Zinc in PDB 5pz6: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 102)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 102), PDB code: 5pz6 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)	39.01 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.680, 45.470, 83.590, 90.00, 101.83, 90.00
R / Rfree (%)	17.5 / 21.4

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 102) (pdb code 5pz6). 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 102), PDB code: 5pz6:
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 102)


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 102) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.8 occ:1.00 ND1 A:HIS725 2.2 33.0 1.0 SG A:CYS705 2.2 26.2 1.0 SG A:CYS728 2.2 26.3 1.0 SG A:CYS708 2.4 28.0 1.0 CB A:CYS705 3.1 27.7 1.0 CE1 A:HIS725 3.1 32.1 1.0 CB A:CYS728 3.2 25.9 1.0 CG A:HIS725 3.2 34.2 1.0 CB A:CYS708 3.3 25.8 1.0 CB A:HIS725 3.6 31.6 1.0 N A:CYS708 3.8 23.5 1.0 O A:HOH1284 3.9 50.2 1.0 CA A:CYS708 4.1 26.8 1.0 N A:HIS725 4.1 29.2 1.0 NE2 A:HIS725 4.2 36.3 1.0 CD2 A:HIS725 4.3 36.1 1.0 CA A:HIS725 4.4 29.1 1.0 CA A:CYS705 4.5 28.4 1.0 O A:HOH1255 4.5 37.6 1.0 CB A:VAL707 4.6 21.1 1.0 CA A:CYS728 4.6 22.7 1.0 C A:CYS708 4.8 30.0 1.0 C A:VAL707 4.9 26.5 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 102)


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 102) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:33.6 occ:1.00 SG A:CYS720 2.2 36.1 1.0 SG A:CYS717 2.2 36.6 1.0 SG A:CYS745 2.3 36.1 1.0 SG A:CYS742 2.5 28.4 1.0 CB A:CYS717 3.2 37.5 1.0 CB A:CYS720 3.3 39.4 1.0 CB A:CYS742 3.4 24.3 1.0 CB A:CYS745 3.5 29.4 1.0 N A:CYS742 3.8 29.8 1.0 N A:CYS720 3.8 39.2 1.0 OG1 A:THR719 4.0 42.4 1.0 N A:CYS745 4.0 29.6 1.0 CA A:CYS720 4.1 37.9 1.0 CA A:CYS742 4.1 28.9 1.0 CA A:CYS745 4.3 30.6 1.0 O A:CYS742 4.4 23.4 1.0 C A:THR719 4.4 40.6 1.0 C A:CYS742 4.5 25.9 1.0 O A:HOH1241 4.6 47.0 1.0 NH1 A:ARG722 4.6 31.6 1.0 C A:CYS720 4.6 31.5 1.0 O A:CYS720 4.6 35.9 1.0 CA A:CYS717 4.6 42.7 1.0 N A:THR719 4.9 45.8 1.0 C A:SER741 4.9 30.9 1.0 O A:THR719 5.0 39.0 1.0 CB A:PHE744 5.0 26.7 1.0 CA A:THR719 5.0 41.8 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 102)


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 102) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:77.5 occ:0.43 OE2 A:GLU756 2.5 70.3 1.0 SG A:CYS754 2.8 49.0 0.6 OE1 A:GLU756 3.1 57.5 1.0 CD A:GLU756 3.2 56.3 1.0 SG A:CYS754 3.4 31.5 0.5 CB A:CYS754 3.5 38.2 0.6 CA A:CYS754 3.6 34.5 0.5 CA A:CYS754 3.6 37.4 0.6 CB A:CYS754 3.6 32.5 0.5 O A:ARG753 3.8 52.5 1.0 C A:ARG753 4.6 43.1 1.0 N A:CYS754 4.6 34.9 1.0 C A:CYS754 4.6 35.5 1.0 CG A:GLU756 4.6 49.7 1.0 CD A:PRO755 4.7 35.0 1.0 O A:HOH1092 5.0 55.9 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 102)


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 102) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:23.2 occ:1.00 ND1 B:HIS725 2.2 30.9 1.0 SG B:CYS705 2.3 21.5 1.0 SG B:CYS728 2.3 23.3 1.0 SG B:CYS708 2.3 21.5 1.0 CE1 B:HIS725 3.1 30.8 1.0 CB B:CYS705 3.1 24.6 1.0 CB B:CYS728 3.2 20.9 1.0 CG B:HIS725 3.2 27.6 1.0 CB B:CYS708 3.4 20.9 1.0 CB B:HIS725 3.5 22.3 1.0 N B:CYS708 3.8 21.0 1.0 CA B:CYS708 4.1 21.1 1.0 NE2 B:HIS725 4.2 31.1 1.0 N B:HIS725 4.2 22.3 1.0 CD2 B:HIS725 4.3 28.8 1.0 CA B:HIS725 4.5 21.6 1.0 CA B:CYS705 4.5 24.1 1.0 O B:HOH1210 4.6 26.4 1.0 CA B:CYS728 4.6 19.4 1.0 CB B:VAL707 4.7 21.2 1.0 C B:CYS708 4.8 23.3 1.0 C B:VAL707 4.9 22.2 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 102)


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 102) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:27.2 occ:1.00 SG B:CYS717 2.2 26.6 1.0 SG B:CYS720 2.3 28.6 1.0 SG B:CYS742 2.4 22.7 1.0 SG B:CYS745 2.4 28.7 1.0 CB B:CYS717 3.2 28.3 1.0 CB B:CYS720 3.3 32.8 1.0 CB B:CYS742 3.4 22.4 1.0 CB B:CYS745 3.5 24.6 1.0 N B:CYS742 3.8 25.7 1.0 N B:CYS720 3.8 36.2 1.0 CA B:CYS720 4.1 32.1 1.0 N B:CYS745 4.1 21.4 1.0 OG1 B:THR719 4.1 31.9 1.0 CA B:CYS742 4.2 20.4 1.0 CA B:CYS745 4.3 23.9 1.0 C B:THR719 4.4 32.2 1.0 O B:CYS742 4.5 21.2 1.0 C B:CYS742 4.6 22.4 1.0 O B:HOH1190 4.6 33.2 1.0 CA B:CYS717 4.6 29.9 1.0 C B:CYS720 4.6 33.5 1.0 NH1 B:ARG722 4.7 31.1 1.0 O B:CYS720 4.7 30.7 1.0 N B:THR719 4.8 36.1 1.0 CB B:PHE744 4.9 21.6 1.0 C B:SER741 4.9 26.5 1.0 CA B:THR719 4.9 32.3 1.0 CB B:ARG722 5.0 27.8 1.0 CD B:ARG722 5.0 26.9 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