Zinc in PDB 5pz8: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 104)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 104), PDB code: 5pz8 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)	45.42 / 1.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.930, 45.540, 83.720, 90.00, 101.90, 90.00
R / Rfree (%)	17.2 / 20.3

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 104) (pdb code 5pz8). 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 104), PDB code: 5pz8:
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 104)


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 104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.5 occ:1.00 ND1 A:HIS725 2.1 22.0 1.0 SG A:CYS708 2.3 26.1 1.0 SG A:CYS705 2.3 24.5 1.0 SG A:CYS728 2.4 25.8 1.0 CE1 A:HIS725 3.0 31.3 1.0 CB A:CYS705 3.0 22.6 1.0 CG A:HIS725 3.2 30.6 1.0 CB A:CYS728 3.3 24.3 1.0 CB A:CYS708 3.4 25.0 1.0 CB A:HIS725 3.6 27.4 1.0 N A:CYS708 3.8 24.0 1.0 O A:HOH1273 4.0 61.6 1.0 NE2 A:HIS725 4.1 29.5 1.0 N A:HIS725 4.1 25.1 1.0 CA A:CYS708 4.1 25.1 1.0 CD2 A:HIS725 4.2 28.9 1.0 CA A:HIS725 4.4 24.6 1.0 CA A:CYS705 4.5 24.0 1.0 CA A:CYS728 4.6 20.9 1.0 O A:HOH1257 4.6 37.2 1.0 CB A:VAL707 4.7 20.3 1.0 C A:CYS708 4.9 29.3 1.0 C A:VAL707 4.9 24.4 1.0 N A:ASN709 5.0 25.3 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 104)


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 104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.4 occ:1.00 SG A:CYS742 2.3 24.7 1.0 SG A:CYS717 2.3 33.0 1.0 SG A:CYS720 2.4 37.0 1.0 SG A:CYS745 2.4 30.7 1.0 CB A:CYS717 3.2 32.6 1.0 CB A:CYS742 3.2 22.9 1.0 CB A:CYS720 3.3 35.5 1.0 CB A:CYS745 3.4 25.8 1.0 N A:CYS742 3.7 29.3 1.0 N A:CYS720 3.8 33.4 1.0 CA A:CYS742 4.0 25.6 1.0 OG1 A:THR719 4.0 40.3 1.0 N A:CYS745 4.1 23.9 1.0 CA A:CYS720 4.1 34.7 1.0 CA A:CYS745 4.3 27.0 1.0 O A:CYS742 4.4 25.1 1.0 C A:CYS742 4.5 26.9 1.0 C A:THR719 4.5 36.0 1.0 NH1 A:ARG722 4.6 29.2 1.0 O A:CYS720 4.6 37.9 1.0 C A:CYS720 4.6 27.6 1.0 CA A:CYS717 4.6 34.7 1.0 O A:HOH1235 4.7 43.5 1.0 C A:SER741 4.8 26.1 1.0 CB A:PHE744 4.9 25.5 1.0 N A:THR719 5.0 39.6 1.0 CD A:ARG722 5.0 27.7 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 104)


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 104) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:42.4 occ:0.43 OE2 A:GLU756 1.9 53.7 1.0 SG A:CYS754 2.5 42.9 0.6 CD A:GLU756 2.6 49.6 1.0 OE1 A:GLU756 2.7 49.1 1.0 SG A:CYS754 2.8 32.7 0.5 CB A:CYS754 3.2 37.2 0.6 CB A:CYS754 3.4 33.7 0.5 CA A:CYS754 3.4 32.9 0.5 CA A:CYS754 3.4 34.7 0.6 CG A:GLU756 4.1 42.8 1.0 O A:ARG753 4.1 44.5 1.0 C A:CYS754 4.3 32.8 1.0 CD A:PRO755 4.5 31.2 1.0 N A:CYS754 4.5 35.0 1.0 O A:HOH1101 4.6 51.0 1.0 N A:PRO755 4.7 30.8 1.0 C A:ARG753 4.7 37.1 1.0 O A:CYS754 5.0 30.3 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 104)


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 104) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.2 occ:1.00 ND1 B:HIS725 2.1 22.3 1.0 SG B:CYS728 2.3 21.3 1.0 SG B:CYS708 2.3 23.0 1.0 SG B:CYS705 2.4 20.1 1.0 CE1 B:HIS725 3.1 24.3 1.0 CB B:CYS705 3.1 19.2 1.0 CG B:HIS725 3.1 21.8 1.0 CB B:CYS728 3.2 20.1 1.0 CB B:CYS708 3.4 21.5 1.0 CB B:HIS725 3.5 19.7 1.0 N B:CYS708 3.8 21.0 1.0 CA B:CYS708 4.2 22.0 1.0 N B:HIS725 4.2 19.4 1.0 NE2 B:HIS725 4.2 24.8 1.0 CD2 B:HIS725 4.2 22.5 1.0 CA B:HIS725 4.4 18.3 1.0 CA B:CYS705 4.5 20.3 1.0 O B:HOH1207 4.6 29.6 1.0 CA B:CYS728 4.7 18.1 1.0 CB B:VAL707 4.8 19.5 1.0 C B:CYS708 4.9 25.9 1.0 C B:VAL707 4.9 23.3 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 104)


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 104) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:23.8 occ:1.00 SG B:CYS717 2.3 25.4 1.0 SG B:CYS720 2.3 25.3 1.0 SG B:CYS742 2.3 20.6 1.0 SG B:CYS745 2.3 25.4 1.0 CB B:CYS717 3.2 21.8 1.0 CB B:CYS720 3.3 25.4 1.0 CB B:CYS742 3.4 20.6 1.0 CB B:CYS745 3.5 20.5 1.0 N B:CYS742 3.8 21.4 1.0 N B:CYS720 3.8 27.3 1.0 N B:CYS745 4.0 20.5 1.0 CA B:CYS720 4.1 28.1 1.0 CA B:CYS742 4.1 21.5 1.0 OG1 B:THR719 4.1 28.6 1.0 CA B:CYS745 4.3 23.4 1.0 C B:THR719 4.5 28.6 1.0 O B:HOH1188 4.5 36.8 1.0 O B:CYS742 4.6 19.6 1.0 NH1 B:ARG722 4.6 25.9 1.0 C B:CYS742 4.6 19.8 1.0 C B:CYS720 4.6 27.7 1.0 CA B:CYS717 4.7 23.1 1.0 O B:CYS720 4.7 28.2 1.0 CB B:PHE744 4.9 20.8 1.0 N B:THR719 4.9 31.2 1.0 C B:SER741 4.9 23.2 1.0 CA B:THR719 5.0 28.8 1.0 CB B:ARG722 5.0 23.3 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