Zinc in PDB 5pwy: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 22)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 22), PDB code: 5pwy 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)	28.41 / 1.98
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.578, 45.327, 83.288, 90.00, 102.28, 90.00
R / Rfree (%)	16.8 / 21.5

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 22) (pdb code 5pwy). 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 22), PDB code: 5pwy:
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 22)


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 22) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:22.5 occ:1.00 SG A:CYS705 2.2 24.9 1.0 ND1 A:HIS725 2.2 27.5 1.0 SG A:CYS728 2.2 19.4 1.0 SG A:CYS708 2.3 24.2 1.0 CB A:CYS705 3.0 26.4 1.0 CE1 A:HIS725 3.1 26.1 1.0 CB A:CYS728 3.2 19.2 1.0 CG A:HIS725 3.3 27.7 1.0 CB A:CYS708 3.3 22.2 1.0 CB A:HIS725 3.6 26.4 1.0 N A:CYS708 3.8 22.2 1.0 O A:HOH1272 3.9 54.0 1.0 N A:HIS725 4.1 27.0 1.0 CA A:CYS708 4.1 23.6 1.0 NE2 A:HIS725 4.2 29.4 1.0 CD2 A:HIS725 4.4 30.1 1.0 CA A:CYS705 4.5 24.2 1.0 CA A:HIS725 4.5 24.8 1.0 O A:HOH1246 4.6 29.3 1.0 CB A:VAL707 4.7 18.6 1.0 CA A:CYS728 4.7 19.6 1.0 C A:CYS708 4.9 25.9 1.0 C A:VAL707 4.9 21.2 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 22)


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 22) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:27.3 occ:1.00 SG A:CYS720 2.2 31.0 1.0 SG A:CYS717 2.2 30.0 1.0 SG A:CYS745 2.4 32.0 1.0 SG A:CYS742 2.4 23.6 1.0 CB A:CYS717 3.2 33.9 1.0 CB A:CYS720 3.3 32.8 1.0 CB A:CYS742 3.5 21.9 1.0 CB A:CYS745 3.5 27.7 1.0 N A:CYS720 3.8 33.5 1.0 N A:CYS742 3.8 26.2 1.0 N A:CYS745 4.0 24.3 1.0 CA A:CYS720 4.0 34.1 1.0 OG1 A:THR719 4.1 35.6 1.0 CA A:CYS742 4.2 25.8 1.0 CA A:CYS745 4.3 27.4 1.0 C A:THR719 4.4 34.2 1.0 O A:CYS742 4.5 21.1 1.0 O A:HOH1206 4.5 43.6 1.0 C A:CYS742 4.6 24.2 1.0 NH1 A:ARG722 4.6 27.1 1.0 C A:CYS720 4.6 30.1 1.0 O A:CYS720 4.6 33.6 1.0 CA A:CYS717 4.6 36.9 1.0 CB A:PHE744 4.8 21.2 1.0 CD A:ARG722 4.8 26.4 1.0 O A:THR719 4.9 37.1 1.0 N A:THR719 4.9 39.5 1.0 C A:SER741 4.9 27.4 1.0 C A:PHE744 5.0 22.1 1.0 CB A:ARG722 5.0 31.2 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 22)


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 22) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:88.0 occ:0.43 OE2 A:GLU756 3.3 62.1 1.0 OE1 A:GLU756 3.5 53.9 1.0 SG A:CYS754 3.8 52.2 0.6 CD A:GLU756 3.8 54.8 1.0 O A:ARG753 3.8 48.2 1.0 CA A:CYS754 4.3 34.5 0.6 CA A:CYS754 4.3 29.8 0.5 CB A:CYS754 4.6 39.0 0.6 CD A:PRO755 4.7 29.7 1.0 SG A:CYS754 4.7 24.8 0.5 CB A:CYS754 4.8 28.7 0.5 C A:ARG753 4.8 40.6 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 22)


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 22) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:18.8 occ:1.00 ND1 B:HIS725 2.2 26.4 1.0 SG B:CYS705 2.3 19.6 1.0 SG B:CYS728 2.3 18.0 1.0 SG B:CYS708 2.3 22.0 1.0 CB B:CYS705 3.0 22.1 1.0 CE1 B:HIS725 3.1 26.0 1.0 CB B:CYS728 3.2 17.5 1.0 CG B:HIS725 3.2 25.1 1.0 CB B:CYS708 3.3 21.3 1.0 CB B:HIS725 3.6 22.2 1.0 N B:CYS708 3.8 19.5 1.0 CA B:CYS708 4.1 20.8 1.0 N B:HIS725 4.2 19.7 1.0 NE2 B:HIS725 4.2 26.0 1.0 CD2 B:HIS725 4.3 23.7 1.0 CA B:HIS725 4.5 20.4 1.0 CA B:CYS705 4.5 22.7 1.0 O B:HOH1209 4.6 27.8 1.0 CA B:CYS728 4.6 17.0 1.0 CB B:VAL707 4.7 17.8 1.0 C B:CYS708 4.8 23.1 1.0 C B:VAL707 4.9 20.0 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 22)


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 22) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.1 occ:1.00 SG B:CYS717 2.2 23.6 1.0 SG B:CYS745 2.3 25.3 1.0 SG B:CYS742 2.3 21.0 1.0 SG B:CYS720 2.4 25.0 1.0 CB B:CYS717 3.2 24.3 1.0 CB B:CYS720 3.2 26.5 1.0 CB B:CYS742 3.3 20.0 1.0 CB B:CYS745 3.5 21.2 1.0 N B:CYS742 3.7 20.8 1.0 N B:CYS720 3.8 28.9 1.0 N B:CYS745 4.0 18.2 1.0 CA B:CYS742 4.0 18.3 1.0 OG1 B:THR719 4.1 26.4 1.0 CA B:CYS720 4.1 27.1 1.0 CA B:CYS745 4.3 20.5 1.0 C B:THR719 4.4 26.4 1.0 O B:HOH1183 4.5 35.8 1.0 O B:CYS742 4.5 16.9 1.0 C B:CYS742 4.6 18.3 1.0 NH1 B:ARG722 4.6 26.2 1.0 C B:CYS720 4.7 26.5 1.0 CA B:CYS717 4.7 26.7 1.0 O B:CYS720 4.8 27.3 1.0 N B:THR719 4.8 31.0 1.0 C B:SER741 4.9 25.0 1.0 CB B:PHE744 4.9 18.5 1.0 CA B:THR719 4.9 27.3 1.0 CB B:ARG722 5.0 23.0 1.0 O B:THR719 5.0 26.4 1.0 CB B:THR719 5.0 29.1 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