Zinc in PDB 5px4: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 28)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 28), PDB code: 5px4 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 / 1.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.681, 45.392, 83.333, 90.00, 102.06, 90.00
R / Rfree (%)	18.2 / 20.8

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 28) (pdb code 5px4). 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 28), PDB code: 5px4:
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 28)


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 28) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:21.0 occ:1.00 ND1 A:HIS725 2.1 19.5 1.0 SG A:CYS708 2.3 21.7 1.0 SG A:CYS728 2.3 21.5 1.0 SG A:CYS705 2.4 20.3 1.0 CE1 A:HIS725 2.9 24.4 1.0 CB A:CYS705 3.0 19.4 1.0 CG A:HIS725 3.2 24.7 1.0 CB A:CYS728 3.3 19.1 1.0 CB A:CYS708 3.4 18.1 1.0 CB A:HIS725 3.6 25.1 1.0 N A:CYS708 3.8 18.6 1.0 O A:HOH1280 4.0 52.1 1.0 N A:HIS725 4.1 24.1 1.0 NE2 A:HIS725 4.1 24.8 1.0 CA A:CYS708 4.1 19.8 1.0 CD2 A:HIS725 4.2 25.9 1.0 CA A:HIS725 4.4 21.9 1.0 CA A:CYS705 4.5 19.9 1.0 O A:HOH1252 4.6 33.3 1.0 CA A:CYS728 4.7 16.3 1.0 CB A:VAL707 4.7 15.6 1.0 C A:VAL707 4.9 19.8 1.0 C A:CYS708 4.9 24.3 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 28)


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 28) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:27.4 occ:1.00 SG A:CYS720 2.2 32.8 1.0 SG A:CYS717 2.3 29.2 1.0 SG A:CYS742 2.3 21.4 1.0 SG A:CYS745 2.4 27.1 1.0 CB A:CYS720 3.2 32.5 1.0 CB A:CYS717 3.2 30.7 1.0 CB A:CYS742 3.2 18.8 1.0 CB A:CYS745 3.5 22.5 1.0 N A:CYS742 3.8 25.1 1.0 N A:CYS720 3.8 32.8 1.0 CA A:CYS720 4.0 32.4 1.0 CA A:CYS742 4.0 22.1 1.0 OG1 A:THR719 4.1 32.9 1.0 N A:CYS745 4.1 23.8 1.0 CA A:CYS745 4.3 23.7 1.0 O A:CYS742 4.4 22.0 1.0 C A:THR719 4.5 34.8 1.0 C A:CYS720 4.5 26.2 1.0 C A:CYS742 4.6 22.5 1.0 O A:CYS720 4.6 32.4 1.0 NH1 A:ARG722 4.6 29.0 1.0 CA A:CYS717 4.7 33.3 1.0 O A:HOH1224 4.7 39.8 1.0 CB A:PHE744 4.8 22.4 1.0 C A:SER741 4.9 22.0 1.0 N A:THR719 4.9 36.0 1.0 O A:THR719 5.0 34.8 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 28)


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 28) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:94.3 occ:0.43 OE2 A:GLU756 2.6 59.7 1.0 SG A:CYS754 2.8 44.0 0.6 OE1 A:GLU756 3.0 39.2 1.0 CD A:GLU756 3.2 45.5 1.0 CB A:CYS754 3.5 34.4 0.6 SG A:CYS754 3.5 24.6 0.5 CA A:CYS754 3.6 27.6 0.5 CA A:CYS754 3.6 31.0 0.6 O A:ARG753 3.6 36.0 1.0 CB A:CYS754 3.8 27.3 0.5 C A:ARG753 4.4 33.8 1.0 CD A:PRO755 4.5 29.1 1.0 N A:CYS754 4.5 29.5 1.0 C A:CYS754 4.5 28.5 1.0 CG A:GLU756 4.7 36.6 1.0 N A:PRO755 4.8 27.8 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 28)


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 28) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:16.8 occ:1.00 ND1 B:HIS725 2.1 16.2 1.0 SG B:CYS728 2.3 16.4 1.0 SG B:CYS708 2.3 18.7 1.0 SG B:CYS705 2.4 15.6 1.0 CB B:CYS705 3.0 14.1 1.0 CE1 B:HIS725 3.1 21.1 1.0 CG B:HIS725 3.1 18.1 1.0 CB B:CYS728 3.3 14.7 1.0 CB B:CYS708 3.4 16.4 1.0 CB B:HIS725 3.5 15.9 1.0 N B:CYS708 3.8 16.7 1.0 N B:HIS725 4.2 16.3 1.0 CA B:CYS708 4.2 18.4 1.0 NE2 B:HIS725 4.2 21.5 1.0 CD2 B:HIS725 4.2 19.7 1.0 CA B:HIS725 4.4 15.4 1.0 CA B:CYS705 4.5 16.8 1.0 O B:HOH1203 4.5 24.1 1.0 CA B:CYS728 4.7 15.4 1.0 CB B:VAL707 4.7 15.1 1.0 C B:CYS708 4.8 22.0 1.0 C B:VAL707 4.9 18.4 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 28)


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 28) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:20.0 occ:1.00 SG B:CYS717 2.3 20.6 1.0 SG B:CYS720 2.3 21.0 1.0 SG B:CYS742 2.4 17.3 1.0 SG B:CYS745 2.4 21.4 1.0 CB B:CYS717 3.2 18.7 1.0 CB B:CYS720 3.3 23.1 1.0 CB B:CYS742 3.3 18.3 1.0 CB B:CYS745 3.5 16.6 1.0 N B:CYS742 3.8 18.8 1.0 N B:CYS720 3.8 24.9 1.0 N B:CYS745 4.0 16.4 1.0 CA B:CYS720 4.0 23.6 1.0 CA B:CYS742 4.1 16.6 1.0 OG1 B:THR719 4.1 23.6 1.0 CA B:CYS745 4.3 20.4 1.0 C B:THR719 4.5 23.3 1.0 O B:CYS742 4.5 16.0 1.0 O B:HOH1194 4.6 31.4 1.0 NH1 B:ARG722 4.6 22.7 1.0 C B:CYS720 4.6 23.3 1.0 C B:CYS742 4.6 16.4 1.0 CA B:CYS717 4.7 18.7 1.0 O B:CYS720 4.7 23.6 1.0 CB B:PHE744 4.9 15.8 1.0 C B:SER741 4.9 21.6 1.0 N B:THR719 4.9 25.3 1.0 CB B:ARG722 5.0 19.7 1.0 CA B:THR719 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