Zinc in PDB 5pzi: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 114)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 114), PDB code: 5pzi 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)	28.48 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.751, 45.441, 83.437, 90.00, 102.22, 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 114) (pdb code 5pzi). 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 114), PDB code: 5pzi:
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 114)


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 114) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:24.4 occ:1.00 ND1 A:HIS725 2.2 25.2 1.0 SG A:CYS705 2.3 23.8 1.0 SG A:CYS708 2.3 24.0 1.0 SG A:CYS728 2.3 25.5 1.0 CE1 A:HIS725 3.0 27.2 1.0 CB A:CYS705 3.0 25.2 1.0 CG A:HIS725 3.2 27.6 1.0 CB A:CYS728 3.2 23.1 1.0 CB A:CYS708 3.3 24.9 1.0 CB A:HIS725 3.6 28.2 1.0 N A:CYS708 3.8 24.1 1.0 O A:HOH1278 4.0 52.3 1.0 CA A:CYS708 4.1 23.2 1.0 N A:HIS725 4.1 24.8 1.0 NE2 A:HIS725 4.2 27.1 1.0 CD2 A:HIS725 4.3 29.3 1.0 CA A:HIS725 4.4 23.8 1.0 CA A:CYS705 4.5 24.1 1.0 O A:HOH1244 4.6 40.4 1.0 CA A:CYS728 4.7 19.6 1.0 CB A:VAL707 4.7 19.2 1.0 C A:CYS708 4.9 28.8 1.0 C A:VAL707 4.9 22.7 1.0 N A:ASN709 5.0 25.6 1.0 C A:CYS705 5.0 25.1 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 114)


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 114) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.2 occ:1.00 SG A:CYS720 2.2 34.0 1.0 SG A:CYS742 2.4 22.5 1.0 SG A:CYS717 2.4 33.9 1.0 SG A:CYS745 2.4 30.8 1.0 CB A:CYS717 3.2 33.9 1.0 CB A:CYS720 3.2 34.8 1.0 CB A:CYS742 3.3 20.2 1.0 CB A:CYS745 3.4 27.8 1.0 N A:CYS742 3.8 26.1 1.0 N A:CYS720 3.9 36.8 1.0 N A:CYS745 4.0 26.6 1.0 CA A:CYS720 4.0 37.2 1.0 OG1 A:THR719 4.1 36.0 1.0 CA A:CYS742 4.1 25.8 1.0 CA A:CYS745 4.3 27.0 1.0 O A:CYS742 4.4 22.2 1.0 O A:HOH1241 4.4 44.9 1.0 C A:THR719 4.5 37.6 1.0 O A:CYS720 4.6 38.0 1.0 NH1 A:ARG722 4.6 32.8 1.0 C A:CYS720 4.6 28.9 1.0 C A:CYS742 4.6 24.9 1.0 CA A:CYS717 4.7 39.1 1.0 CB A:PHE744 4.8 25.4 1.0 N A:THR719 4.9 39.2 1.0 C A:SER741 4.9 25.0 1.0 O A:THR719 5.0 43.4 1.0 CD A:ARG722 5.0 29.1 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 114)


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 114) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:75.8 occ:0.43 OE2 A:GLU756 2.2 59.5 1.0 SG A:CYS754 2.7 48.4 0.6 CD A:GLU756 2.8 52.8 1.0 OE1 A:GLU756 2.9 46.5 1.0 SG A:CYS754 2.9 30.6 0.5 CB A:CYS754 3.2 39.8 0.6 CA A:CYS754 3.3 34.0 0.5 CA A:CYS754 3.3 37.5 0.6 CB A:CYS754 3.4 32.9 0.5 O A:ARG753 3.8 51.7 1.0 C A:CYS754 4.2 33.9 1.0 CG A:GLU756 4.3 43.2 1.0 N A:CYS754 4.4 34.6 1.0 C A:ARG753 4.5 43.2 1.0 CD A:PRO755 4.6 31.4 1.0 N A:PRO755 4.7 31.5 1.0 O A:HOH1145 4.9 51.9 1.0 O A:CYS754 5.0 30.9 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 114)


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 114) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:20.9 occ:1.00 ND1 B:HIS725 2.2 23.6 1.0 SG B:CYS728 2.2 22.0 1.0 SG B:CYS708 2.3 22.7 1.0 SG B:CYS705 2.3 19.9 1.0 CE1 B:HIS725 3.1 25.1 1.0 CB B:CYS705 3.1 19.6 1.0 CG B:HIS725 3.2 22.3 1.0 CB B:CYS728 3.2 20.8 1.0 CB B:CYS708 3.4 20.9 1.0 CB B:HIS725 3.6 20.0 1.0 N B:CYS708 3.8 21.8 1.0 CA B:CYS708 4.1 21.6 1.0 N B:HIS725 4.2 20.5 1.0 NE2 B:HIS725 4.2 22.8 1.0 CD2 B:HIS725 4.3 22.2 1.0 CA B:HIS725 4.5 18.6 1.0 CA B:CYS705 4.5 21.1 1.0 CA B:CYS728 4.7 18.8 1.0 O B:HOH1210 4.7 29.8 1.0 CB B:VAL707 4.7 19.4 1.0 C B:CYS708 4.8 24.6 1.0 C B:VAL707 4.9 21.9 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 114)


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 114) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:24.6 occ:1.00 SG B:CYS717 2.2 25.7 1.0 SG B:CYS720 2.3 25.3 1.0 SG B:CYS745 2.3 26.9 1.0 SG B:CYS742 2.4 21.7 1.0 CB B:CYS717 3.2 22.7 1.0 CB B:CYS720 3.3 29.1 1.0 CB B:CYS742 3.4 20.6 1.0 CB B:CYS745 3.4 22.5 1.0 N B:CYS742 3.7 21.8 1.0 N B:CYS720 3.8 32.8 1.0 N B:CYS745 4.0 20.1 1.0 CA B:CYS720 4.1 30.0 1.0 CA B:CYS742 4.1 19.8 1.0 OG1 B:THR719 4.1 28.6 1.0 CA B:CYS745 4.3 21.3 1.0 C B:THR719 4.5 30.2 1.0 O B:CYS742 4.5 19.0 1.0 O B:HOH1191 4.6 35.8 1.0 NH1 B:ARG722 4.6 26.6 1.0 C B:CYS742 4.6 18.1 1.0 C B:CYS720 4.6 30.8 1.0 CA B:CYS717 4.6 23.9 1.0 O B:CYS720 4.7 28.9 1.0 CB B:PHE744 4.9 19.9 1.0 N B:THR719 4.9 30.8 1.0 C B:SER741 4.9 23.3 1.0 CB B:ARG722 4.9 23.9 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