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

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 5), PDB code: 5pwi 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)	31.44 / 1.62
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.670, 45.380, 83.220, 90.00, 102.28, 90.00
R / Rfree (%)	16.9 / 20

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


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 5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:23.2 occ:1.00 ND1 A:HIS725 2.1 24.4 1.0 SG A:CYS728 2.3 23.3 1.0 SG A:CYS705 2.3 22.6 1.0 SG A:CYS708 2.3 23.9 1.0 CE1 A:HIS725 3.0 27.8 1.0 CB A:CYS705 3.1 23.6 1.0 CG A:HIS725 3.2 26.6 1.0 CB A:CYS728 3.2 20.8 1.0 CB A:CYS708 3.4 23.6 1.0 CB A:HIS725 3.6 27.3 1.0 N A:CYS708 3.8 22.1 1.0 N A:HIS725 4.1 24.5 1.0 O A:HOH1285 4.1 46.6 1.0 CA A:CYS708 4.1 22.5 1.0 NE2 A:HIS725 4.2 25.6 1.0 CD2 A:HIS725 4.3 30.2 1.0 CA A:HIS725 4.4 22.9 1.0 CA A:CYS705 4.5 23.0 1.0 O A:HOH1245 4.6 36.0 1.0 CA A:CYS728 4.6 19.0 1.0 CB A:VAL707 4.7 19.9 1.0 C A:VAL707 4.9 22.4 1.0 C A:CYS708 4.9 24.4 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 5)


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 5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:28.9 occ:1.00 SG A:CYS720 2.3 33.7 1.0 SG A:CYS742 2.3 22.5 1.0 SG A:CYS717 2.4 31.6 1.0 SG A:CYS745 2.4 29.4 1.0 CB A:CYS717 3.2 30.1 1.0 CB A:CYS720 3.3 31.8 1.0 CB A:CYS742 3.3 19.3 1.0 CB A:CYS745 3.4 27.1 1.0 N A:CYS742 3.8 25.6 1.0 N A:CYS720 3.8 35.0 1.0 N A:CYS745 4.0 26.6 1.0 CA A:CYS720 4.0 35.9 1.0 CA A:CYS742 4.1 24.1 1.0 OG1 A:THR719 4.1 34.0 1.0 CA A:CYS745 4.3 25.8 1.0 O A:CYS742 4.4 22.0 1.0 C A:THR719 4.5 32.1 1.0 O A:CYS720 4.5 32.9 1.0 C A:CYS720 4.6 28.1 1.0 C A:CYS742 4.6 24.0 1.0 O A:HOH1215 4.6 43.8 1.0 CA A:CYS717 4.6 36.6 1.0 NH1 A:ARG722 4.7 29.1 1.0 CB A:PHE744 4.8 23.2 1.0 N A:THR719 4.9 36.4 1.0 C A:SER741 4.9 23.1 1.0 CD A:ARG722 4.9 26.8 1.0 CB A:ARG722 5.0 26.2 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 5)


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 5) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:94.2 occ:0.43 O A:ARG753 3.4 46.2 1.0 OE2 A:GLU756 3.4 66.7 1.0 OE1 A:GLU756 3.4 46.0 1.0 SG A:CYS754 3.5 46.7 0.6 CD A:GLU756 3.9 52.3 1.0 CA A:CYS754 4.0 34.4 0.6 CA A:CYS754 4.0 30.4 0.5 CB A:CYS754 4.2 37.1 0.6 CD A:PRO755 4.4 28.5 1.0 C A:ARG753 4.4 40.2 1.0 CB A:CYS754 4.5 28.8 0.5 SG A:CYS754 4.5 25.5 0.5 N A:CYS754 4.7 32.8 1.0 C A:CYS754 4.9 30.8 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 5)


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 5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:19.5 occ:1.00 ND1 B:HIS725 2.2 22.9 1.0 SG B:CYS728 2.3 19.2 1.0 SG B:CYS708 2.3 21.0 1.0 SG B:CYS705 2.4 19.0 1.0 CE1 B:HIS725 3.1 24.6 1.0 CB B:CYS705 3.1 18.4 1.0 CB B:CYS728 3.2 18.4 1.0 CG B:HIS725 3.2 21.2 1.0 CB B:CYS708 3.4 19.7 1.0 CB B:HIS725 3.6 19.2 1.0 N B:CYS708 3.8 19.8 1.0 CA B:CYS708 4.1 21.2 1.0 N B:HIS725 4.1 18.9 1.0 NE2 B:HIS725 4.2 21.5 1.0 CD2 B:HIS725 4.3 20.2 1.0 CA B:HIS725 4.4 17.4 1.0 CA B:CYS705 4.6 20.6 1.0 CA B:CYS728 4.6 18.3 1.0 O B:HOH1207 4.6 29.0 1.0 CB B:VAL707 4.7 17.7 1.0 C B:CYS708 4.8 22.3 1.0 C B:VAL707 4.9 20.8 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 5)


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 5) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.1 occ:1.00 SG B:CYS717 2.3 23.6 1.0 SG B:CYS742 2.3 18.7 1.0 SG B:CYS720 2.3 23.7 1.0 SG B:CYS745 2.4 24.7 1.0 CB B:CYS717 3.2 20.9 1.0 CB B:CYS720 3.4 23.8 1.0 CB B:CYS742 3.4 18.9 1.0 CB B:CYS745 3.5 19.2 1.0 N B:CYS742 3.7 19.3 1.0 N B:CYS720 3.8 26.8 1.0 N B:CYS745 4.0 18.1 1.0 CA B:CYS720 4.1 24.7 1.0 CA B:CYS742 4.1 18.7 1.0 OG1 B:THR719 4.2 25.5 1.0 CA B:CYS745 4.3 20.0 1.0 C B:THR719 4.5 25.6 1.0 O B:CYS742 4.5 18.9 1.0 O B:HOH1199 4.6 33.6 1.0 C B:CYS742 4.6 18.4 1.0 NH1 B:ARG722 4.6 26.7 1.0 C B:CYS720 4.6 24.7 1.0 CA B:CYS717 4.7 20.9 1.0 O B:CYS720 4.7 25.1 1.0 C B:SER741 4.9 22.4 1.0 CB B:PHE744 4.9 19.0 1.0 N B:THR719 4.9 26.0 1.0 CB B:ARG722 4.9 22.0 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