Zinc in PDB 5pyu: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 90)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 90), PDB code: 5pyu 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)	45.24 / 1.74
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.630, 45.480, 83.370, 90.00, 101.99, 90.00
R / Rfree (%)	17.1 / 20.4

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 90) (pdb code 5pyu). 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 90), PDB code: 5pyu:
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 90)


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 90) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.4 occ:1.00 ND1 A:HIS725 2.2 26.7 1.0 SG A:CYS728 2.2 26.0 1.0 SG A:CYS705 2.3 24.9 1.0 SG A:CYS708 2.3 25.2 1.0 CE1 A:HIS725 3.0 31.6 1.0 CB A:CYS705 3.1 26.2 1.0 CB A:CYS728 3.2 23.1 1.0 CG A:HIS725 3.2 30.6 1.0 CB A:CYS708 3.3 22.7 1.0 CB A:HIS725 3.6 30.1 1.0 N A:CYS708 3.8 22.7 1.0 O A:HOH1269 3.8 53.9 1.0 CA A:CYS708 4.1 24.1 1.0 N A:HIS725 4.1 27.1 1.0 NE2 A:HIS725 4.2 28.8 1.0 CD2 A:HIS725 4.3 33.6 1.0 CA A:HIS725 4.4 25.8 1.0 CA A:CYS705 4.5 27.7 1.0 O A:HOH1255 4.6 39.3 1.0 CA A:CYS728 4.6 21.3 1.0 CB A:VAL707 4.7 20.9 1.0 C A:CYS708 4.9 28.2 1.0 C A:VAL707 4.9 23.7 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 90)


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 90) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:31.5 occ:1.00 SG A:CYS720 2.2 35.1 1.0 SG A:CYS717 2.3 35.6 1.0 SG A:CYS745 2.4 32.9 1.0 SG A:CYS742 2.4 24.5 1.0 CB A:CYS717 3.2 36.8 1.0 CB A:CYS720 3.2 34.7 1.0 CB A:CYS742 3.4 21.5 1.0 CB A:CYS745 3.5 29.2 1.0 N A:CYS742 3.8 26.8 1.0 N A:CYS720 3.9 36.3 1.0 N A:CYS745 4.0 28.4 1.0 CA A:CYS720 4.0 36.5 1.0 CA A:CYS742 4.1 26.1 1.0 OG1 A:THR719 4.2 39.7 1.0 CA A:CYS745 4.3 29.1 1.0 O A:CYS742 4.4 24.3 1.0 C A:THR719 4.5 40.1 1.0 O A:CYS720 4.6 35.7 1.0 C A:CYS720 4.6 29.5 1.0 O A:HOH1241 4.6 40.5 1.0 C A:CYS742 4.6 25.1 1.0 NH1 A:ARG722 4.6 34.3 1.0 CA A:CYS717 4.7 43.6 1.0 C A:SER741 4.9 26.9 1.0 N A:THR719 4.9 42.8 1.0 CB A:PHE744 4.9 25.9 1.0 O A:THR719 4.9 39.3 1.0 CD A:ARG722 5.0 29.6 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 90)


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 90) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:0.1 occ:0.43 OE2 A:GLU756 2.9 70.5 1.0 SG A:CYS754 3.3 50.9 0.6 OE1 A:GLU756 3.3 47.8 1.0 CD A:GLU756 3.5 53.2 1.0 O A:ARG753 3.7 47.2 1.0 CA A:CYS754 3.9 33.1 0.5 CA A:CYS754 3.9 37.1 0.6 CB A:CYS754 4.0 38.8 0.6 SG A:CYS754 4.1 29.4 0.5 CB A:CYS754 4.2 30.6 0.5 C A:ARG753 4.6 41.3 1.0 CD A:PRO755 4.6 34.1 1.0 N A:CYS754 4.8 34.3 1.0 C A:CYS754 4.9 34.6 1.0

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 90)


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 90) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.6 occ:1.00 ND1 B:HIS725 2.2 26.9 1.0 SG B:CYS728 2.3 21.2 1.0 SG B:CYS705 2.3 21.2 1.0 SG B:CYS708 2.3 21.8 1.0 CE1 B:HIS725 3.0 28.4 1.0 CB B:CYS705 3.1 19.2 1.0 CB B:CYS728 3.2 18.4 1.0 CG B:HIS725 3.2 26.4 1.0 CB B:CYS708 3.4 20.7 1.0 CB B:HIS725 3.6 20.7 1.0 N B:CYS708 3.8 20.6 1.0 CA B:CYS708 4.1 21.2 1.0 N B:HIS725 4.2 20.4 1.0 NE2 B:HIS725 4.2 26.0 1.0 CD2 B:HIS725 4.3 23.4 1.0 CA B:HIS725 4.5 19.4 1.0 CA B:CYS705 4.6 22.1 1.0 CA B:CYS728 4.6 19.3 1.0 O B:HOH1207 4.6 31.4 1.0 CB B:VAL707 4.7 18.2 1.0 C B:VAL707 4.9 21.4 1.0 C B:CYS708 4.9 25.6 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 90)


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 90) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:24.5 occ:1.00 SG B:CYS717 2.2 25.3 1.0 SG B:CYS720 2.3 27.9 1.0 SG B:CYS745 2.4 26.3 1.0 SG B:CYS742 2.4 21.9 1.0 CB B:CYS717 3.2 24.2 1.0 CB B:CYS720 3.3 30.5 1.0 CB B:CYS742 3.4 21.2 1.0 CB B:CYS745 3.4 23.1 1.0 N B:CYS742 3.8 23.1 1.0 N B:CYS720 3.8 33.8 1.0 N B:CYS745 4.0 20.4 1.0 CA B:CYS720 4.1 29.2 1.0 CA B:CYS742 4.1 21.0 1.0 OG1 B:THR719 4.1 28.7 1.0 CA B:CYS745 4.3 23.4 1.0 C B:THR719 4.5 28.5 1.0 O B:CYS742 4.5 19.9 1.0 C B:CYS742 4.6 20.4 1.0 NH1 B:ARG722 4.6 28.7 1.0 C B:CYS720 4.6 30.0 1.0 O B:HOH1192 4.7 36.2 1.0 CA B:CYS717 4.7 23.3 1.0 O B:CYS720 4.7 27.4 1.0 N B:THR719 4.9 31.2 1.0 CB B:PHE744 4.9 20.9 1.0 C B:SER741 4.9 26.7 1.0 CB B:ARG722 5.0 26.0 1.0 CA B:THR719 5.0 29.0 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