Zinc in PDB 5pz9: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 105)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 105), PDB code: 5pz9 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)	28.58 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.780, 45.603, 83.559, 90.00, 101.96, 90.00
R / Rfree (%)	16.9 / 21.6

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 105) (pdb code 5pz9). 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 105), PDB code: 5pz9:
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 105)


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 105) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:33.5 occ:1.00 ND1 A:HIS725 2.2 42.5 1.0 SG A:CYS705 2.2 35.4 1.0 SG A:CYS728 2.3 33.9 1.0 SG A:CYS708 2.4 34.9 1.0 CB A:CYS705 3.0 39.7 1.0 CE1 A:HIS725 3.1 42.7 1.0 CB A:CYS728 3.2 33.3 1.0 CG A:HIS725 3.2 43.8 1.0 CB A:CYS708 3.3 33.2 1.0 CB A:HIS725 3.6 40.0 1.0 N A:CYS708 3.8 31.6 1.0 O A:HOH1283 3.8 65.2 1.0 N A:HIS725 4.1 37.0 1.0 CA A:CYS708 4.1 34.3 1.0 NE2 A:HIS725 4.2 48.7 1.0 CD2 A:HIS725 4.3 49.1 1.0 CA A:CYS705 4.4 37.4 1.0 O A:HOH1244 4.5 44.9 1.0 CA A:HIS725 4.5 35.6 1.0 CB A:VAL707 4.6 28.1 1.0 CA A:CYS728 4.7 31.7 1.0 C A:CYS708 4.9 35.8 1.0 C A:VAL707 4.9 35.9 1.0 C A:CYS705 5.0 34.3 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 105)


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 105) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:42.0 occ:1.00 SG A:CYS717 2.1 46.8 1.0 SG A:CYS720 2.2 44.9 1.0 SG A:CYS745 2.3 45.1 1.0 SG A:CYS742 2.4 36.7 1.0 CB A:CYS717 3.2 50.4 1.0 CB A:CYS720 3.3 48.9 1.0 CB A:CYS742 3.4 34.0 1.0 CB A:CYS745 3.5 39.1 1.0 N A:CYS720 3.8 47.2 1.0 N A:CYS742 3.9 36.5 1.0 N A:CYS745 4.0 39.9 1.0 CA A:CYS720 4.1 46.8 1.0 OG1 A:THR719 4.1 56.1 1.0 CA A:CYS742 4.1 41.5 1.0 CA A:CYS745 4.3 42.8 1.0 O A:CYS742 4.4 31.5 1.0 C A:THR719 4.4 48.1 1.0 O A:HOH1237 4.5 55.7 1.0 NH1 A:ARG722 4.5 41.5 1.0 C A:CYS742 4.5 35.2 1.0 CA A:CYS717 4.6 57.3 1.0 C A:CYS720 4.6 37.4 1.0 O A:CYS720 4.7 40.3 1.0 CB A:PHE744 4.8 34.6 1.0 N A:THR719 4.9 56.5 1.0 C A:SER741 4.9 39.9 1.0 CD A:ARG722 5.0 39.9 1.0 O A:THR719 5.0 54.0 1.0 CA A:THR719 5.0 51.1 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 105)


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 105) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:86.4 occ:0.43 OE2 A:GLU756 2.8 84.2 1.0 SG A:CYS754 2.9 68.8 0.6 OE1 A:GLU756 3.3 73.8 1.0 CD A:GLU756 3.5 72.6 1.0 O A:ARG753 3.6 76.5 1.0 SG A:CYS754 3.8 48.1 0.5 CB A:CYS754 3.8 56.5 0.6 CA A:CYS754 3.8 48.9 0.5 CA A:CYS754 3.8 52.3 0.6 CB A:CYS754 3.9 48.7 0.5 C A:ARG753 4.6 60.7 1.0 N A:CYS754 4.7 49.9 1.0 C A:CYS754 4.9 50.4 1.0 CG A:GLU756 5.0 61.2 1.0 CD A:PRO755 5.0 49.7 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 105)


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 105) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:29.4 occ:1.00 ND1 B:HIS725 2.2 42.4 1.0 SG B:CYS705 2.2 29.1 1.0 SG B:CYS728 2.3 30.0 1.0 SG B:CYS708 2.4 32.0 1.0 CB B:CYS705 3.0 35.0 1.0 CE1 B:HIS725 3.0 40.7 1.0 CB B:CYS728 3.2 28.2 1.0 CG B:HIS725 3.2 38.4 1.0 CB B:CYS708 3.4 28.0 1.0 CB B:HIS725 3.6 32.2 1.0 N B:CYS708 3.8 29.4 1.0 CA B:CYS708 4.1 30.7 1.0 N B:HIS725 4.2 31.0 1.0 NE2 B:HIS725 4.2 44.7 1.0 CD2 B:HIS725 4.3 39.5 1.0 CA B:CYS705 4.4 33.8 1.0 CA B:HIS725 4.5 29.6 1.0 CB B:VAL707 4.6 30.0 1.0 CA B:CYS728 4.7 27.2 1.0 O B:HOH1212 4.8 37.8 1.0 C B:CYS708 4.8 31.8 1.0 C B:VAL707 4.9 33.3 1.0 C B:CYS705 5.0 33.5 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 105)


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 105) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:37.4 occ:1.00 SG B:CYS717 2.1 36.0 1.0 SG B:CYS745 2.3 40.4 1.0 SG B:CYS742 2.4 34.6 1.0 SG B:CYS720 2.4 38.7 1.0 CB B:CYS720 3.2 41.3 1.0 CB B:CYS717 3.2 38.3 1.0 CB B:CYS745 3.4 36.4 1.0 CB B:CYS742 3.5 31.8 1.0 N B:CYS742 3.8 35.4 1.0 N B:CYS720 3.9 44.2 1.0 CA B:CYS720 4.0 39.6 1.0 OG1 B:THR719 4.1 43.5 1.0 CA B:CYS742 4.2 32.0 1.0 N B:CYS745 4.2 33.4 1.0 CA B:CYS745 4.4 35.7 1.0 C B:THR719 4.4 39.2 1.0 O B:HOH1186 4.5 43.4 1.0 O B:CYS742 4.6 28.9 1.0 C B:CYS742 4.6 27.2 1.0 C B:CYS720 4.7 41.2 1.0 CA B:CYS717 4.7 43.5 1.0 NH1 B:ARG722 4.7 38.5 1.0 O B:CYS720 4.8 39.1 1.0 N B:THR719 4.9 48.8 1.0 C B:SER741 4.9 40.3 1.0 CA B:THR719 5.0 41.4 1.0 CB B:PHE744 5.0 29.7 1.0 O B:THR719 5.0 43.1 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