Zinc in PDB 5pz0: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 96)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 96), PDB code: 5pz0 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)	39.05 / 2.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.720, 45.510, 83.630, 90.00, 101.90, 90.00
R / Rfree (%)	16.4 / 21.3

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 96) (pdb code 5pz0). 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 96), PDB code: 5pz0:
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 96)


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 96) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.4 occ:1.00 ND1 A:HIS725 2.2 35.1 1.0 SG A:CYS728 2.2 25.4 1.0 SG A:CYS705 2.2 27.1 1.0 SG A:CYS708 2.4 29.3 1.0 CB A:CYS705 3.0 32.5 1.0 CE1 A:HIS725 3.0 34.7 1.0 CB A:CYS728 3.2 23.6 1.0 CG A:HIS725 3.2 33.7 1.0 CB A:CYS708 3.3 25.0 1.0 CB A:HIS725 3.6 31.1 1.0 N A:CYS708 3.7 23.0 1.0 O A:HOH1285 3.9 55.8 1.0 CA A:CYS708 4.1 25.9 1.0 N A:HIS725 4.1 26.1 1.0 NE2 A:HIS725 4.2 38.8 1.0 CD2 A:HIS725 4.3 38.6 1.0 CA A:HIS725 4.5 27.4 1.0 CA A:CYS705 4.5 30.8 1.0 CB A:VAL707 4.6 21.6 1.0 CA A:CYS728 4.6 22.1 1.0 O A:HOH1250 4.6 36.7 1.0 C A:VAL707 4.9 25.0 1.0 C A:CYS708 4.9 29.2 1.0 C A:CYS705 5.0 26.5 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 96)


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 96) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:31.8 occ:1.00 SG A:CYS717 2.2 32.5 1.0 SG A:CYS720 2.2 34.1 1.0 SG A:CYS745 2.4 34.8 1.0 SG A:CYS742 2.5 28.2 1.0 CB A:CYS717 3.3 37.4 1.0 CB A:CYS720 3.3 35.7 1.0 CB A:CYS745 3.5 31.4 1.0 CB A:CYS742 3.5 28.4 1.0 N A:CYS720 3.7 34.9 1.0 N A:CYS742 3.9 28.5 1.0 N A:CYS745 4.0 28.4 1.0 CA A:CYS720 4.0 35.6 1.0 OG1 A:THR719 4.2 43.3 1.0 CA A:CYS742 4.2 28.5 1.0 CA A:CYS745 4.3 32.0 1.0 O A:CYS742 4.4 20.2 1.0 C A:THR719 4.4 39.3 1.0 O A:HOH1242 4.5 45.3 1.0 NH1 A:ARG722 4.5 30.0 1.0 C A:CYS742 4.6 24.9 1.0 C A:CYS720 4.6 31.7 1.0 O A:CYS720 4.6 35.2 1.0 CA A:CYS717 4.7 42.3 1.0 C A:SER741 4.9 32.2 1.0 N A:THR719 4.9 46.0 1.0 CB A:PHE744 4.9 25.9 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 96)


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 96) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:85.3 occ:0.43 OE2 A:GLU756 3.3 76.3 1.0 SG A:CYS754 3.4 56.1 0.6 OE1 A:GLU756 3.7 59.5 1.0 O A:ARG753 3.8 54.7 1.0 CD A:GLU756 3.9 63.9 1.0 CA A:CYS754 4.3 41.6 0.6 CA A:CYS754 4.3 36.4 0.5 CB A:CYS754 4.4 45.4 0.6 SG A:CYS754 4.4 28.9 0.5 CB A:CYS754 4.5 34.5 0.5 C A:ARG753 4.8 44.5 1.0 CD A:PRO755 4.9 37.7 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 96)


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 96) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.5 occ:1.00 ND1 B:HIS725 2.2 25.9 1.0 SG B:CYS705 2.2 22.5 1.0 SG B:CYS728 2.3 21.9 1.0 SG B:CYS708 2.4 23.2 1.0 CB B:CYS705 3.0 24.2 1.0 CE1 B:HIS725 3.1 27.5 1.0 CB B:CYS728 3.2 19.9 1.0 CG B:HIS725 3.2 26.5 1.0 CB B:CYS708 3.4 21.2 1.0 CB B:HIS725 3.5 21.7 1.0 N B:CYS708 3.8 20.2 1.0 N B:HIS725 4.1 22.8 1.0 CA B:CYS708 4.2 21.9 1.0 NE2 B:HIS725 4.2 29.7 1.0 CD2 B:HIS725 4.3 27.7 1.0 CA B:HIS725 4.5 22.5 1.0 CA B:CYS705 4.5 24.4 1.0 CA B:CYS728 4.6 19.2 1.0 O B:HOH1212 4.7 28.3 1.0 CB B:VAL707 4.7 18.2 1.0 C B:CYS708 4.9 24.7 1.0 C B:VAL707 4.9 22.4 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 96)


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 96) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:25.6 occ:1.00 SG B:CYS717 2.2 26.1 1.0 SG B:CYS745 2.3 28.5 1.0 SG B:CYS742 2.3 23.4 1.0 SG B:CYS720 2.3 26.2 1.0 CB B:CYS720 3.2 29.5 1.0 CB B:CYS717 3.3 30.0 1.0 CB B:CYS742 3.4 22.9 1.0 CB B:CYS745 3.5 23.1 1.0 N B:CYS742 3.8 25.1 1.0 N B:CYS720 3.8 31.1 1.0 CA B:CYS720 4.1 29.3 1.0 OG1 B:THR719 4.1 36.3 1.0 N B:CYS745 4.1 21.4 1.0 CA B:CYS742 4.1 21.8 1.0 CA B:CYS745 4.3 21.8 1.0 C B:THR719 4.4 29.3 1.0 O B:HOH1186 4.6 35.6 1.0 O B:CYS742 4.6 21.1 1.0 C B:CYS742 4.6 21.7 1.0 NH1 B:ARG722 4.6 26.0 1.0 C B:CYS720 4.7 28.7 1.0 CA B:CYS717 4.7 31.5 1.0 O B:CYS720 4.8 29.9 1.0 CB B:PHE744 4.9 18.6 1.0 C B:SER741 4.9 27.1 1.0 N B:THR719 4.9 35.8 1.0 CB B:ARG722 5.0 26.0 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