Zinc in PDB 5pya: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 70)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 70), PDB code: 5pya 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)	28.51 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.784, 45.426, 83.508, 90.00, 102.05, 90.00
R / Rfree (%)	17.8 / 20.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 70) (pdb code 5pya). 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 70), PDB code: 5pya:
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 70)


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 70) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:23.2 occ:1.00 ND1 A:HIS725 2.1 23.6 1.0 SG A:CYS728 2.3 22.9 1.0 SG A:CYS708 2.3 23.4 1.0 SG A:CYS705 2.3 22.4 1.0 CE1 A:HIS725 3.0 28.9 1.0 CB A:CYS705 3.1 22.4 1.0 CG A:HIS725 3.2 27.9 1.0 CB A:CYS728 3.2 21.0 1.0 CB A:CYS708 3.4 22.7 1.0 CB A:HIS725 3.6 27.9 1.0 N A:CYS708 3.8 22.2 1.0 O A:HOH1285 4.1 55.7 1.0 N A:HIS725 4.1 25.9 1.0 CA A:CYS708 4.1 22.4 1.0 NE2 A:HIS725 4.2 27.8 1.0 CD2 A:HIS725 4.3 27.4 1.0 CA A:HIS725 4.4 23.7 1.0 CA A:CYS705 4.5 21.9 1.0 CA A:CYS728 4.6 19.0 1.0 O A:HOH1250 4.6 38.3 1.0 CB A:VAL707 4.7 17.6 1.0 C A:CYS708 4.9 26.4 1.0 C A:VAL707 4.9 21.9 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 70)


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 70) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.1 occ:1.00 SG A:CYS720 2.2 35.3 1.0 SG A:CYS717 2.3 33.4 1.0 SG A:CYS742 2.3 23.5 1.0 SG A:CYS745 2.4 31.4 1.0 CB A:CYS717 3.2 32.8 1.0 CB A:CYS720 3.3 36.5 1.0 CB A:CYS742 3.3 20.8 1.0 CB A:CYS745 3.4 26.1 1.0 N A:CYS742 3.8 28.3 1.0 N A:CYS720 3.8 36.5 1.0 N A:CYS745 4.0 27.1 1.0 CA A:CYS720 4.0 34.9 1.0 CA A:CYS742 4.1 25.0 1.0 OG1 A:THR719 4.1 37.4 1.0 CA A:CYS745 4.3 27.6 1.0 O A:CYS742 4.4 23.5 1.0 C A:THR719 4.4 37.0 1.0 C A:CYS742 4.6 25.2 1.0 C A:CYS720 4.6 27.6 1.0 O A:CYS720 4.6 34.6 1.0 O A:HOH1236 4.6 41.5 1.0 CA A:CYS717 4.6 36.9 1.0 NH1 A:ARG722 4.7 29.3 1.0 C A:SER741 4.9 26.2 1.0 CB A:PHE744 4.9 24.6 1.0 N A:THR719 4.9 39.8 1.0 O A:THR719 4.9 36.4 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 70)


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 70) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:35.4 occ:0.43 OE2 A:GLU756 1.8 47.5 1.0 SG A:CYS754 2.4 36.5 0.6 CD A:GLU756 2.6 42.7 1.0 SG A:CYS754 2.7 30.2 0.5 OE1 A:GLU756 2.7 43.1 1.0 CB A:CYS754 3.1 33.8 0.6 CB A:CYS754 3.3 31.8 0.5 CA A:CYS754 3.4 32.6 0.5 CA A:CYS754 3.4 33.5 0.6 CG A:GLU756 4.0 39.2 1.0 O A:ARG753 4.1 49.1 1.0 C A:CYS754 4.3 33.2 1.0 O A:HOH1153 4.5 46.2 1.0 N A:CYS754 4.5 33.7 1.0 C A:ARG753 4.8 42.3 1.0 CD A:PRO755 4.8 33.8 1.0 N A:PRO755 4.8 31.6 1.0 O A:CYS754 5.0 28.6 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 70)


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 70) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:18.9 occ:1.00 ND1 B:HIS725 2.1 21.1 1.0 SG B:CYS708 2.3 19.9 1.0 SG B:CYS728 2.3 18.2 1.0 SG B:CYS705 2.4 18.6 1.0 CE1 B:HIS725 3.0 22.3 1.0 CB B:CYS705 3.1 17.7 1.0 CG B:HIS725 3.2 19.9 1.0 CB B:CYS728 3.2 17.9 1.0 CB B:CYS708 3.4 19.2 1.0 CB B:HIS725 3.5 18.4 1.0 N B:CYS708 3.8 18.1 1.0 CA B:CYS708 4.1 20.4 1.0 NE2 B:HIS725 4.2 21.8 1.0 N B:HIS725 4.2 19.1 1.0 CD2 B:HIS725 4.3 20.7 1.0 CA B:HIS725 4.5 17.4 1.0 CA B:CYS705 4.5 19.5 1.0 CA B:CYS728 4.6 17.5 1.0 O B:HOH1203 4.6 25.9 1.0 CB B:VAL707 4.7 17.2 1.0 C B:CYS708 4.8 23.6 1.0 C B:VAL707 4.9 20.6 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 70)


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 70) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.9 occ:1.00 SG B:CYS717 2.2 24.3 1.0 SG B:CYS720 2.3 24.4 1.0 SG B:CYS742 2.3 19.6 1.0 SG B:CYS745 2.4 23.7 1.0 CB B:CYS717 3.2 19.9 1.0 CB B:CYS720 3.3 28.9 1.0 CB B:CYS742 3.4 19.7 1.0 CB B:CYS745 3.5 19.4 1.0 N B:CYS742 3.7 21.1 1.0 N B:CYS720 3.8 30.1 1.0 CA B:CYS720 4.0 28.2 1.0 N B:CYS745 4.1 20.1 1.0 CA B:CYS742 4.1 20.1 1.0 OG1 B:THR719 4.1 26.4 1.0 CA B:CYS745 4.3 21.6 1.0 C B:THR719 4.5 28.0 1.0 O B:CYS742 4.5 18.6 1.0 C B:CYS742 4.6 18.9 1.0 O B:HOH1195 4.6 34.2 1.0 C B:CYS720 4.6 27.4 1.0 NH1 B:ARG722 4.6 25.3 1.0 CA B:CYS717 4.7 20.9 1.0 O B:CYS720 4.7 24.2 1.0 CB B:PHE744 4.9 20.1 1.0 C B:SER741 4.9 24.0 1.0 N B:THR719 4.9 28.7 1.0 CA B:THR719 5.0 27.6 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