Zinc in PDB 5pz5: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 101)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 101), PDB code: 5pz5 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)	40.68 / 2.64
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.740, 45.730, 83.210, 90.00, 102.11, 90.00
R / Rfree (%)	29.3 / 34.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 101) (pdb code 5pz5). 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 101), PDB code: 5pz5:
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 101)


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 101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.6 occ:1.00 SG A:CYS708 2.2 31.6 1.0 ND1 A:HIS725 2.2 29.4 1.0 SG A:CYS728 2.2 36.8 1.0 SG A:CYS705 2.3 29.9 1.0 CB A:CYS705 3.1 33.4 1.0 CE1 A:HIS725 3.1 30.5 1.0 CB A:CYS728 3.2 33.7 1.0 CG A:HIS725 3.2 29.5 1.0 CB A:CYS708 3.2 34.1 1.0 CB A:HIS725 3.6 30.2 1.0 N A:CYS708 3.8 33.1 1.0 CA A:CYS708 4.1 34.9 1.0 N A:HIS725 4.2 28.3 1.0 NE2 A:HIS725 4.2 31.1 1.0 CD2 A:HIS725 4.3 29.8 1.0 O A:HOH1253 4.4 33.1 1.0 CA A:HIS725 4.5 29.6 1.0 CA A:CYS705 4.6 35.1 1.0 CB A:VAL707 4.7 29.0 1.0 CA A:CYS728 4.7 32.6 1.0 C A:CYS708 4.9 35.7 1.0 C A:VAL707 5.0 31.5 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 101)


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 101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:33.2 occ:1.00 SG A:CYS717 2.0 36.0 1.0 SG A:CYS745 2.2 39.3 1.0 SG A:CYS720 2.2 41.3 1.0 SG A:CYS742 2.2 38.3 1.0 CB A:CYS717 3.1 40.0 1.0 CB A:CYS745 3.4 37.2 1.0 CB A:CYS720 3.4 44.8 1.0 CB A:CYS742 3.4 34.9 1.0 N A:CYS742 3.6 35.1 1.0 OG1 A:THR719 3.6 48.9 1.0 N A:CYS720 3.7 44.0 1.0 N A:CYS745 4.0 35.4 1.0 CA A:CYS742 4.0 35.1 1.0 CA A:CYS720 4.1 43.5 1.0 CA A:CYS745 4.3 36.0 1.0 C A:THR719 4.4 47.1 1.0 C A:CYS742 4.5 35.1 1.0 O A:CYS742 4.5 36.0 1.0 CA A:CYS717 4.6 40.3 1.0 O A:HOH1225 4.6 71.4 1.0 NH1 A:ARG722 4.7 33.9 1.0 C A:SER741 4.7 35.6 1.0 N A:THR719 4.7 48.4 1.0 C A:CYS720 4.8 43.7 1.0 CB A:THR719 4.8 48.6 1.0 CA A:THR719 4.8 46.4 1.0 CA A:SER741 4.9 39.2 1.0 CB A:PHE744 4.9 31.7 1.0 O A:CYS720 4.9 44.5 1.0 CB A:ARG722 5.0 39.6 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 101)


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 101) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:83.7 occ:0.43 OE2 A:GLU756 3.6 60.6 1.0 SG A:CYS754 3.6 40.1 0.6 O A:HOH1128 4.5 79.3 1.0 CD A:GLU756 4.5 57.9 1.0 O A:ARG753 4.5 50.9 1.0 SG A:CYS754 4.6 34.0 0.5 OE1 A:GLU756 4.7 59.5 1.0 CB A:CYS754 5.0 39.3 0.6

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 101)


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 101) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:29.4 occ:1.00 ND1 B:HIS725 2.2 54.5 1.0 SG B:CYS708 2.3 41.3 1.0 SG B:CYS728 2.3 40.0 1.0 SG B:CYS705 2.3 31.3 1.0 CE1 B:HIS725 3.0 54.2 1.0 CB B:CYS705 3.1 35.4 1.0 CG B:HIS725 3.1 49.6 1.0 CB B:CYS728 3.2 38.3 1.0 CB B:CYS708 3.3 40.2 1.0 CB B:HIS725 3.5 43.5 1.0 N B:CYS708 3.8 37.2 1.0 CA B:CYS708 4.1 39.0 1.0 NE2 B:HIS725 4.1 52.7 1.0 CD2 B:HIS725 4.2 54.7 1.0 N B:HIS725 4.2 37.6 1.0 O B:HOH1219 4.2 44.3 1.0 CA B:HIS725 4.5 39.7 1.0 CA B:CYS705 4.6 35.4 1.0 CA B:CYS728 4.7 36.9 1.0 CB B:VAL707 4.7 32.8 1.0 C B:CYS708 4.8 39.4 1.0 C B:VAL707 4.9 37.8 1.0 O B:HOH1270 5.0 48.0 1.0 N B:ASN709 5.0 42.5 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 101)


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 101) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:39.3 occ:1.00 SG B:CYS717 2.1 49.4 1.0 SG B:CYS742 2.2 35.2 1.0 SG B:CYS720 2.3 34.3 1.0 SG B:CYS745 2.3 46.0 1.0 CB B:CYS717 3.0 52.6 1.0 CB B:CYS720 3.3 40.3 1.0 CB B:CYS742 3.3 36.1 1.0 CB B:CYS745 3.7 40.5 1.0 N B:CYS742 3.8 38.0 1.0 N B:CYS720 3.8 41.2 1.0 OG1 B:THR719 4.0 49.8 1.0 CA B:CYS720 4.1 42.2 1.0 CA B:CYS742 4.1 35.1 1.0 N B:CYS745 4.3 34.7 1.0 CA B:CYS717 4.4 52.9 1.0 C B:THR719 4.5 44.6 1.0 C B:CYS742 4.6 34.0 1.0 CA B:CYS745 4.6 37.1 1.0 C B:CYS720 4.7 43.1 1.0 O B:CYS742 4.7 38.2 1.0 O B:HOH1104 4.7 36.2 1.0 NH1 B:ARG722 4.7 38.5 1.0 O B:CYS720 4.8 44.2 1.0 N B:THR719 4.9 52.3 1.0 CD B:ARG722 4.9 38.6 1.0 C B:SER741 4.9 39.1 1.0 C B:CYS717 5.0 55.1 1.0 CB B:ARG722 5.0 39.8 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