Zinc in PDB 5pzc: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 108)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 108), PDB code: 5pzc 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)	40.82 / 1.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.860, 45.430, 83.540, 90.00, 102.23, 90.00
R / Rfree (%)	17.1 / 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 108) (pdb code 5pzc). 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 108), PDB code: 5pzc:
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 108)


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 108) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:24.0 occ:1.00 ND1 A:HIS725 2.1 22.6 1.0 SG A:CYS728 2.3 24.5 1.0 SG A:CYS705 2.3 22.4 1.0 SG A:CYS708 2.3 24.2 1.0 CE1 A:HIS725 3.0 27.3 1.0 CB A:CYS705 3.1 21.1 1.0 CG A:HIS725 3.2 26.8 1.0 CB A:CYS728 3.3 23.2 1.0 CB A:CYS708 3.3 23.5 1.0 CB A:HIS725 3.6 27.1 1.0 N A:CYS708 3.8 21.4 1.0 O A:HOH1282 4.1 53.9 1.0 CA A:CYS708 4.1 23.2 1.0 N A:HIS725 4.1 23.8 1.0 NE2 A:HIS725 4.2 28.1 1.0 CD2 A:HIS725 4.3 28.8 1.0 CA A:HIS725 4.4 24.2 1.0 CA A:CYS705 4.5 22.6 1.0 CB A:VAL707 4.7 18.4 1.0 CA A:CYS728 4.7 19.6 1.0 O A:HOH1248 4.7 38.3 1.0 C A:VAL707 4.9 22.2 1.0 C A:CYS708 4.9 27.1 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 108)


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 108) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.0 occ:1.00 SG A:CYS720 2.2 36.0 1.0 SG A:CYS717 2.3 34.3 1.0 SG A:CYS742 2.3 22.4 1.0 SG A:CYS745 2.4 30.3 1.0 CB A:CYS720 3.2 38.6 1.0 CB A:CYS717 3.2 32.1 1.0 CB A:CYS742 3.3 19.1 1.0 CB A:CYS745 3.4 26.8 1.0 N A:CYS742 3.8 27.9 1.0 N A:CYS720 3.9 37.6 1.0 N A:CYS745 4.0 24.7 1.0 CA A:CYS720 4.1 37.3 1.0 CA A:CYS742 4.1 24.8 1.0 OG1 A:THR719 4.2 36.3 1.0 CA A:CYS745 4.3 26.0 1.0 O A:CYS742 4.4 21.4 1.0 C A:THR719 4.5 35.9 1.0 C A:CYS742 4.6 23.1 1.0 O A:CYS720 4.6 35.8 1.0 C A:CYS720 4.6 29.1 1.0 O A:HOH1233 4.6 41.5 1.0 CA A:CYS717 4.7 38.6 1.0 NH1 A:ARG722 4.7 29.3 1.0 C A:SER741 4.9 23.4 1.0 CB A:PHE744 4.9 25.0 1.0 O A:THR719 5.0 37.9 1.0 N A:THR719 5.0 38.1 1.0 CD A:ARG722 5.0 27.0 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 108)


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 108) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:50.3 occ:0.43 OE2 A:GLU756 2.1 61.4 1.0 SG A:CYS754 2.4 42.8 0.6 CD A:GLU756 2.7 48.8 1.0 OE1 A:GLU756 2.8 45.2 1.0 SG A:CYS754 2.8 31.5 0.5 CB A:CYS754 3.1 36.9 0.6 CB A:CYS754 3.3 32.9 0.5 CA A:CYS754 3.3 33.3 0.5 CA A:CYS754 3.4 35.3 0.6 O A:ARG753 4.0 47.5 1.0 CG A:GLU756 4.1 40.2 1.0 C A:CYS754 4.2 34.3 1.0 N A:CYS754 4.5 33.7 1.0 CD A:PRO755 4.6 31.6 1.0 N A:PRO755 4.6 31.8 1.0 C A:ARG753 4.6 41.5 1.0 O A:HOH1129 4.7 56.1 1.0 O A:CYS754 4.9 28.8 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 108)


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 108) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:20.4 occ:1.00 ND1 B:HIS725 2.2 24.0 1.0 SG B:CYS728 2.3 20.5 1.0 SG B:CYS708 2.3 22.3 1.0 SG B:CYS705 2.3 19.4 1.0 CE1 B:HIS725 3.1 25.7 1.0 CB B:CYS705 3.1 18.4 1.0 CG B:HIS725 3.2 23.8 1.0 CB B:CYS728 3.2 19.3 1.0 CB B:CYS708 3.4 22.6 1.0 CB B:HIS725 3.5 21.4 1.0 N B:CYS708 3.8 20.6 1.0 N B:HIS725 4.1 19.0 1.0 CA B:CYS708 4.1 22.9 1.0 NE2 B:HIS725 4.2 24.6 1.0 CD2 B:HIS725 4.3 23.6 1.0 CA B:HIS725 4.4 19.0 1.0 CA B:CYS705 4.5 19.4 1.0 CA B:CYS728 4.6 17.7 1.0 O B:HOH1211 4.7 28.7 1.0 CB B:VAL707 4.7 17.7 1.0 C B:VAL707 4.9 21.3 1.0 C B:CYS708 4.9 23.7 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 108)


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 108) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:23.4 occ:1.00 SG B:CYS717 2.2 24.7 1.0 SG B:CYS720 2.3 25.0 1.0 SG B:CYS745 2.3 25.4 1.0 SG B:CYS742 2.4 20.4 1.0 CB B:CYS717 3.2 20.2 1.0 CB B:CYS720 3.3 30.0 1.0 CB B:CYS742 3.4 20.3 1.0 CB B:CYS745 3.5 19.6 1.0 N B:CYS742 3.8 21.3 1.0 N B:CYS720 3.8 30.9 1.0 N B:CYS745 4.0 19.6 1.0 CA B:CYS720 4.1 29.8 1.0 CA B:CYS742 4.1 20.5 1.0 OG1 B:THR719 4.1 28.3 1.0 CA B:CYS745 4.3 21.8 1.0 C B:THR719 4.5 28.5 1.0 O B:CYS742 4.5 18.9 1.0 O B:HOH1192 4.6 37.1 1.0 C B:CYS742 4.6 18.8 1.0 NH1 B:ARG722 4.6 26.4 1.0 C B:CYS720 4.6 29.6 1.0 CA B:CYS717 4.7 21.5 1.0 O B:CYS720 4.7 27.2 1.0 N B:THR719 4.9 28.9 1.0 CB B:PHE744 4.9 20.3 1.0 C B:SER741 4.9 23.6 1.0 CB B:ARG722 4.9 24.7 1.0 CA B:THR719 5.0 27.4 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