Zinc in PDB 5pxy: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 58)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 58), PDB code: 5pxy 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)	42.57 / 2.14
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.670, 45.290, 83.360, 90.00, 102.42, 90.00
R / Rfree (%)	16.4 / 21.8

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 58) (pdb code 5pxy). 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 58), PDB code: 5pxy:
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 58)


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 58) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.6 occ:1.00 ND1 A:HIS725 2.2 36.1 1.0 SG A:CYS728 2.2 23.5 1.0 SG A:CYS705 2.3 25.4 1.0 SG A:CYS708 2.4 29.4 1.0 CB A:CYS705 3.0 29.7 1.0 CE1 A:HIS725 3.1 33.6 1.0 CB A:CYS728 3.1 24.7 1.0 CG A:HIS725 3.2 33.6 1.0 CB A:CYS708 3.4 27.2 1.0 CB A:HIS725 3.6 30.3 1.0 N A:CYS708 3.8 26.8 1.0 O A:HOH1268 3.8 47.1 1.0 N A:HIS725 4.1 27.7 1.0 CA A:CYS708 4.1 27.9 1.0 NE2 A:HIS725 4.2 35.7 1.0 CD2 A:HIS725 4.3 38.4 1.0 CA A:CYS705 4.4 28.1 1.0 CA A:HIS725 4.4 28.7 1.0 O A:HOH1246 4.6 34.3 1.0 CA A:CYS728 4.6 24.6 1.0 CB A:VAL707 4.7 22.0 1.0 C A:VAL707 4.9 26.2 1.0 C A:CYS708 4.9 29.2 1.0 C A:CYS705 5.0 27.4 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 58)


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 58) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:32.6 occ:1.00 SG A:CYS720 2.2 33.9 1.0 SG A:CYS717 2.3 34.3 1.0 SG A:CYS745 2.3 37.4 1.0 SG A:CYS742 2.4 30.7 1.0 CB A:CYS720 3.2 36.7 1.0 CB A:CYS717 3.3 40.7 1.0 CB A:CYS745 3.5 30.4 1.0 CB A:CYS742 3.5 30.4 1.0 N A:CYS720 3.8 35.9 1.0 N A:CYS742 3.9 36.8 1.0 CA A:CYS720 4.0 35.9 1.0 N A:CYS745 4.0 28.1 1.0 CA A:CYS742 4.2 34.1 1.0 OG1 A:THR719 4.2 43.2 1.0 CA A:CYS745 4.3 30.4 1.0 O A:CYS742 4.4 24.6 1.0 C A:THR719 4.4 38.7 1.0 C A:CYS742 4.5 29.4 1.0 C A:CYS720 4.5 32.8 1.0 O A:CYS720 4.6 35.5 1.0 CA A:CYS717 4.7 41.3 1.0 NH1 A:ARG722 4.7 29.5 1.0 O A:HOH1154 4.7 47.1 1.0 CB A:PHE744 4.8 25.9 1.0 CD A:ARG722 4.9 30.8 1.0 C A:SER741 4.9 36.1 1.0 O A:THR719 4.9 41.4 1.0 N A:THR719 5.0 42.0 1.0 CB A:ARG722 5.0 34.9 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 58)


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 58) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:81.1 occ:0.43 OE2 A:GLU756 2.4 65.1 1.0 OE1 A:GLU756 3.0 50.6 1.0 CD A:GLU756 3.1 58.6 1.0 SG A:CYS754 3.2 50.5 0.6 SG A:CYS754 3.8 32.1 0.5 CA A:CYS754 3.9 41.7 0.6 CB A:CYS754 4.0 44.1 0.6 CA A:CYS754 4.0 38.2 0.5 O A:ARG753 4.0 65.0 1.0 CB A:CYS754 4.2 36.8 0.5 CG A:GLU756 4.6 48.9 1.0 CD A:PRO755 4.7 42.4 1.0 C A:CYS754 4.8 39.7 1.0 C A:ARG753 4.9 49.7 1.0 N A:CYS754 4.9 42.5 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 58)


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 58) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:23.1 occ:1.00 ND1 B:HIS725 2.1 30.2 1.0 SG B:CYS728 2.2 22.0 1.0 SG B:CYS705 2.3 21.9 1.0 SG B:CYS708 2.4 27.3 1.0 CB B:CYS705 3.0 25.0 1.0 CE1 B:HIS725 3.0 30.4 1.0 CB B:CYS728 3.1 20.7 1.0 CG B:HIS725 3.2 27.9 1.0 CB B:CYS708 3.4 23.9 1.0 CB B:HIS725 3.5 23.9 1.0 N B:CYS708 3.8 22.6 1.0 CA B:CYS708 4.2 24.9 1.0 N B:HIS725 4.2 22.9 1.0 NE2 B:HIS725 4.2 33.2 1.0 CD2 B:HIS725 4.3 28.7 1.0 CA B:HIS725 4.5 21.2 1.0 CA B:CYS705 4.5 25.1 1.0 CA B:CYS728 4.6 19.9 1.0 CB B:VAL707 4.6 19.6 1.0 O B:HOH1193 4.6 38.1 1.0 C B:CYS708 4.8 26.4 1.0 C B:VAL707 4.9 23.7 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 58)


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 58) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:27.4 occ:1.00 SG B:CYS717 2.2 27.3 1.0 SG B:CYS742 2.3 27.4 1.0 SG B:CYS745 2.3 31.8 1.0 SG B:CYS720 2.3 30.4 1.0 CB B:CYS717 3.2 31.1 1.0 CB B:CYS720 3.3 30.1 1.0 CB B:CYS742 3.3 24.5 1.0 CB B:CYS745 3.4 27.6 1.0 N B:CYS742 3.7 25.2 1.0 N B:CYS720 3.8 31.6 1.0 CA B:CYS742 4.0 24.3 1.0 CA B:CYS720 4.1 29.6 1.0 OG1 B:THR719 4.1 32.3 1.0 N B:CYS745 4.1 24.1 1.0 CA B:CYS745 4.4 24.3 1.0 C B:THR719 4.4 31.1 1.0 O B:HOH1184 4.5 37.8 1.0 C B:CYS742 4.6 21.9 1.0 O B:CYS742 4.6 23.1 1.0 CA B:CYS717 4.6 34.0 1.0 C B:CYS720 4.7 28.2 1.0 NH1 B:ARG722 4.7 30.5 1.0 O B:CYS720 4.8 30.4 1.0 C B:SER741 4.8 31.8 1.0 N B:THR719 4.9 36.2 1.0 CB B:PHE744 4.9 20.4 1.0 O B:THR719 5.0 31.5 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