Zinc in PDB 5pyg: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 76)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 76), PDB code: 5pyg 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)	42.67 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.720, 45.410, 83.600, 90.00, 102.27, 90.00
R / Rfree (%)	17.7 / 22.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 76) (pdb code 5pyg). 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 76), PDB code: 5pyg:
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 76)


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 76) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:28.4 occ:1.00 ND1 A:HIS725 2.2 35.2 1.0 SG A:CYS728 2.3 24.2 1.0 SG A:CYS705 2.3 29.3 1.0 SG A:CYS708 2.4 31.2 1.0 CB A:CYS705 3.0 33.7 1.0 CB A:CYS728 3.1 23.7 1.0 CE1 A:HIS725 3.2 31.6 1.0 CG A:HIS725 3.2 31.7 1.0 CB A:CYS708 3.3 26.3 1.0 CB A:HIS725 3.5 29.0 1.0 N A:CYS708 3.8 23.0 1.0 O A:HOH1289 4.1 46.6 1.0 CA A:CYS708 4.1 27.5 1.0 N A:HIS725 4.1 31.5 1.0 NE2 A:HIS725 4.3 40.7 1.0 CD2 A:HIS725 4.4 38.4 1.0 CA A:HIS725 4.4 28.7 1.0 CA A:CYS705 4.5 31.4 1.0 CA A:CYS728 4.6 23.2 1.0 CB A:VAL707 4.6 19.1 1.0 O A:HOH1243 4.7 42.1 1.0 C A:CYS708 4.9 31.0 1.0 C A:VAL707 4.9 25.7 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 76)


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 76) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:35.7 occ:1.00 SG A:CYS717 2.2 42.9 1.0 SG A:CYS720 2.2 35.4 1.0 SG A:CYS745 2.4 40.6 1.0 SG A:CYS742 2.4 30.8 1.0 CB A:CYS717 3.2 45.1 1.0 CB A:CYS720 3.2 36.5 1.0 CB A:CYS742 3.4 27.4 1.0 CB A:CYS745 3.5 35.3 1.0 N A:CYS720 3.7 39.0 1.0 N A:CYS742 3.8 36.3 1.0 CA A:CYS720 4.0 37.4 1.0 N A:CYS745 4.0 34.8 1.0 CA A:CYS742 4.1 35.4 1.0 OG1 A:THR719 4.2 47.3 1.0 CA A:CYS745 4.3 37.4 1.0 C A:THR719 4.4 41.1 1.0 O A:CYS742 4.5 23.3 1.0 O A:CYS720 4.5 32.6 1.0 O A:HOH1059 4.6 52.4 1.0 C A:CYS720 4.6 31.1 1.0 C A:CYS742 4.6 29.2 1.0 NH1 A:ARG722 4.6 36.7 1.0 CA A:CYS717 4.6 46.0 1.0 N A:THR719 4.9 47.4 1.0 CB A:PHE744 4.9 26.3 1.0 C A:SER741 4.9 35.6 1.0 CD A:ARG722 4.9 35.7 1.0 CA A:THR719 5.0 41.4 1.0 O A:THR719 5.0 43.9 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 76)


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 76) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:94.4 occ:0.43 OE2 A:GLU756 2.5 80.8 1.0 SG A:CYS754 3.1 65.2 0.6 OE1 A:GLU756 3.2 72.0 1.0 CD A:GLU756 3.2 70.3 1.0 SG A:CYS754 3.6 41.6 0.5 CB A:CYS754 3.6 53.0 0.6 CA A:CYS754 3.8 48.5 0.6 CA A:CYS754 3.8 44.5 0.5 CB A:CYS754 3.9 45.0 0.5 O A:ARG753 4.0 67.1 1.0 CG A:GLU756 4.6 61.9 1.0 C A:CYS754 4.8 45.8 1.0 N A:CYS754 4.8 46.8 1.0 C A:ARG753 4.8 55.5 1.0 CD A:PRO755 4.9 52.2 1.0 O A:HOH1077 5.0 57.2 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 76)


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 76) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:27.6 occ:1.00 SG B:CYS705 2.2 27.1 1.0 ND1 B:HIS725 2.2 44.4 1.0 SG B:CYS728 2.3 25.9 1.0 SG B:CYS708 2.4 27.9 1.0 CB B:CYS705 2.9 31.5 1.0 CE1 B:HIS725 3.1 39.0 1.0 CB B:CYS728 3.1 23.6 1.0 CG B:HIS725 3.2 37.3 1.0 CB B:CYS708 3.3 25.4 1.0 CB B:HIS725 3.6 28.9 1.0 N B:CYS708 3.8 26.6 1.0 CA B:CYS708 4.1 26.8 1.0 N B:HIS725 4.1 29.8 1.0 NE2 B:HIS725 4.2 47.7 1.0 CD2 B:HIS725 4.2 42.0 1.0 CA B:CYS705 4.4 31.7 1.0 CA B:HIS725 4.5 28.0 1.0 CA B:CYS728 4.6 21.9 1.0 CB B:VAL707 4.7 21.4 1.0 O B:HOH1206 4.7 42.4 1.0 C B:CYS708 4.8 30.2 1.0 C B:VAL707 4.9 28.1 1.0 C B:CYS705 5.0 29.9 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 76)


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 76) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:33.0 occ:1.00 SG B:CYS717 2.1 32.9 1.0 SG B:CYS745 2.3 34.5 1.0 SG B:CYS720 2.4 32.5 1.0 SG B:CYS742 2.4 27.8 1.0 CB B:CYS720 3.2 39.9 1.0 CB B:CYS717 3.3 34.3 1.0 CB B:CYS742 3.4 27.4 1.0 CB B:CYS745 3.4 33.0 1.0 N B:CYS742 3.8 32.6 1.0 N B:CYS720 3.8 41.0 1.0 CA B:CYS720 4.0 37.8 1.0 OG1 B:THR719 4.1 39.7 1.0 N B:CYS745 4.1 28.1 1.0 CA B:CYS742 4.1 28.5 1.0 CA B:CYS745 4.3 27.9 1.0 C B:THR719 4.4 38.3 1.0 O B:HOH1192 4.5 44.2 1.0 O B:CYS742 4.6 27.0 1.0 C B:CYS742 4.6 26.1 1.0 C B:CYS720 4.7 35.1 1.0 CA B:CYS717 4.7 39.4 1.0 NH1 B:ARG722 4.7 35.1 1.0 O B:CYS720 4.8 34.5 1.0 N B:THR719 4.8 42.6 1.0 CB B:PHE744 4.9 25.6 1.0 C B:SER741 4.9 35.0 1.0 CA B:THR719 4.9 39.0 1.0 O B:THR719 4.9 39.1 1.0 CB B:ARG722 5.0 34.0 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