Zinc in PDB 5pxe: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 38)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 38), PDB code: 5pxe 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)	28.43 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.624, 45.409, 83.233, 90.00, 102.19, 90.00
R / Rfree (%)	17.5 / 20.5

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 38) (pdb code 5pxe). 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 38), PDB code: 5pxe:
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 38)


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 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:23.7 occ:1.00 ND1 A:HIS725 2.2 23.9 1.0 SG A:CYS728 2.3 23.6 1.0 SG A:CYS705 2.3 22.4 1.0 SG A:CYS708 2.3 23.4 1.0 CB A:CYS705 3.0 22.7 1.0 CE1 A:HIS725 3.0 28.6 1.0 CB A:CYS728 3.2 21.1 1.0 CG A:HIS725 3.2 28.2 1.0 CB A:CYS708 3.3 24.6 1.0 CB A:HIS725 3.6 27.9 1.0 N A:CYS708 3.8 22.2 1.0 O A:HOH1283 4.1 48.6 1.0 N A:HIS725 4.1 24.4 1.0 CA A:CYS708 4.2 23.4 1.0 NE2 A:HIS725 4.2 26.6 1.0 CD2 A:HIS725 4.3 28.6 1.0 CA A:HIS725 4.4 23.4 1.0 CA A:CYS705 4.5 21.6 1.0 O A:HOH1250 4.6 36.7 1.0 CA A:CYS728 4.6 19.3 1.0 CB A:VAL707 4.7 18.3 1.0 C A:CYS708 4.9 27.1 1.0 C A:VAL707 4.9 22.7 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 38)


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 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.9 occ:1.00 SG A:CYS720 2.3 35.7 1.0 SG A:CYS717 2.3 33.7 1.0 SG A:CYS742 2.3 24.0 1.0 SG A:CYS745 2.4 31.3 1.0 CB A:CYS717 3.2 33.8 1.0 CB A:CYS742 3.2 18.8 1.0 CB A:CYS720 3.2 37.7 1.0 CB A:CYS745 3.4 26.6 1.0 N A:CYS742 3.8 27.8 1.0 N A:CYS720 3.8 37.3 1.0 N A:CYS745 4.0 28.1 1.0 CA A:CYS720 4.0 36.5 1.0 CA A:CYS742 4.0 26.4 1.0 OG1 A:THR719 4.1 37.2 1.0 CA A:CYS745 4.3 26.0 1.0 O A:CYS742 4.4 23.5 1.0 C A:THR719 4.5 37.1 1.0 C A:CYS742 4.6 26.1 1.0 O A:HOH1230 4.6 41.5 1.0 C A:CYS720 4.6 28.8 1.0 O A:CYS720 4.6 36.2 1.0 CA A:CYS717 4.6 39.8 1.0 NH1 A:ARG722 4.7 33.2 1.0 C A:SER741 4.9 26.4 1.0 CB A:PHE744 4.9 24.3 1.0 N A:THR719 4.9 39.7 1.0 O 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 38)


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 38) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:86.3 occ:0.43 OE2 A:GLU756 2.4 62.5 1.0 SG A:CYS754 2.8 47.7 0.6 OE1 A:GLU756 2.9 42.8 1.0 CD A:GLU756 3.0 50.1 1.0 SG A:CYS754 3.3 28.1 0.5 CB A:CYS754 3.4 37.7 0.6 CA A:CYS754 3.5 34.5 0.6 CA A:CYS754 3.5 31.1 0.5 CB A:CYS754 3.7 30.9 0.5 O A:ARG753 3.7 47.8 1.0 C A:CYS754 4.4 32.3 1.0 CD A:PRO755 4.4 30.1 1.0 CG A:GLU756 4.5 42.2 1.0 N A:CYS754 4.5 33.2 1.0 C A:ARG753 4.5 41.5 1.0 N A:PRO755 4.7 29.4 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 38)


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 38) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:19.8 occ:1.00 ND1 B:HIS725 2.1 20.7 1.0 SG B:CYS728 2.3 19.5 1.0 SG B:CYS708 2.3 21.2 1.0 SG B:CYS705 2.4 18.8 1.0 CE1 B:HIS725 3.1 24.0 1.0 CB B:CYS705 3.1 18.1 1.0 CG B:HIS725 3.2 21.2 1.0 CB B:CYS728 3.2 17.6 1.0 CB B:CYS708 3.4 21.7 1.0 CB B:HIS725 3.5 19.7 1.0 N B:CYS708 3.8 20.2 1.0 CA B:CYS708 4.1 20.2 1.0 N B:HIS725 4.2 19.0 1.0 NE2 B:HIS725 4.2 22.7 1.0 CD2 B:HIS725 4.3 21.5 1.0 CA B:HIS725 4.4 17.6 1.0 CA B:CYS705 4.5 20.9 1.0 CA B:CYS728 4.6 17.6 1.0 O B:HOH1204 4.6 28.0 1.0 CB B:VAL707 4.7 17.1 1.0 C B:CYS708 4.8 23.6 1.0 C B:VAL707 4.9 21.1 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 38)


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 38) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:23.4 occ:1.00 SG B:CYS717 2.3 24.1 1.0 SG B:CYS742 2.3 19.8 1.0 SG B:CYS720 2.3 23.5 1.0 SG B:CYS745 2.4 24.7 1.0 CB B:CYS717 3.2 20.3 1.0 CB B:CYS720 3.4 25.5 1.0 CB B:CYS742 3.4 18.8 1.0 CB B:CYS745 3.5 20.0 1.0 N B:CYS742 3.7 20.3 1.0 N B:CYS720 3.8 28.9 1.0 N B:CYS745 4.0 20.3 1.0 CA B:CYS720 4.1 27.9 1.0 CA B:CYS742 4.1 19.7 1.0 OG1 B:THR719 4.1 26.1 1.0 CA B:CYS745 4.3 21.6 1.0 C B:THR719 4.5 27.1 1.0 O B:CYS742 4.5 19.6 1.0 C B:CYS742 4.6 18.6 1.0 O B:HOH1196 4.6 35.0 1.0 NH1 B:ARG722 4.6 27.2 1.0 C B:CYS720 4.6 27.1 1.0 CA B:CYS717 4.6 21.7 1.0 O B:CYS720 4.7 27.5 1.0 N B:THR719 4.9 27.5 1.0 CB B:PHE744 4.9 19.4 1.0 C B:SER741 4.9 23.6 1.0 CB B:ARG722 4.9 22.1 1.0 CA B:THR719 5.0 27.2 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