Zinc in PDB 5pzb: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 107)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 107), PDB code: 5pzb 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)	39.02 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.620, 45.480, 83.420, 90.00, 102.15, 90.00
R / Rfree (%)	16 / 21

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 107) (pdb code 5pzb). 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 107), PDB code: 5pzb:
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 107)


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 107) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:30.1 occ:1.00 ND1 A:HIS725 2.2 38.8 1.0 SG A:CYS728 2.2 28.2 1.0 SG A:CYS705 2.3 31.8 1.0 SG A:CYS708 2.4 30.9 1.0 CB A:CYS705 3.0 35.6 1.0 CE1 A:HIS725 3.1 34.6 1.0 CB A:CYS728 3.1 29.5 1.0 CG A:HIS725 3.2 36.2 1.0 CB A:CYS708 3.3 29.1 1.0 CB A:HIS725 3.6 34.0 1.0 N A:CYS708 3.8 31.2 1.0 O A:HOH1277 3.8 56.6 1.0 CA A:CYS708 4.1 30.8 1.0 N A:HIS725 4.2 28.9 1.0 NE2 A:HIS725 4.2 38.6 1.0 CD2 A:HIS725 4.3 41.3 1.0 CA A:HIS725 4.5 29.2 1.0 CA A:CYS705 4.5 34.0 1.0 O A:HOH1254 4.6 36.0 1.0 CA A:CYS728 4.6 29.1 1.0 CB A:VAL707 4.6 24.8 1.0 O A:HOH1260 4.8 56.3 1.0 C A:VAL707 4.9 31.8 1.0 C A:CYS708 4.9 32.5 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 107)


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 107) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:36.2 occ:1.00 SG A:CYS720 2.2 36.1 1.0 SG A:CYS717 2.2 38.9 1.0 SG A:CYS745 2.3 41.8 1.0 SG A:CYS742 2.5 32.0 1.0 CB A:CYS720 3.3 42.1 1.0 CB A:CYS717 3.3 44.3 1.0 CB A:CYS745 3.5 34.9 1.0 CB A:CYS742 3.5 30.3 1.0 N A:CYS720 3.8 42.0 1.0 N A:CYS742 3.9 34.1 1.0 N A:CYS745 4.0 32.0 1.0 CA A:CYS720 4.1 43.0 1.0 OG1 A:THR719 4.2 45.9 1.0 CA A:CYS742 4.2 34.0 1.0 CA A:CYS745 4.3 34.8 1.0 O A:CYS742 4.4 28.2 1.0 C A:THR719 4.4 43.9 1.0 NH1 A:ARG722 4.5 38.5 1.0 O A:CYS720 4.5 41.0 1.0 O A:HOH1205 4.6 48.9 1.0 C A:CYS720 4.6 34.9 1.0 C A:CYS742 4.6 31.2 1.0 CA A:CYS717 4.7 49.8 1.0 CB A:PHE744 4.8 29.4 1.0 N A:THR719 4.9 49.4 1.0 C A:SER741 4.9 35.0 1.0 O A:THR719 5.0 48.0 1.0 C A:PHE744 5.0 31.2 1.0 CD A:ARG722 5.0 32.9 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 107)


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 107) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:92.0 occ:0.43 OE2 A:GLU756 2.7 79.0 1.0 OE1 A:GLU756 3.1 64.7 1.0 CD A:GLU756 3.3 61.8 1.0 SG A:CYS754 3.4 60.8 0.6 O A:ARG753 3.6 57.5 1.0 CA A:CYS754 3.7 45.9 0.6 CA A:CYS754 3.7 40.7 0.5 SG A:CYS754 3.8 33.6 0.5 CB A:CYS754 3.9 50.6 0.6 CB A:CYS754 4.0 39.3 0.5 CD A:PRO755 4.4 47.1 1.0 C A:ARG753 4.5 47.9 1.0 N A:CYS754 4.6 43.3 1.0 C A:CYS754 4.6 41.9 1.0 CG A:GLU756 4.9 54.7 1.0 N A:PRO755 4.9 45.4 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 107)


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 107) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:25.6 occ:1.00 ND1 B:HIS725 2.2 32.8 1.0 SG B:CYS705 2.2 24.8 1.0 SG B:CYS728 2.3 26.0 1.0 SG B:CYS708 2.3 28.5 1.0 CB B:CYS705 3.0 28.4 1.0 CE1 B:HIS725 3.1 34.8 1.0 CB B:CYS728 3.2 23.5 1.0 CG B:HIS725 3.2 30.7 1.0 CB B:CYS708 3.3 26.6 1.0 CB B:HIS725 3.6 25.1 1.0 N B:CYS708 3.8 25.4 1.0 CA B:CYS708 4.1 27.1 1.0 N B:HIS725 4.2 24.8 1.0 NE2 B:HIS725 4.2 35.8 1.0 CD2 B:HIS725 4.3 30.9 1.0 CA B:CYS705 4.5 30.1 1.0 CA B:HIS725 4.5 23.9 1.0 CA B:CYS728 4.6 21.4 1.0 O B:HOH1205 4.7 36.7 1.0 CB B:VAL707 4.7 22.2 1.0 C B:CYS708 4.8 29.8 1.0 C B:VAL707 4.9 29.2 1.0 C B:CYS705 5.0 29.3 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 107)


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 107) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:30.7 occ:1.00 SG B:CYS717 2.1 28.8 1.0 SG B:CYS720 2.3 34.4 1.0 SG B:CYS745 2.3 33.7 1.0 SG B:CYS742 2.4 30.5 1.0 CB B:CYS717 3.2 31.6 1.0 CB B:CYS720 3.2 38.2 1.0 CB B:CYS742 3.4 28.2 1.0 CB B:CYS745 3.5 29.5 1.0 N B:CYS720 3.8 35.9 1.0 N B:CYS742 3.8 28.7 1.0 CA B:CYS720 4.0 37.2 1.0 N B:CYS745 4.1 27.3 1.0 CA B:CYS742 4.1 25.7 1.0 OG1 B:THR719 4.1 42.3 1.0 CA B:CYS745 4.4 27.4 1.0 C B:THR719 4.4 34.4 1.0 O B:HOH1181 4.5 39.0 1.0 NH1 B:ARG722 4.6 35.6 1.0 O B:CYS742 4.6 24.4 1.0 C B:CYS742 4.6 24.4 1.0 CA B:CYS717 4.6 32.3 1.0 C B:CYS720 4.6 35.0 1.0 O B:CYS720 4.7 32.5 1.0 N B:THR719 4.8 39.4 1.0 C B:SER741 4.9 34.6 1.0 CB B:PHE744 4.9 27.4 1.0 CA B:THR719 5.0 37.0 1.0 O B:THR719 5.0 34.6 1.0 CB B:ARG722 5.0 30.0 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