.5 45.2 1.0 CE1 A:HIS68 3.6 42.1 1.0 CB A:HIS70 3.7 40.4 1.0 CB A:ASP184 3.8 43.3 1.0 CD2 A:HIS73 4.2 36.0 1.0 CG A:HIS163 4.2 49.4 1.0 NE2 A:HIS73 4.3 42.2 1.0 ND1 A:HIS163 4.3 46.7 1.0 O A:HOH743 4.4 65.8 1.0 NE2 A:HIS70 4.5 54.8 1.0 CD2 A:HIS70 4.5 52.8 1.0 CG A:HIS68 4.6 46.0 1.0 NE2 A:HIS408 4.6 51.7 1.0 OD1 A:ASP72 4.6 61.7 1.0 CE1 A:HIS408 4.6 49.0 1.0 O A:HOH677 4.6 57.1 1.0 ND1 A:HIS68 4.7 49.2 1.0 OD1 A:ASP184 4.7 45.9 1.0 O A:HOH747 4.7 65.2 1.0 OD2 A:ASP72 4.8 46.3 1.0

C.H.Hill, V.Boreikaite, A.Kumar, A.Casanal, P.Kubik, G.Degliesposti, S.Maslen, A.Mariani, O.Von Loeffelholz, M.Girbig, M.Skehel, L.A.Passmore. Activation of the Endonuclease That Defines Mrna 3' Ends Requires Incorporation Into An 8-Subunit Core Cleavage and Polyadenylation Factor Complex. Mol.Cell V. 73 1217 2019.
ISSN: ISSN 1097-2765
PubMed: 30737185
DOI: 10.1016/J.MOLCEL.2018.12.023