Zinc in PDB 7zyh: Crystal Structure of Human CPSF30 in Complex with HFIP1

The structure of Crystal Structure of Human CPSF30 in Complex with HFIP1, PDB code: 7zyh was solved by L.M.Muckenfuss, M.Jinek, A.C.Migenda Herranz, M.Clerici, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.65 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.127, 115.125, 66.444, 90, 116.78, 90
R / Rfree (%)	24.7 / 26.4

The binding sites of Zinc atom in the Crystal Structure of Human CPSF30 in Complex with HFIP1 (pdb code 7zyh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Human CPSF30 in Complex with HFIP1, PDB code: 7zyh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:54.0 occ:1.00 NE2 A:HIS142 2.1 47.3 1.0 SG A:CYS132 2.3 44.6 1.0 SG A:CYS138 2.3 58.3 1.0 SG A:CYS124 2.3 68.9 1.0 HB2 A:CYS138 2.8 68.5 1.0 CD2 A:HIS142 3.0 46.2 1.0 CB A:CYS138 3.0 57.1 1.0 CE1 A:HIS142 3.0 49.2 1.0 HB2 A:CYS132 3.2 52.8 1.0 HD2 A:HIS142 3.2 55.5 1.0 HB3 A:CYS138 3.2 68.5 1.0 HE1 A:HIS142 3.2 59.1 1.0 CB A:CYS132 3.3 44.0 1.0 HB2 A:CYS124 3.4 81.1 1.0 CB A:CYS124 3.5 67.6 1.0 HB3 A:CYS132 3.6 52.8 1.0 HB2 A:TYR127 3.7 51.9 1.0 HB3 A:CYS124 3.8 81.1 1.0 HB2 A:TRP126 3.9 50.1 1.0 H A:TYR127 4.0 55.1 1.0 ND1 A:HIS142 4.1 42.9 1.0 CG A:HIS142 4.2 45.4 1.0 H A:GLY135 4.3 58.7 1.0 HB2 A:HIS140 4.3 77.1 1.0 HB2 A:HIS134 4.4 64.9 1.0 CA A:CYS138 4.4 58.4 1.0 HA A:CYS138 4.6 70.0 1.0 CB A:TYR127 4.6 43.3 1.0 H A:HIS140 4.6 73.3 1.0 N A:TYR127 4.7 46.0 1.0 CA A:CYS132 4.7 40.4 1.0 O A:HIS140 4.7 66.8 1.0 HA A:CYS132 4.8 48.5 1.0 H A:TRP126 4.8 58.8 1.0 HD1 A:TRP126 4.8 48.1 1.0 HB3 A:TYR127 4.8 51.9 1.0 CB A:TRP126 4.9 41.8 1.0 CA A:CYS124 4.9 61.5 1.0 HD1 A:HIS142 4.9 51.4 1.0 HA A:CYS124 5.0 73.8 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:46.4 occ:1.00 NE2 A:HIS166 2.1 41.3 1.0 SG A:CYS162 2.3 53.2 1.0 SG A:CYS148 2.3 44.2 1.0 SG A:CYS156 2.3 45.2 1.0 HB2 A:CYS148 3.0 46.8 1.0 HB2 A:CYS162 3.0 57.8 1.0 CE1 A:HIS166 3.0 44.3 1.0 CB A:CYS162 3.1 48.2 1.0 CB A:CYS148 3.1 39.0 1.0 HB2 A:CYS156 3.1 49.2 1.0 CD2 A:HIS166 3.1 39.3 1.0 CB A:CYS156 3.2 41.0 1.0 HB3 A:CYS162 3.2 57.8 1.0 HE1 A:HIS166 3.2 53.2 1.0 HB3 A:CYS156 3.3 49.2 1.0 HB3 A:CYS148 3.3 46.8 1.0 HD2 A:HIS166 3.3 47.2 1.0 HB2 A:TYR151 3.7 43.9 1.0 HB2 A:PHE164 4.1 53.1 1.0 H A:TYR151 4.1 45.4 1.0 HB2 A:ASN150 4.2 45.9 1.0 ND1 A:HIS166 4.2 38.7 1.0 O A:PHE164 4.2 52.4 1.0 HB2 A:GLU158 4.2 56.3 1.0 CG A:HIS166 4.3 36.3 1.0 H A:PHE164 4.4 63.4 1.0 HD2 A:PHE164 4.4 52.6 1.0 CA A:CYS148 4.6 35.7 1.0 CA A:CYS162 4.6 52.0 1.0 CB A:TYR151 4.6 36.6 1.0 CA A:CYS156 4.6 42.1 1.0 N A:TYR151 4.7 37.8 1.0 HA A:CYS148 4.7 42.8 1.0 HA A:CYS162 4.8 62.4 1.0 HB3 A:TYR151 4.8 43.9 1.0 O A:HOH1106 4.8 36.3 1.0 H A:GLY159 4.8 53.4 1.0 HA A:CYS156 4.8 50.5 1.0 HD1 A:HIS166 5.0 46.5 1.0 C A:PHE164 5.0 40.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:69.1 occ:1.00 NE2 D:HIS142 2.0 67.8 1.0 SG D:CYS132 2.3 60.8 1.0 SG D:CYS138 2.3 67.7 1.0 SG D:CYS124 2.3 62.6 1.0 HB2 D:CYS124 2.5 69.1 1.0 HB2 D:CYS132 2.8 80.2 1.0 HB2 D:CYS138 2.8 82.0 1.0 CB D:CYS124 2.8 57.6 1.0 CB D:CYS132 2.9 66.8 1.0 HB3 D:CYS124 3.0 69.1 1.0 CD2 D:HIS142 3.0 67.6 1.0 CE1 D:HIS142 3.0 71.2 1.0 CB D:CYS138 3.0 68.3 1.0 HB3 D:CYS132 3.1 80.2 1.0 HD2 D:HIS142 3.2 81.1 1.0 HE1 D:HIS142 3.2 85.5 1.0 HB3 D:CYS138 3.4 82.0 1.0 HB2 D:TYR127 3.4 65.4 1.0 H D:TYR127 3.9 61.3 1.0 HB2 D:TRP126 4.0 66.8 1.0 HD2 D:HIS134 4.0 95.5 1.0 HB2 D:HIS134 4.0 85.5 1.0 ND1 D:HIS142 4.1 66.4 1.0 CG D:HIS142 4.2 64.2 1.0 CA D:CYS124 4.2 57.1 1.0 CA D:CYS132 4.4 63.9 1.0 CB D:TYR127 4.4 54.5 1.0 CA D:CYS138 4.4 70.0 1.0 HB2 D:HIS140 4.4 81.3 1.0 HA D:CYS124 4.4 68.5 1.0 CD2 D:HIS134 4.4 79.6 1.0 HA D:CYS138 4.5 84.0 1.0 N D:TYR127 4.5 51.1 1.0 HA D:CYS132 4.6 76.6 1.0 H D:HIS140 4.6 90.0 1.0 H D:HIS134 4.6 82.4 1.0 HB3 D:TYR127 4.7 65.4 1.0 HD1 D:TRP126 4.7 86.1 1.0 H D:TRP126 4.8 65.5 1.0 H D:GLY135 4.8 87.3 1.0 CG D:HIS134 4.8 74.8 1.0 CB D:HIS134 4.8 71.3 1.0 HD1 D:HIS142 4.9 79.7 1.0 CB D:TRP126 4.9 55.7 1.0 HD1 D:TYR127 5.0 61.7 1.0 H D:CYS124 5.0 71.4 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:54.8 occ:1.00 NE2 D:HIS166 2.1 45.9 1.0 SG D:CYS162 2.3 48.1 1.0 SG D:CYS148 2.3 67.5 1.0 SG D:CYS156 2.3 52.1 1.0 HB2 D:CYS148 2.8 68.0 1.0 HB2 D:CYS162 2.9 58.5 1.0 CB D:CYS148 3.0 56.6 1.0 CD2 D:HIS166 3.0 43.8 1.0 CE1 D:HIS166 3.1 48.9 1.0 CB D:CYS162 3.1 48.7 1.0 HB3 D:CYS148 3.1 68.0 1.0 HD2 D:HIS166 3.2 52.6 1.0 HB2 D:CYS156 3.2 47.4 1.0 HB3 D:CYS162 3.2 58.5 1.0 HE1 D:HIS166 3.3 58.7 1.0 CB D:CYS156 3.3 39.5 1.0 HB3 D:CYS156 3.5 47.4 1.0 HB2 D:TYR151 3.6 51.1 1.0 HB2 D:GLU158 3.9 50.7 1.0 H D:TYR151 4.1 48.8 1.0 HB2 D:PHE164 4.1 61.6 1.0 ND1 D:HIS166 4.1 48.0 1.0 CG D:HIS166 4.2 42.6 1.0 O D:PHE164 4.2 55.7 1.0 HB2 D:ASN150 4.3 54.4 1.0 CA D:CYS148 4.4 49.9 1.0 HD1 D:PHE164 4.5 68.2 1.0 CA D:CYS162 4.5 44.5 1.0 CB D:TYR151 4.6 42.5 1.0 H D:PHE164 4.6 62.4 1.0 HA D:CYS148 4.6 59.9 1.0 O C:HOH212 4.6 47.3 1.0 HA D:CYS162 4.7 53.4 1.0 CA D:CYS156 4.7 43.0 1.0 HB3 D:TYR151 4.7 51.1 1.0 N D:TYR151 4.7 40.7 1.0 CB D:GLU158 4.8 42.2 1.0 HA D:CYS156 4.9 51.6 1.0 H D:GLY159 4.9 57.2 1.0 H D:GLU158 4.9 53.5 1.0 HD1 D:HIS166 4.9 57.5 1.0 HG3 D:GLU158 5.0 53.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1001 b:60.0 occ:1.00 NE2 G:HIS142 2.1 49.1 1.0 SG G:CYS132 2.3 48.5 1.0 SG G:CYS138 2.3 56.7 1.0 SG G:CYS124 2.3 57.2 1.0 HB2 G:CYS138 2.7 71.4 1.0 CB G:CYS138 2.9 59.5 1.0 CE1 G:HIS142 3.0 52.8 1.0 HB2 G:CYS132 3.0 69.6 1.0 HE1 G:HIS142 3.1 63.3 1.0 CB G:CYS132 3.1 58.0 1.0 HB3 G:CYS138 3.1 71.4 1.0 CD2 G:HIS142 3.2 52.5 1.0 HB2 G:CYS124 3.2 67.6 1.0 HB3 G:CYS132 3.2 69.6 1.0 CB G:CYS124 3.4 56.3 1.0 HD2 G:HIS142 3.4 62.9 1.0 HB3 G:CYS124 3.7 67.6 1.0 HB2 G:TYR127 3.7 66.1 1.0 HB2 G:HIS134 4.1 65.8 1.0 H G:GLY135 4.1 67.9 1.0 ND1 G:HIS142 4.1 54.2 1.0 H G:TYR127 4.2 64.6 1.0 HB2 G:TRP126 4.2 71.6 1.0 CG G:HIS142 4.2 52.5 1.0 HB2 G:HIS140 4.3 85.5 1.0 HD2 G:HIS134 4.3 80.3 1.0 CA G:CYS138 4.4 63.0 1.0 H G:HIS140 4.5 91.8 1.0 CA G:CYS132 4.5 58.7 1.0 HA G:CYS138 4.6 75.6 1.0 CB G:TYR127 4.7 55.0 1.0 CA G:CYS124 4.7 57.5 1.0 O G:HIS140 4.7 61.5 1.0 HA G:CYS124 4.8 68.9 1.0 HA G:CYS132 4.8 70.5 1.0 CD2 G:HIS134 4.8 66.9 1.0 N G:TYR127 4.8 53.8 1.0 HD2 G:HIS140 4.8 80.9 1.0 HD1 G:HIS142 4.8 65.1 1.0 H G:HIS134 4.9 68.2 1.0 N G:GLY135 4.9 56.6 1.0 HB3 G:TYR127 4.9 66.1 1.0 HD1 G:TRP126 4.9 73.2 1.0 H G:TRP126 4.9 70.3 1.0 CB G:HIS134 5.0 54.8 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1002 b:54.6 occ:1.00 NE2 G:HIS166 2.0 46.9 1.0 SG G:CYS162 2.3 48.5 1.0 SG G:CYS148 2.3 40.3 1.0 SG G:CYS156 2.3 45.7 1.0 HB2 G:CYS148 2.7 56.4 1.0 CB G:CYS148 2.9 47.0 1.0 CE1 G:HIS166 3.0 50.8 1.0 CD2 G:HIS166 3.0 48.2 1.0 HB3 G:CYS148 3.0 56.4 1.0 HB2 G:CYS156 3.1 58.3 1.0 HB2 G:CYS162 3.1 64.0 1.0 HE1 G:HIS166 3.1 61.0 1.0 CB G:CYS162 3.2 53.4 1.0 CB G:CYS156 3.2 48.6 1.0 HD2 G:HIS166 3.2 57.8 1.0 HB3 G:CYS162 3.3 64.0 1.0 HB3 G:CYS156 3.5 58.3 1.0 HB2 G:TYR151 3.5 54.1 1.0 HB2 G:PHE164 3.9 61.8 1.0 H G:TYR151 4.0 47.9 1.0 ND1 G:HIS166 4.1 48.9 1.0 CG G:HIS166 4.1 47.8 1.0 HD2 G:PHE164 4.2 64.7 1.0 O G:PHE164 4.2 57.0 1.0 HB2 G:GLU158 4.3 64.0 1.0 HB2 G:ASN150 4.3 50.8 1.0 H G:PHE164 4.4 74.0 1.0 CA G:CYS148 4.4 42.1 1.0 CB G:TYR151 4.4 45.1 1.0 HB3 G:TYR151 4.5 54.1 1.0 HA G:CYS148 4.6 50.5 1.0 CA G:CYS156 4.6 44.8 1.0 CA G:CYS162 4.6 50.5 1.0 N G:TYR151 4.7 39.9 1.0 HA G:CYS156 4.8 53.8 1.0 HA G:CYS162 4.8 60.6 1.0 CB G:PHE164 4.8 51.5 1.0 HD1 G:HIS166 4.9 58.6 1.0 C G:PHE164 4.9 49.5 1.0 H G:GLY159 4.9 60.9 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1001 b:56.0 occ:1.00 NE2 J:HIS142 2.0 52.3 1.0 SG J:CYS132 2.3 113.7 1.0 SG J:CYS138 2.3 52.5 1.0 SG J:CYS124 2.3 48.8 1.0 HB2 J:CYS138 2.9 65.2 1.0 CD2 J:HIS142 2.9 49.4 1.0 HB2 J:CYS132 3.0 60.3 1.0 CB J:CYS138 3.0 54.3 1.0 HD2 J:HIS142 3.1 59.3 1.0 HB3 J:CYS138 3.1 65.2 1.0 CE1 J:HIS142 3.1 54.3 1.0 CB J:CYS132 3.1 50.2 1.0 HB2 J:CYS124 3.3 67.2 1.0 HB3 J:CYS132 3.3 60.3 1.0 HE1 J:HIS142 3.3 65.2 1.0 CB J:CYS124 3.4 56.0 1.0 HB2 J:TYR127 3.6 56.9 1.0 HB2 J:TRP126 3.7 70.2 1.0 HB3 J:CYS124 3.7 67.2 1.0 HB2 J:HIS140 3.9 67.5 1.0 H J:TYR127 4.0 60.1 1.0 CG J:HIS142 4.1 52.0 1.0 ND1 J:HIS142 4.2 53.3 1.0 HD2 J:HIS140 4.2 64.8 1.0 HD2 J:HIS134 4.2 71.3 1.0 H J:HIS140 4.3 80.9 1.0 CA J:CYS138 4.5 54.3 1.0 CB J:TYR127 4.5 47.4 1.0 CA J:CYS132 4.5 47.2 1.0 HD1 J:TRP126 4.6 112.9 1.0 N J:TYR127 4.6 50.1 1.0 HE2 J:HIS134 4.7 72.4 1.0 HA J:CYS132 4.7 56.7 1.0 CB J:TRP126 4.7 58.5 1.0 HA J:CYS138 4.7 65.2 1.0 HB3 J:TYR127 4.8 56.9 1.0 CA J:CYS124 4.8 54.7 1.0 CD2 J:HIS134 4.8 59.4 1.0 HA2 J:GLY135 4.8 58.3 1.0 CB J:HIS140 4.8 56.2 1.0 HA J:CYS124 4.9 65.7 1.0 H J:TRP126 4.9 64.7 1.0 HD1 J:HIS142 5.0 63.9 1.0 O J:HIS134 5.0 52.1 1.0 O J:HIS140 5.0 63.0 1.0 CD2 J:HIS140 5.0 54.0 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Human CPSF30 in Complex with HFIP1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human CPSF30 in Complex with HFIP1 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1002 b:60.4 occ:1.00 NE2 J:HIS166 2.0 45.9 1.0 SG J:CYS162 2.3 68.9 1.0 SG J:CYS156 2.3 49.3 1.0 SG J:CYS148 2.3 59.3 1.0 CE1 J:HIS166 2.7 47.4 1.0 HE1 J:HIS166 2.7 56.9 1.0 HB2 J:CYS148 2.9 60.1 1.0 HB2 J:CYS162 3.1 67.2 1.0 CB J:CYS148 3.1 50.1 1.0 HB2 J:CYS156 3.2 60.1 1.0 CB J:CYS162 3.2 56.0 1.0 HB3 J:CYS148 3.2 60.1 1.0 CD2 J:HIS166 3.2 44.5 1.0 CB J:CYS156 3.3 50.1 1.0 HB3 J:CYS162 3.4 67.2 1.0 HB3 J:CYS156 3.5 60.1 1.0 HD2 J:HIS166 3.6 53.3 1.0 HB2 J:GLU158 3.8 64.8 1.0 HB2 J:TYR151 3.8 54.6 1.0 HB2 J:ASN150 3.9 57.6 1.0 ND1 J:HIS166 3.9 43.6 1.0 HB2 J:PHE164 4.0 60.7 1.0 H J:TYR151 4.0 53.7 1.0 HD2 J:PHE164 4.1 74.0 1.0 CG J:HIS166 4.2 40.3 1.0 H J:PHE164 4.4 66.8 1.0 O J:PHE164 4.4 44.0 1.0 CA J:CYS148 4.5 50.2 1.0 OE2 J:GLU158 4.6 66.0 1.0 CA J:CYS162 4.6 57.6 1.0 N J:TYR151 4.6 44.8 1.0 HD1 J:HIS166 4.6 52.3 1.0 HG3 J:GLU158 4.7 71.4 1.0 CA J:CYS156 4.7 49.4 1.0 CB J:TYR151 4.7 45.5 1.0 CB J:GLU158 4.7 54.0 1.0 HA J:CYS148 4.7 60.3 1.0 HA J:CYS162 4.7 69.2 1.0 CB J:ASN150 4.8 48.0 1.0 HA J:CYS156 4.8 59.2 1.0 HB3 J:ASN150 4.8 57.6 1.0 H J:GLU158 4.9 63.5 1.0 HB3 J:TYR151 4.9 54.6 1.0 CB J:PHE164 4.9 50.6 1.0 H J:ASN150 4.9 57.8 1.0 CD2 J:PHE164 5.0 61.6 1.0

L.M.Muckenfuss, A.C.Migenda Herranz, F.M.Boneberg, M.Clerici, M.Jinek. FIP1 Is A Multivalent Interaction Scaffold For Processing Factors in Human Mrna 3' End Biogenesis. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36073787
DOI: 10.7554/ELIFE.80332