Zinc in PDB 5pwf: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 2)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 2), PDB code: 5pwf 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)	28.40 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.589, 45.330, 83.178, 90.00, 102.22, 90.00
R / Rfree (%)	17.9 / 20.6

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 2) (pdb code 5pwf). 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 2), PDB code: 5pwf:
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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:21.6 occ:1.00 ND1 A:HIS725 2.1 20.7 1.0 SG A:CYS708 2.3 21.9 1.0 SG A:CYS728 2.3 21.1 1.0 SG A:CYS705 2.4 20.6 1.0 CE1 A:HIS725 3.0 26.8 1.0 CB A:CYS705 3.0 21.4 1.0 CG A:HIS725 3.2 26.1 1.0 CB A:CYS728 3.2 19.0 1.0 CB A:CYS708 3.4 20.9 1.0 CB A:HIS725 3.6 26.2 1.0 N A:CYS708 3.8 20.1 1.0 O A:HOH1275 4.0 42.8 1.0 N A:HIS725 4.1 22.7 1.0 CA A:CYS708 4.2 21.3 1.0 NE2 A:HIS725 4.2 25.9 1.0 CD2 A:HIS725 4.3 27.1 1.0 CA A:HIS725 4.4 23.5 1.0 CA A:CYS705 4.5 20.4 1.0 CB A:VAL707 4.6 16.1 1.0 O A:HOH1245 4.7 37.2 1.0 CA A:CYS728 4.7 17.7 1.0 C A:VAL707 4.9 21.2 1.0 C A:CYS708 4.9 24.0 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:28.0 occ:1.00 SG A:CYS717 2.3 31.7 1.0 SG A:CYS720 2.3 33.2 1.0 SG A:CYS742 2.3 22.3 1.0 SG A:CYS745 2.4 27.8 1.0 CB A:CYS717 3.2 34.2 1.0 CB A:CYS742 3.3 18.9 1.0 CB A:CYS720 3.3 31.1 1.0 CB A:CYS745 3.5 25.9 1.0 N A:CYS720 3.8 34.6 1.0 N A:CYS742 3.8 25.7 1.0 OG1 A:THR719 4.1 35.2 1.0 CA A:CYS720 4.1 35.9 1.0 N A:CYS745 4.1 23.0 1.0 CA A:CYS742 4.1 22.5 1.0 CA A:CYS745 4.3 24.8 1.0 O A:CYS742 4.3 22.5 1.0 C A:THR719 4.4 36.3 1.0 C A:CYS742 4.6 23.7 1.0 C A:CYS720 4.6 28.3 1.0 NH1 A:ARG722 4.6 30.4 1.0 O A:CYS720 4.6 35.7 1.0 CA A:CYS717 4.7 38.2 1.0 O A:HOH1238 4.7 40.0 1.0 CB A:PHE744 4.9 22.7 1.0 N A:THR719 4.9 39.8 1.0 C A:SER741 4.9 20.4 1.0 O A:THR719 5.0 36.2 1.0 CD A:ARG722 5.0 24.5 1.0 CB A:ARG722 5.0 27.8 1.0 CA A:THR719 5.0 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:93.9 occ:0.43 OE2 A:GLU756 2.8 55.8 1.0 OE1 A:GLU756 2.8 38.8 1.0 SG A:CYS754 3.1 46.0 0.6 CD A:GLU756 3.2 44.0 1.0 CA A:CYS754 3.5 32.0 0.6 CA A:CYS754 3.5 28.1 0.5 O A:ARG753 3.5 40.1 1.0 CB A:CYS754 3.7 34.4 0.6 SG A:CYS754 3.8 24.4 0.5 CB A:CYS754 3.9 26.6 0.5 CD A:PRO755 4.2 28.2 1.0 C A:ARG753 4.4 35.0 1.0 C A:CYS754 4.4 29.4 1.0 N A:CYS754 4.4 31.1 1.0 N A:PRO755 4.6 26.4 1.0 CG A:GLU756 4.7 35.4 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:18.3 occ:1.00 ND1 B:HIS725 2.1 20.7 1.0 SG B:CYS708 2.3 20.0 1.0 SG B:CYS728 2.3 18.2 1.0 SG B:CYS705 2.4 17.6 1.0 CE1 B:HIS725 3.0 23.1 1.0 CB B:CYS705 3.1 16.7 1.0 CG B:HIS725 3.2 21.5 1.0 CB B:CYS728 3.3 15.5 1.0 CB B:CYS708 3.4 17.3 1.0 CB B:HIS725 3.6 18.1 1.0 N B:CYS708 3.8 18.9 1.0 CA B:CYS708 4.1 19.3 1.0 N B:HIS725 4.2 19.1 1.0 NE2 B:HIS725 4.2 21.8 1.0 CD2 B:HIS725 4.3 21.6 1.0 CA B:HIS725 4.5 17.1 1.0 CA B:CYS705 4.5 18.9 1.0 O B:HOH1208 4.6 26.9 1.0 CA B:CYS728 4.7 16.6 1.0 CB B:VAL707 4.7 15.9 1.0 C B:CYS708 4.8 23.0 1.0 C B:VAL707 4.9 19.2 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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.0 occ:1.00 SG B:CYS717 2.3 23.2 1.0 SG B:CYS720 2.3 22.9 1.0 SG B:CYS742 2.3 18.6 1.0 SG B:CYS745 2.4 23.5 1.0 CB B:CYS717 3.2 19.6 1.0 CB B:CYS720 3.3 23.2 1.0 CB B:CYS742 3.4 18.3 1.0 CB B:CYS745 3.5 16.2 1.0 N B:CYS742 3.7 19.1 1.0 N B:CYS720 3.8 26.4 1.0 N B:CYS745 4.0 17.7 1.0 CA B:CYS720 4.0 25.3 1.0 CA B:CYS742 4.1 18.1 1.0 OG1 B:THR719 4.1 25.2 1.0 CA B:CYS745 4.3 19.6 1.0 C B:THR719 4.5 26.0 1.0 O B:CYS742 4.5 17.0 1.0 O B:HOH1189 4.6 34.7 1.0 C B:CYS742 4.6 17.2 1.0 NH1 B:ARG722 4.6 23.2 1.0 C B:CYS720 4.6 25.6 1.0 CA B:CYS717 4.6 20.6 1.0 O B:CYS720 4.7 25.5 1.0 CB B:PHE744 4.9 18.2 1.0 C B:SER741 4.9 21.6 1.0 N B:THR719 4.9 27.5 1.0 CB B:ARG722 5.0 21.5 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