Zinc in PDB 6m8q: Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531

The structure of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531, PDB code: 6m8q was solved by W.A.Weihofen, M.Salcius, G.Michaud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.95 / 2.49
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.222, 106.222, 206.035, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 22.1

The structure of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Zinc atom in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 (pdb code 6m8q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531, PDB code: 6m8q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:45.4 occ:1.00 NE2 A:HIS76 2.0 26.2 1.0 O A:HOH630 2.2 59.7 1.0 OD2 A:ASP75 2.2 43.5 1.0 NE2 A:HIS418 2.2 36.6 1.0 OD2 A:ASP179 2.3 34.7 1.0 O2 A:PO4505 2.4 48.0 1.0 CE1 A:HIS418 2.9 36.2 1.0 CD2 A:HIS76 3.0 26.5 1.0 CE1 A:HIS76 3.1 26.4 1.0 CG A:ASP75 3.1 38.8 1.0 CG A:ASP179 3.2 33.6 1.0 CD2 A:HIS418 3.3 36.9 1.0 OD1 A:ASP75 3.4 36.5 1.0 ZN A:ZN502 3.4 41.6 1.0 OD1 A:ASP179 3.5 34.4 1.0 P A:PO4505 3.5 48.3 1.0 O4 A:PO4505 3.8 53.2 1.0 O3 A:PO4505 3.9 53.8 1.0 ND1 A:HIS418 4.1 37.0 1.0 CG A:HIS76 4.1 27.3 1.0 ND1 A:HIS76 4.2 28.4 1.0 O A:HOH666 4.2 43.1 1.0 CG A:HIS418 4.3 35.5 1.0 NE2 A:HIS71 4.3 32.7 1.0 CE1 A:HIS71 4.4 32.4 1.0 CB A:ASP75 4.5 30.9 1.0 CB A:ASP179 4.6 30.3 1.0 CE1 A:HIS396 4.7 33.6 1.0 O1 A:PO4505 4.9 45.9 1.0 ND1 A:HIS73 5.0 32.1 1.0 CG1 A:VAL23 5.0 40.5 1.0

Zinc binding site 2 out of 4 in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:41.6 occ:1.00 O A:HOH630 2.1 59.7 1.0 ND1 A:HIS73 2.2 32.1 1.0 O4 A:PO4505 2.2 53.2 1.0 NE2 A:HIS71 2.2 32.7 1.0 NE2 A:HIS158 2.2 28.7 1.0 OD2 A:ASP179 2.5 34.7 1.0 CD2 A:HIS71 3.1 32.9 1.0 CE1 A:HIS73 3.1 31.2 1.0 CE1 A:HIS158 3.2 28.7 1.0 CG A:HIS73 3.2 30.9 1.0 CD2 A:HIS158 3.2 28.4 1.0 CE1 A:HIS71 3.3 32.4 1.0 P A:PO4505 3.4 48.3 1.0 ZN A:ZN501 3.4 45.4 1.0 CG A:ASP179 3.5 33.6 1.0 CB A:HIS73 3.6 27.6 1.0 O2 A:PO4505 3.6 48.0 1.0 CB A:ASP179 3.7 30.3 1.0 O3 A:PO4505 3.9 53.8 1.0 NE2 A:HIS76 4.0 26.2 1.0 CD2 A:HIS76 4.1 26.5 1.0 O A:HOH608 4.2 50.0 1.0 CG A:HIS71 4.3 31.4 1.0 NE2 A:HIS73 4.3 31.6 1.0 ND1 A:HIS158 4.3 29.9 1.0 CG A:HIS158 4.3 28.3 1.0 CD2 A:HIS73 4.4 32.1 1.0 ND1 A:HIS71 4.4 32.9 1.0 CE1 A:HIS396 4.5 33.6 1.0 OD1 A:ASP179 4.6 34.4 1.0 OD1 A:ASP75 4.7 36.5 1.0 O1 A:PO4505 4.7 45.9 1.0

Zinc binding site 3 out of 4 in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:47.7 occ:1.00 O B:HOH603 1.9 70.1 1.0 NE2 B:HIS418 2.2 33.3 1.0 OD2 B:ASP179 2.2 38.6 1.0 OD2 B:ASP75 2.3 43.7 1.0 O2 B:PO4504 2.3 50.9 1.0 NE2 B:HIS76 2.5 36.4 1.0 CD2 B:HIS76 3.0 36.6 1.0 CG B:ASP75 3.1 46.0 1.0 CD2 B:HIS418 3.2 34.1 1.0 CE1 B:HIS418 3.2 32.7 1.0 CG B:ASP179 3.2 37.3 1.0 OD1 B:ASP75 3.3 48.2 1.0 ZN B:ZN502 3.3 45.0 1.0 P B:PO4504 3.5 48.1 1.0 OD1 B:ASP179 3.5 42.0 1.0 CE1 B:HIS76 3.7 36.2 1.0 O3 B:PO4504 3.7 49.6 1.0 O1 B:PO4504 4.0 50.7 1.0 O B:HOH634 4.1 35.5 1.0 CG B:HIS418 4.3 32.6 1.0 CG B:HIS76 4.3 35.9 1.0 ND1 B:HIS418 4.3 33.2 1.0 NE2 B:HIS71 4.3 31.0 1.0 CB B:ASP75 4.5 35.0 1.0 CB B:ASP179 4.6 32.7 1.0 CE1 B:HIS71 4.6 30.8 1.0 CE1 B:HIS396 4.6 34.0 1.0 ND1 B:HIS76 4.6 37.2 1.0 O4 B:PO4504 4.8 49.8 1.0

Zinc binding site 4 out of 4 in the Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cleavage and Polyadenylation Specificity Factor Subunit 3 (CPSF3) in Complex with Nvp-LTM531 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:45.0 occ:1.00 O B:HOH603 2.0 70.1 1.0 O3 B:PO4504 2.3 49.6 1.0 ND1 B:HIS73 2.3 44.5 1.0 NE2 B:HIS158 2.3 41.7 1.0 NE2 B:HIS71 2.3 31.0 1.0 OD2 B:ASP179 2.5 38.6 1.0 CD2 B:HIS71 3.2 31.6 1.0 CD2 B:HIS158 3.2 41.6 1.0 CE1 B:HIS73 3.3 44.2 1.0 CG B:HIS73 3.3 42.4 1.0 CE1 B:HIS158 3.3 41.1 1.0 ZN B:ZN501 3.3 47.7 1.0 CE1 B:HIS71 3.4 30.8 1.0 P B:PO4504 3.4 48.1 1.0 CG B:ASP179 3.4 37.3 1.0 CB B:HIS73 3.5 39.0 1.0 CB B:ASP179 3.7 32.7 1.0 O2 B:PO4504 3.7 50.9 1.0 O1 B:PO4504 4.0 50.7 1.0 O B:HOH618 4.3 36.8 1.0 CD2 B:HIS76 4.3 36.6 1.0 NE2 B:HIS76 4.4 36.4 1.0 CG B:HIS158 4.4 39.8 1.0 ND1 B:HIS158 4.4 41.7 1.0 CG B:HIS71 4.4 30.9 1.0 NE2 B:HIS73 4.4 44.4 1.0 CD2 B:HIS73 4.4 44.1 1.0 ND1 B:HIS71 4.5 31.9 1.0 OD1 B:ASP75 4.5 48.2 1.0 CE1 B:HIS396 4.5 34.0 1.0 OD1 B:ASP179 4.6 42.0 1.0 O4 B:PO4504 4.8 49.8 1.0 NE2 B:HIS396 4.9 34.4 1.0

N.T.Ross, F.Lohmann, S.Carbonneau, A.Fazal, W.A.Weihofen. CPSF3-Dependent Pre-Mrna Processing As A Druggable Node in Translocation Driven Aml and Ewing'S Sarcoma To Be Published.