Zinc in PDB 5pzf: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 111)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 111), PDB code: 5pzf 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)	40.70 / 1.84
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.640, 45.460, 83.250, 90.00, 102.09, 90.00
R / Rfree (%)	16.7 / 20.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 111) (pdb code 5pzf). 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 111), PDB code: 5pzf:
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 111)


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 111) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:27.8 occ:1.00 ND1 A:HIS725 2.2 33.9 1.0 SG A:CYS728 2.2 26.9 1.0 SG A:CYS705 2.2 27.2 1.0 SG A:CYS708 2.4 28.2 1.0 CB A:CYS705 3.1 30.6 1.0 CE1 A:HIS725 3.1 31.2 1.0 CB A:CYS728 3.2 26.6 1.0 CG A:HIS725 3.2 32.8 1.0 CB A:CYS708 3.3 28.5 1.0 CB A:HIS725 3.6 32.0 1.0 N A:CYS708 3.8 27.9 1.0 O A:HOH1284 3.9 52.1 1.0 CA A:CYS708 4.1 30.3 1.0 N A:HIS725 4.2 30.0 1.0 NE2 A:HIS725 4.2 34.0 1.0 CD2 A:HIS725 4.3 35.3 1.0 CA A:HIS725 4.5 28.7 1.0 CA A:CYS705 4.5 29.4 1.0 CA A:CYS728 4.6 23.7 1.0 O A:HOH1254 4.6 41.7 1.0 CB A:VAL707 4.7 23.1 1.0 C A:VAL707 4.9 27.7 1.0 C A:CYS708 4.9 31.3 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 111)


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 111) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:33.2 occ:1.00 SG A:CYS720 2.2 36.5 1.0 SG A:CYS717 2.3 37.4 1.0 SG A:CYS745 2.4 36.5 1.0 SG A:CYS742 2.4 28.7 1.0 CB A:CYS717 3.2 40.5 1.0 CB A:CYS720 3.3 36.2 1.0 CB A:CYS742 3.4 24.9 1.0 CB A:CYS745 3.5 29.9 1.0 N A:CYS742 3.8 26.6 1.0 N A:CYS720 3.9 37.1 1.0 N A:CYS745 4.0 30.8 1.0 CA A:CYS720 4.1 37.2 1.0 CA A:CYS742 4.1 29.3 1.0 OG1 A:THR719 4.1 38.5 1.0 CA A:CYS745 4.3 29.9 1.0 O A:CYS742 4.4 25.3 1.0 C A:THR719 4.4 41.5 1.0 C A:CYS742 4.5 29.2 1.0 O A:CYS720 4.6 34.3 1.0 NH1 A:ARG722 4.6 36.9 1.0 C A:CYS720 4.6 31.8 1.0 CA A:CYS717 4.7 44.1 1.0 O A:HOH1215 4.7 43.9 1.0 C A:SER741 4.9 31.1 1.0 CB A:PHE744 4.9 27.0 1.0 N A:THR719 4.9 45.6 1.0 O A:THR719 5.0 42.0 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 111)


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 111) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:56.8 occ:0.43 OE2 A:GLU756 1.9 61.3 1.0 SG A:CYS754 2.6 46.7 0.6 CD A:GLU756 2.7 51.0 1.0 OE1 A:GLU756 2.8 53.0 1.0 SG A:CYS754 3.0 34.6 0.5 CB A:CYS754 3.2 39.8 0.6 CA A:CYS754 3.4 39.1 0.6 CB A:CYS754 3.4 36.5 0.5 CA A:CYS754 3.4 37.2 0.5 O A:ARG753 4.0 56.7 1.0 CG A:GLU756 4.1 45.6 1.0 C A:CYS754 4.3 36.8 1.0 N A:CYS754 4.5 38.3 1.0 O A:HOH1144 4.6 50.9 1.0 CD A:PRO755 4.7 38.8 1.0 C A:ARG753 4.7 48.2 1.0 N A:PRO755 4.8 36.2 1.0 O A:CYS754 5.0 32.5 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 111)


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 111) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:24.4 occ:1.00 ND1 B:HIS725 2.2 31.0 1.0 SG B:CYS705 2.3 23.0 1.0 SG B:CYS728 2.3 24.4 1.0 SG B:CYS708 2.3 24.9 1.0 CE1 B:HIS725 3.1 30.6 1.0 CB B:CYS705 3.1 22.7 1.0 CB B:CYS728 3.1 21.7 1.0 CG B:HIS725 3.2 27.1 1.0 CB B:CYS708 3.4 23.7 1.0 CB B:HIS725 3.5 22.1 1.0 N B:CYS708 3.8 25.8 1.0 CA B:CYS708 4.1 25.5 1.0 NE2 B:HIS725 4.2 29.7 1.0 N B:HIS725 4.2 23.4 1.0 CD2 B:HIS725 4.3 25.9 1.0 CA B:HIS725 4.5 20.0 1.0 CA B:CYS705 4.5 25.4 1.0 CA B:CYS728 4.6 21.8 1.0 O B:HOH1209 4.7 36.1 1.0 CB B:VAL707 4.7 22.9 1.0 C B:CYS708 4.8 27.8 1.0 C B:VAL707 4.9 26.4 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 111)


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 111) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:28.5 occ:1.00 SG B:CYS717 2.1 28.4 1.0 SG B:CYS745 2.3 31.4 1.0 SG B:CYS720 2.4 31.0 1.0 SG B:CYS742 2.4 25.6 1.0 CB B:CYS717 3.2 27.9 1.0 CB B:CYS720 3.3 34.5 1.0 CB B:CYS742 3.4 24.3 1.0 CB B:CYS745 3.4 28.3 1.0 N B:CYS742 3.8 26.8 1.0 N B:CYS720 3.8 36.8 1.0 N B:CYS745 4.0 24.2 1.0 OG1 B:THR719 4.1 33.8 1.0 CA B:CYS720 4.1 34.1 1.0 CA B:CYS742 4.1 23.4 1.0 CA B:CYS745 4.3 26.6 1.0 C B:THR719 4.5 33.9 1.0 O B:CYS742 4.5 21.8 1.0 C B:CYS742 4.6 23.4 1.0 NH1 B:ARG722 4.6 31.8 1.0 C B:CYS720 4.7 32.8 1.0 CA B:CYS717 4.7 29.0 1.0 O B:HOH1189 4.7 40.4 1.0 O B:CYS720 4.7 30.3 1.0 N B:THR719 4.9 36.8 1.0 C B:SER741 4.9 29.3 1.0 CB B:PHE744 4.9 25.4 1.0 CB B:ARG722 5.0 29.2 1.0 CA B:THR719 5.0 32.3 1.0 CD B:ARG722 5.0 27.3 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