Zinc in PDB 5pz3: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 99)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 99), PDB code: 5pz3 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)	40.83 / 1.93
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.740, 45.450, 83.500, 90.00, 102.05, 90.00
R / Rfree (%)	17.7 / 22.6

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 99) (pdb code 5pz3). 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 99), PDB code: 5pz3:
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 99)


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 99) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.0 occ:1.00 ND1 A:HIS725 2.2 27.9 1.0 SG A:CYS705 2.2 25.3 1.0 SG A:CYS728 2.3 28.7 1.0 SG A:CYS708 2.3 26.5 1.0 CB A:CYS705 3.0 31.7 1.0 CE1 A:HIS725 3.1 29.2 1.0 CB A:CYS728 3.2 26.0 1.0 CG A:HIS725 3.2 30.1 1.0 CB A:CYS708 3.3 22.3 1.0 CB A:HIS725 3.6 27.6 1.0 N A:CYS708 3.8 21.2 1.0 O A:HOH1295 3.9 50.3 1.0 N A:HIS725 4.1 24.7 1.0 CA A:CYS708 4.1 24.0 1.0 NE2 A:HIS725 4.2 32.5 1.0 CD2 A:HIS725 4.3 34.5 1.0 CA A:HIS725 4.4 25.5 1.0 O A:HOH1254 4.5 36.8 1.0 CA A:CYS705 4.5 31.0 1.0 CB A:VAL707 4.6 18.8 1.0 CA A:CYS728 4.7 24.6 1.0 C A:VAL707 4.8 24.0 1.0 C A:CYS708 4.9 28.0 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 99)


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 99) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:29.4 occ:1.00 SG A:CYS717 2.3 33.9 1.0 SG A:CYS720 2.3 31.7 1.0 SG A:CYS745 2.3 33.3 1.0 SG A:CYS742 2.5 26.7 1.0 CB A:CYS717 3.3 40.2 1.0 CB A:CYS720 3.3 34.1 1.0 CB A:CYS745 3.5 30.4 1.0 CB A:CYS742 3.5 26.6 1.0 N A:CYS742 3.8 27.8 1.0 N A:CYS720 3.9 35.9 1.0 N A:CYS745 4.0 28.6 1.0 OG1 A:THR719 4.1 40.1 1.0 CA A:CYS720 4.1 36.6 1.0 CA A:CYS742 4.2 27.4 1.0 CA A:CYS745 4.3 30.4 1.0 O A:CYS742 4.4 21.6 1.0 C A:THR719 4.4 38.7 1.0 C A:CYS742 4.6 23.7 1.0 NH1 A:ARG722 4.6 32.3 1.0 O A:CYS720 4.6 34.0 1.0 C A:CYS720 4.6 30.4 1.0 CA A:CYS717 4.7 42.2 1.0 CB A:PHE744 4.9 25.3 1.0 O A:HOH1224 4.9 38.8 1.0 C A:SER741 4.9 30.2 1.0 O A:THR719 4.9 42.7 1.0 N A:THR719 4.9 41.2 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 99)


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 99) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:86.7 occ:0.43 OE2 A:GLU756 3.4 80.3 1.0 O A:ARG753 3.7 54.4 1.0 OE1 A:GLU756 3.7 60.8 1.0 SG A:CYS754 4.0 56.4 0.6 CD A:GLU756 4.0 65.4 1.0 CA A:CYS754 4.4 38.0 0.6 CA A:CYS754 4.5 33.4 0.5 CB A:CYS754 4.7 43.1 0.6 C A:ARG753 4.8 44.1 1.0 SG A:CYS754 4.8 29.9 0.5 CB A:CYS754 4.9 33.0 0.5 CD A:PRO755 4.9 34.1 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 99)


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 99) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:24.9 occ:1.00 SG B:CYS705 2.2 24.5 1.0 ND1 B:HIS725 2.2 32.9 1.0 SG B:CYS728 2.3 25.1 1.0 SG B:CYS708 2.4 25.7 1.0 CB B:CYS705 3.1 27.6 1.0 CB B:CYS728 3.1 21.5 1.0 CE1 B:HIS725 3.2 36.0 1.0 CG B:HIS725 3.2 32.6 1.0 CB B:CYS708 3.3 23.2 1.0 CB B:HIS725 3.6 26.6 1.0 N B:CYS708 3.8 22.9 1.0 CA B:CYS708 4.1 24.4 1.0 N B:HIS725 4.2 24.1 1.0 NE2 B:HIS725 4.3 34.1 1.0 CD2 B:HIS725 4.3 31.7 1.0 CA B:HIS725 4.5 22.7 1.0 CA B:CYS705 4.5 27.8 1.0 CB B:VAL707 4.6 20.4 1.0 O B:HOH1209 4.6 32.6 1.0 CA B:CYS728 4.6 19.8 1.0 C B:CYS708 4.8 25.9 1.0 C B:VAL707 4.9 25.0 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 99)


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 99) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:26.5 occ:1.00 SG B:CYS717 2.2 26.0 1.0 SG B:CYS720 2.3 30.8 1.0 SG B:CYS742 2.3 23.5 1.0 SG B:CYS745 2.3 31.6 1.0 CB B:CYS720 3.2 35.1 1.0 CB B:CYS717 3.3 26.9 1.0 CB B:CYS742 3.4 25.8 1.0 CB B:CYS745 3.4 27.9 1.0 N B:CYS720 3.8 37.4 1.0 N B:CYS742 3.9 27.7 1.0 CA B:CYS720 4.1 33.7 1.0 OG1 B:THR719 4.1 39.5 1.0 N B:CYS745 4.1 21.7 1.0 CA B:CYS742 4.1 24.0 1.0 CA B:CYS745 4.3 25.3 1.0 C B:THR719 4.4 35.1 1.0 O B:CYS742 4.5 24.0 1.0 O B:HOH1187 4.5 36.8 1.0 C B:CYS742 4.6 23.2 1.0 NH1 B:ARG722 4.6 32.0 1.0 C B:CYS720 4.7 34.3 1.0 CA B:CYS717 4.7 31.5 1.0 O B:CYS720 4.8 33.6 1.0 N B:THR719 4.9 37.5 1.0 CB B:PHE744 4.9 21.3 1.0 CA B:THR719 5.0 37.6 1.0 C B:SER741 5.0 29.2 1.0 CB B:THR719 5.0 42.7 1.0 O B:THR719 5.0 32.0 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