Zinc in PDB 5pyn: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 83)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 83), PDB code: 5pyn 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)	40.84 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.770, 45.530, 83.460, 90.00, 101.85, 90.00
R / Rfree (%)	22.9 / 27

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 83) (pdb code 5pyn). 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 83), PDB code: 5pyn:
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 83)


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 83) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:22.1 occ:1.00 ND1 A:HIS725 2.2 28.0 1.0 SG A:CYS728 2.2 22.6 1.0 SG A:CYS705 2.2 24.8 1.0 SG A:CYS708 2.3 24.2 1.0 CE1 A:HIS725 3.1 29.4 1.0 CB A:CYS705 3.1 26.2 1.0 CB A:CYS728 3.2 21.9 1.0 CG A:HIS725 3.2 30.2 1.0 CB A:CYS708 3.3 23.7 1.0 O A:HOH1269 3.5 45.2 1.0 CB A:HIS725 3.6 27.7 1.0 N A:CYS708 3.8 22.1 1.0 CA A:CYS708 4.1 25.1 1.0 N A:HIS725 4.2 26.0 1.0 NE2 A:HIS725 4.2 31.6 1.0 CD2 A:HIS725 4.3 32.6 1.0 CA A:HIS725 4.5 26.8 1.0 O A:HOH1253 4.5 32.3 1.0 CA A:CYS705 4.6 25.2 1.0 CA A:CYS728 4.6 20.8 1.0 CB A:VAL707 4.6 18.7 1.0 O A:HOH1277 4.8 53.8 1.0 C A:CYS708 4.9 27.2 1.0 C A:VAL707 4.9 23.2 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 83)


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 83) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:28.2 occ:1.00 SG A:CYS717 2.2 34.7 1.0 SG A:CYS720 2.2 29.2 1.0 SG A:CYS745 2.4 31.5 1.0 SG A:CYS742 2.4 25.4 1.0 CB A:CYS717 3.2 35.5 1.0 CB A:CYS720 3.3 34.9 1.0 CB A:CYS742 3.5 23.4 1.0 CB A:CYS745 3.5 25.3 1.0 N A:CYS742 3.7 24.5 1.0 N A:CYS720 3.8 32.3 1.0 N A:CYS745 4.0 23.9 1.0 CA A:CYS742 4.1 25.7 1.0 CA A:CYS720 4.1 33.0 1.0 OG1 A:THR719 4.1 35.5 1.0 CA A:CYS745 4.3 25.9 1.0 C A:THR719 4.4 34.5 1.0 O A:CYS742 4.4 19.6 1.0 C A:CYS742 4.5 23.3 1.0 O A:HOH1244 4.6 38.5 1.0 CA A:CYS717 4.6 41.3 1.0 C A:CYS720 4.7 28.9 1.0 NH1 A:ARG722 4.7 30.0 1.0 O A:CYS720 4.7 33.0 1.0 C A:SER741 4.8 27.2 1.0 CB A:PHE744 4.9 23.6 1.0 N A:THR719 4.9 41.3 1.0 O A:THR719 4.9 35.3 1.0 CD A:ARG722 5.0 27.6 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 83)


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 83) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:84.1 occ:0.43 SG A:CYS754 3.2 48.7 0.6 OE2 A:GLU756 3.3 60.9 1.0 O A:ARG753 3.6 40.9 1.0 OE1 A:GLU756 3.6 50.6 1.0 CD A:GLU756 3.9 52.6 1.0 CA A:CYS754 3.9 34.7 0.6 CA A:CYS754 3.9 30.6 0.5 CB A:CYS754 4.0 36.3 0.6 CB A:CYS754 4.2 28.1 0.5 SG A:CYS754 4.2 25.5 0.5 C A:ARG753 4.5 38.9 1.0 N A:CYS754 4.7 32.7 1.0 CD A:PRO755 4.7 33.5 1.0 C A:CYS754 5.0 32.5 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 83)


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 83) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:17.2 occ:1.00 ND1 B:HIS725 2.1 24.1 1.0 SG B:CYS705 2.3 19.1 1.0 SG B:CYS728 2.3 19.1 1.0 SG B:CYS708 2.3 19.4 1.0 CE1 B:HIS725 3.0 24.3 1.0 CB B:CYS705 3.1 20.5 1.0 CB B:CYS728 3.2 15.7 1.0 CG B:HIS725 3.2 20.9 1.0 CB B:CYS708 3.3 18.9 1.0 CB B:HIS725 3.6 18.4 1.0 N B:CYS708 3.8 16.8 1.0 CA B:CYS708 4.1 18.6 1.0 NE2 B:HIS725 4.2 22.7 1.0 N B:HIS725 4.2 17.8 1.0 CD2 B:HIS725 4.3 21.5 1.0 CA B:HIS725 4.5 17.8 1.0 CA B:CYS705 4.5 21.4 1.0 O B:HOH1212 4.6 25.8 1.0 CA B:CYS728 4.6 15.6 1.0 CB B:VAL707 4.7 17.1 1.0 C B:CYS708 4.8 20.3 1.0 C B:VAL707 4.9 18.3 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 83)


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 83) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.8 occ:1.00 SG B:CYS717 2.1 23.4 1.0 SG B:CYS720 2.3 22.4 1.0 SG B:CYS742 2.3 17.6 1.0 SG B:CYS745 2.4 24.1 1.0 CB B:CYS717 3.2 22.4 1.0 CB B:CYS720 3.2 24.6 1.0 CB B:CYS742 3.5 18.5 1.0 CB B:CYS745 3.5 20.9 1.0 N B:CYS720 3.7 26.3 1.0 N B:CYS742 3.8 19.4 1.0 CA B:CYS720 4.0 25.0 1.0 OG1 B:THR719 4.0 27.2 1.0 N B:CYS745 4.0 17.5 1.0 CA B:CYS742 4.1 17.4 1.0 CA B:CYS745 4.3 20.2 1.0 C B:THR719 4.4 27.5 1.0 O B:HOH1187 4.5 29.8 1.0 O B:CYS742 4.5 18.8 1.0 C B:CYS742 4.6 18.9 1.0 C B:CYS720 4.6 25.1 1.0 CA B:CYS717 4.6 24.3 1.0 O B:CYS720 4.7 24.6 1.0 NH1 B:ARG722 4.7 25.2 1.0 N B:THR719 4.8 31.6 1.0 C B:SER741 4.9 21.7 1.0 CA B:THR719 4.9 27.6 1.0 CB B:PHE744 4.9 16.3 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