Zinc in PDB 5pyi: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78), PDB code: 5pyi was solved by N.M.Pearce, T.Krojer, R.Talon, A.R.Bradley, M.Fairhead, R.Sethi, N.Wright, E.Maclean, P.Collins, J.Brandao-Neto, A.Douangamath, Z.Renjie, A.Dias, J.Ng, P.E.Brennan, O.Cox, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Vondelft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.06 / 2.29
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.670, 45.540, 83.600, 90.00, 101.87, 90.00
R / Rfree (%)	28.6 / 34.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) (pdb code 5pyi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78), PDB code: 5pyi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:36.4 occ:1.00 SG A:CYS728 2.2 30.4 1.0 SG A:CYS705 2.3 38.6 1.0 ND1 A:HIS725 2.3 32.7 1.0 SG A:CYS708 2.3 40.3 1.0 CB A:CYS708 3.0 40.1 1.0 CB A:CYS705 3.0 38.7 1.0 CE1 A:HIS725 3.1 35.0 1.0 CB A:CYS728 3.2 29.5 1.0 CG A:HIS725 3.3 34.9 1.0 CB A:HIS725 3.7 36.5 1.0 N A:CYS708 3.8 38.9 1.0 O A:HOH1300 3.9 37.9 1.0 CA A:CYS708 4.0 41.5 1.0 NE2 A:HIS725 4.3 35.0 1.0 CD2 A:HIS725 4.4 34.2 1.0 N A:HIS725 4.5 33.1 1.0 O A:HOH1250 4.5 32.7 1.0 CA A:CYS705 4.5 37.0 1.0 CA A:CYS728 4.7 29.8 1.0 CB A:VAL707 4.7 35.1 1.0 CA A:HIS725 4.7 34.4 1.0 C A:CYS708 4.8 45.8 1.0 C A:VAL707 4.9 37.2 1.0 C A:CYS705 5.0 33.8 1.0

Zinc binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:37.2 occ:1.00 SG A:CYS717 2.1 38.6 1.0 SG A:CYS745 2.3 44.4 1.0 SG A:CYS720 2.4 49.3 1.0 SG A:CYS742 2.4 34.5 1.0 CB A:CYS717 3.1 45.4 1.0 CB A:CYS742 3.3 34.6 1.0 CB A:CYS720 3.3 50.1 1.0 N A:CYS742 3.6 37.3 1.0 CB A:CYS745 3.6 40.8 1.0 N A:CYS720 3.8 50.0 1.0 OG1 A:THR719 3.9 44.2 1.0 CA A:CYS742 4.0 35.5 1.0 N A:CYS745 4.0 35.4 1.0 CA A:CYS720 4.0 51.7 1.0 O A:CYS742 4.4 35.0 1.0 CA A:CYS745 4.4 39.6 1.0 C A:CYS742 4.5 35.2 1.0 CA A:CYS717 4.5 48.1 1.0 O A:HOH1253 4.6 31.5 1.0 C A:CYS720 4.6 54.8 1.0 O A:CYS720 4.6 56.6 1.0 NH1 A:ARG722 4.7 43.9 1.0 C A:SER741 4.7 40.0 1.0 CB A:PHE744 4.7 34.5 1.0 C A:THR719 4.8 49.2 1.0 CA A:SER741 4.9 44.6 1.0 C A:PHE744 5.0 34.6 1.0

Zinc binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:66.6 occ:0.43 O A:ARG753 3.8 57.0 1.0 OE1 A:GLU756 4.0 66.7 1.0 OE2 A:GLU756 4.1 58.8 1.0 SG A:CYS754 4.2 45.8 0.6 CA A:CYS754 4.4 48.1 0.6 CA A:CYS754 4.5 47.4 0.5 CD A:GLU756 4.5 59.0 1.0 CD A:PRO755 4.5 48.9 1.0 C A:ARG753 4.8 55.6 1.0 CB A:CYS754 4.9 46.6 0.6

Zinc binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:26.7 occ:1.00 ND1 B:HIS725 2.2 33.0 1.0 SG B:CYS708 2.2 33.0 1.0 SG B:CYS728 2.3 29.7 1.0 SG B:CYS705 2.4 29.9 1.0 CB B:CYS705 3.0 35.0 1.0 CE1 B:HIS725 3.1 35.9 1.0 CB B:CYS728 3.2 30.2 1.0 CG B:HIS725 3.2 35.1 1.0 CB B:CYS708 3.3 32.3 1.0 CB B:HIS725 3.5 33.0 1.0 N B:CYS708 3.9 32.4 1.0 CA B:CYS708 4.2 34.3 1.0 NE2 B:HIS725 4.2 35.6 1.0 CD2 B:HIS725 4.3 36.4 1.0 N B:HIS725 4.3 31.6 1.0 CA B:HIS725 4.5 31.5 1.0 CA B:CYS705 4.5 35.6 1.0 CA B:CYS728 4.6 30.2 1.0 C B:CYS708 4.9 35.1 1.0 CB B:VAL707 4.9 32.3 1.0 O B:HOH1204 5.0 22.2 1.0

Zinc binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 78) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:27.8 occ:1.00 SG B:CYS745 2.2 33.8 1.0 SG B:CYS742 2.4 31.7 1.0 SG B:CYS717 2.4 30.1 1.0 SG B:CYS720 2.4 40.1 1.0 CB B:CYS720 3.0 41.3 1.0 CB B:CYS742 3.2 30.4 1.0 CB B:CYS717 3.3 32.7 1.0 CB B:CYS745 3.5 32.8 1.0 N B:CYS742 3.8 30.0 1.0 N B:CYS720 3.9 38.3 1.0 CA B:CYS720 4.0 40.8 1.0 OG1 B:THR719 4.0 31.3 1.0 CA B:CYS742 4.0 29.2 1.0 O B:HOH1163 4.0 32.1 1.0 N B:CYS745 4.1 27.0 1.0 CA B:CYS745 4.4 30.0 1.0 O B:CYS742 4.4 32.2 1.0 C B:CYS742 4.5 28.1 1.0 C B:THR719 4.6 36.6 1.0 NH1 B:ARG722 4.6 29.7 1.0 C B:CYS720 4.7 42.2 1.0 CA B:CYS717 4.7 34.9 1.0 CB B:PHE744 4.9 23.6 1.0 O B:CYS720 5.0 44.0 1.0

N.M.Pearce, T.Krojer, A.R.Bradley, P.Collins, R.P.Nowak, R.Talon, B.D.Marsden, S.Kelm, J.Shi, C.M.Deane, F.Von Delft. A Multi-Crystal Method For Extracting Obscured Crystallographic States From Conventionally Uninterpretable Electron Density. Nat Commun V. 8 15123 2017.
ISSN: ESSN 2041-1723
PubMed: 28436492
DOI: 10.1038/NCOMMS15123