Zinc in PDB 5pyv: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 91)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 91), PDB code: 5pyv 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)	28.47 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.621, 45.364, 83.305, 90.00, 101.99, 90.00
R / Rfree (%)	20.2 / 26.1

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 91) (pdb code 5pyv). 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 91), PDB code: 5pyv:
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 91)


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 91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:23.1 occ:1.00 ND1 A:HIS725 2.2 31.0 1.0 SG A:CYS728 2.2 21.4 1.0 SG A:CYS705 2.2 24.5 1.0 SG A:CYS708 2.4 26.3 1.0 CB A:CYS705 3.0 28.4 1.0 CE1 A:HIS725 3.1 29.3 1.0 CB A:CYS728 3.2 19.9 1.0 CG A:HIS725 3.2 31.6 1.0 CB A:CYS708 3.3 23.7 1.0 CB A:HIS725 3.6 28.1 1.0 N A:CYS708 3.8 24.2 1.0 O A:HOH1267 3.8 53.8 1.0 CA A:CYS708 4.1 26.1 1.0 N A:HIS725 4.2 26.1 1.0 NE2 A:HIS725 4.2 32.6 1.0 CD2 A:HIS725 4.3 34.7 1.0 CA A:HIS725 4.5 27.8 1.0 CA A:CYS705 4.5 26.8 1.0 O A:HOH1254 4.6 30.9 1.0 CB A:VAL707 4.6 19.4 1.0 CA A:CYS728 4.6 20.1 1.0 C A:CYS708 4.8 27.1 1.0 C A:VAL707 4.9 23.3 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 91)


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 91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:29.3 occ:1.00 SG A:CYS717 2.1 34.9 1.0 SG A:CYS720 2.2 32.2 1.0 SG A:CYS745 2.4 30.3 1.0 SG A:CYS742 2.4 24.9 1.0 CB A:CYS717 3.1 35.8 1.0 CB A:CYS720 3.3 31.8 1.0 CB A:CYS745 3.4 25.0 1.0 CB A:CYS742 3.4 24.1 1.0 N A:CYS742 3.7 24.7 1.0 N A:CYS720 3.8 30.4 1.0 N A:CYS745 4.0 22.8 1.0 OG1 A:THR719 4.0 37.5 1.0 CA A:CYS742 4.0 26.1 1.0 CA A:CYS720 4.1 33.5 1.0 CA A:CYS745 4.2 25.1 1.0 O A:CYS742 4.3 18.7 1.0 C A:THR719 4.4 32.9 1.0 C A:CYS742 4.5 23.9 1.0 CA A:CYS717 4.5 39.3 1.0 O A:HOH1234 4.5 44.7 1.0 NH1 A:ARG722 4.6 27.8 1.0 C A:CYS720 4.7 30.5 1.0 O A:CYS720 4.7 31.3 1.0 C A:SER741 4.8 28.0 1.0 CB A:PHE744 4.8 20.0 1.0 N A:THR719 4.8 40.6 1.0 O A:THR719 4.9 33.2 1.0 CA A:THR719 4.9 35.6 1.0 CA A:SER741 5.0 33.2 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 91)


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 91) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:84.3 occ:0.43 SG A:CYS754 2.5 46.2 0.6 OE2 A:GLU756 2.8 61.1 1.0 SG A:CYS754 3.3 26.5 0.5 CB A:CYS754 3.5 38.3 0.6 CB A:CYS754 3.6 30.4 0.5 O A:ARG753 3.6 46.6 1.0 CD A:GLU756 3.6 51.1 1.0 OE1 A:GLU756 3.6 51.0 1.0 CA A:CYS754 3.7 32.5 0.5 CA A:CYS754 3.7 36.3 0.6 C A:ARG753 4.5 40.6 1.0 N A:CYS754 4.5 34.7 1.0 C A:CYS754 4.8 35.3 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 91)


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 91) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:19.1 occ:1.00 ND1 B:HIS725 2.2 24.8 1.0 SG B:CYS705 2.2 17.9 1.0 SG B:CYS728 2.3 19.2 1.0 SG B:CYS708 2.3 19.6 1.0 CB B:CYS705 3.1 20.8 1.0 CE1 B:HIS725 3.1 24.3 1.0 CB B:CYS728 3.2 17.0 1.0 CG B:HIS725 3.2 21.8 1.0 CB B:CYS708 3.3 20.4 1.0 CB B:HIS725 3.5 18.4 1.0 N B:CYS708 3.8 20.2 1.0 CA B:CYS708 4.1 20.6 1.0 N B:HIS725 4.2 18.1 1.0 NE2 B:HIS725 4.2 24.1 1.0 CD2 B:HIS725 4.3 22.1 1.0 CA B:HIS725 4.5 19.0 1.0 CA B:CYS705 4.5 21.6 1.0 CA B:CYS728 4.6 16.6 1.0 CB B:VAL707 4.7 17.1 1.0 O B:HOH1202 4.8 22.4 1.0 C B:CYS708 4.8 21.8 1.0 C B:VAL707 4.9 19.5 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 91)


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 91) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:22.6 occ:1.00 SG B:CYS717 2.1 20.9 1.0 SG B:CYS720 2.3 24.7 1.0 SG B:CYS745 2.3 25.4 1.0 SG B:CYS742 2.4 19.9 1.0 CB B:CYS717 3.2 23.2 1.0 CB B:CYS720 3.3 26.0 1.0 CB B:CYS742 3.4 20.1 1.0 CB B:CYS745 3.4 21.7 1.0 N B:CYS720 3.7 25.6 1.0 N B:CYS742 3.8 21.9 1.0 OG1 B:THR719 4.0 28.5 1.0 CA B:CYS720 4.0 24.6 1.0 N B:CYS745 4.1 17.8 1.0 CA B:CYS742 4.1 19.8 1.0 CA B:CYS745 4.3 20.3 1.0 C B:THR719 4.4 25.2 1.0 O B:HOH1177 4.5 32.3 1.0 O B:CYS742 4.5 20.0 1.0 NH1 B:ARG722 4.6 27.2 1.0 C B:CYS742 4.6 19.1 1.0 CA B:CYS717 4.6 25.3 1.0 C B:CYS720 4.6 23.9 1.0 O B:CYS720 4.7 23.8 1.0 N B:THR719 4.8 28.7 1.0 C B:SER741 4.9 25.2 1.0 CB B:PHE744 4.9 18.1 1.0 CA B:THR719 4.9 25.6 1.0 CB B:ARG722 5.0 24.1 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