Zinc in PDB 5pzh: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 113)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 113), PDB code: 5pzh 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)	28.53 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.887, 45.451, 83.709, 90.00, 102.21, 90.00
R / Rfree (%)	17.4 / 20.6

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 113) (pdb code 5pzh). 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 113), PDB code: 5pzh:
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 113)


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 113) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.5 occ:1.00 ND1 A:HIS725 2.2 26.9 1.0 SG A:CYS728 2.3 27.5 1.0 SG A:CYS705 2.3 25.8 1.0 SG A:CYS708 2.3 26.9 1.0 CB A:CYS705 3.1 26.5 1.0 CE1 A:HIS725 3.1 31.2 1.0 CG A:HIS725 3.2 30.7 1.0 CB A:CYS728 3.2 25.0 1.0 CB A:CYS708 3.3 25.7 1.0 CB A:HIS725 3.6 30.5 1.0 N A:CYS708 3.8 25.4 1.0 O A:HOH1278 4.0 60.0 1.0 CA A:CYS708 4.1 25.9 1.0 N A:HIS725 4.1 28.2 1.0 NE2 A:HIS725 4.2 30.5 1.0 CD2 A:HIS725 4.3 33.7 1.0 CA A:HIS725 4.4 25.9 1.0 CA A:CYS705 4.5 26.8 1.0 O A:HOH1250 4.6 39.4 1.0 CB A:VAL707 4.6 20.6 1.0 CA A:CYS728 4.6 22.2 1.0 C A:CYS708 4.9 30.8 1.0 C A:VAL707 4.9 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 113)


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 113) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:34.0 occ:1.00 SG A:CYS720 2.3 38.8 1.0 SG A:CYS717 2.3 39.2 1.0 SG A:CYS745 2.4 35.0 1.0 SG A:CYS742 2.4 25.6 1.0 CB A:CYS717 3.2 37.0 1.0 CB A:CYS720 3.3 39.6 1.0 CB A:CYS742 3.3 21.8 1.0 CB A:CYS745 3.5 29.6 1.0 N A:CYS742 3.8 30.5 1.0 N A:CYS720 3.9 41.9 1.0 N A:CYS745 4.1 30.1 1.0 CA A:CYS720 4.1 39.9 1.0 CA A:CYS742 4.1 28.4 1.0 OG1 A:THR719 4.2 42.9 1.0 CA A:CYS745 4.3 30.1 1.0 O A:CYS742 4.4 24.9 1.0 C A:THR719 4.5 42.4 1.0 O A:CYS720 4.6 38.0 1.0 C A:CYS742 4.6 26.9 1.0 C A:CYS720 4.6 29.7 1.0 CA A:CYS717 4.7 41.8 1.0 O A:HOH1232 4.7 45.1 1.0 NH1 A:ARG722 4.7 33.6 1.0 CB A:PHE744 4.9 28.0 1.0 C A:SER741 4.9 27.0 1.0 N A:THR719 4.9 42.8 1.0 O A:THR719 5.0 44.0 1.0 CD A:ARG722 5.0 29.9 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 113)


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 113) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:52.6 occ:0.43 OE2 A:GLU756 2.0 60.4 1.0 SG A:CYS754 2.5 49.5 0.6 CD A:GLU756 2.7 52.6 1.0 OE1 A:GLU756 2.8 53.4 1.0 SG A:CYS754 2.9 38.3 0.5 CB A:CYS754 3.2 43.9 0.6 CA A:CYS754 3.4 39.7 0.5 CA A:CYS754 3.4 41.8 0.6 CB A:CYS754 3.4 39.0 0.5 O A:ARG753 4.0 65.9 1.0 CG A:GLU756 4.1 45.8 1.0 C A:CYS754 4.2 39.9 1.0 N A:CYS754 4.5 39.5 1.0 O A:HOH1112 4.6 55.4 1.0 CD A:PRO755 4.6 39.7 1.0 C A:ARG753 4.6 50.8 1.0 N A:PRO755 4.7 35.9 1.0 O A:CYS754 5.0 36.3 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 113)


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 113) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:23.2 occ:1.00 ND1 B:HIS725 2.1 26.7 1.0 SG B:CYS728 2.3 23.6 1.0 SG B:CYS708 2.3 25.1 1.0 SG B:CYS705 2.3 22.9 1.0 CE1 B:HIS725 3.1 30.3 1.0 CB B:CYS705 3.1 21.6 1.0 CG B:HIS725 3.2 26.7 1.0 CB B:CYS728 3.2 22.2 1.0 CB B:CYS708 3.4 25.1 1.0 CB B:HIS725 3.5 23.8 1.0 N B:CYS708 3.8 23.7 1.0 CA B:CYS708 4.1 24.2 1.0 N B:HIS725 4.2 21.8 1.0 NE2 B:HIS725 4.2 26.0 1.0 CD2 B:HIS725 4.3 25.6 1.0 CA B:HIS725 4.4 20.3 1.0 CA B:CYS705 4.5 22.6 1.0 CA B:CYS728 4.6 21.5 1.0 O B:HOH1207 4.7 34.7 1.0 CB B:VAL707 4.7 20.8 1.0 C B:CYS708 4.9 26.5 1.0 C B:VAL707 4.9 23.3 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 113)


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 113) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:27.1 occ:1.00 SG B:CYS717 2.2 27.7 1.0 SG B:CYS720 2.3 28.8 1.0 SG B:CYS742 2.4 22.9 1.0 SG B:CYS745 2.4 28.7 1.0 CB B:CYS717 3.2 25.0 1.0 CB B:CYS720 3.3 35.1 1.0 CB B:CYS742 3.4 23.0 1.0 CB B:CYS745 3.5 23.9 1.0 N B:CYS742 3.8 23.4 1.0 N B:CYS720 3.8 36.3 1.0 N B:CYS745 4.1 22.2 1.0 CA B:CYS720 4.1 33.6 1.0 OG1 B:THR719 4.1 33.0 1.0 CA B:CYS742 4.1 22.1 1.0 CA B:CYS745 4.3 24.5 1.0 C B:THR719 4.5 33.0 1.0 O B:CYS742 4.5 20.2 1.0 NH1 B:ARG722 4.6 29.9 1.0 C B:CYS742 4.6 20.4 1.0 O B:HOH1197 4.6 38.9 1.0 C B:CYS720 4.7 34.0 1.0 CA B:CYS717 4.7 26.1 1.0 O B:CYS720 4.7 30.3 1.0 N B:THR719 4.8 33.1 1.0 C B:SER741 4.9 27.0 1.0 CB B:PHE744 4.9 23.4 1.0 CB B:ARG722 4.9 26.6 1.0 CA B:THR719 5.0 32.6 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