Zinc in PDB 5pz4: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 100)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 100), PDB code: 5pz4 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)	40.98 / 1.94
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.710, 45.620, 83.740, 90.00, 101.84, 90.00
R / Rfree (%)	16.3 / 20.7

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 100) (pdb code 5pz4). 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 100), PDB code: 5pz4:
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 100)


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 100) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:30.0 occ:1.00 SG A:CYS728 2.2 30.9 1.0 ND1 A:HIS725 2.2 38.1 1.0 SG A:CYS705 2.2 29.6 1.0 SG A:CYS708 2.4 30.2 1.0 CB A:CYS705 3.1 33.0 1.0 CE1 A:HIS725 3.1 35.3 1.0 CB A:CYS728 3.2 29.8 1.0 CG A:HIS725 3.2 37.9 1.0 CB A:CYS708 3.4 26.2 1.0 CB A:HIS725 3.6 30.6 1.0 O A:HOH1279 3.7 60.0 1.0 N A:CYS708 3.8 25.1 1.0 CA A:CYS708 4.1 28.8 1.0 N A:HIS725 4.2 27.4 1.0 NE2 A:HIS725 4.2 43.4 1.0 CD2 A:HIS725 4.3 45.1 1.0 CA A:HIS725 4.5 29.4 1.0 CA A:CYS705 4.5 33.5 1.0 CB A:VAL707 4.6 22.2 1.0 CA A:CYS728 4.6 26.3 1.0 O A:HOH1257 4.6 38.8 1.0 O A:HOH1262 4.7 58.2 1.0 C A:VAL707 4.9 31.9 1.0 C A:CYS708 4.9 31.7 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 100)


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 100) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:35.0 occ:1.00 SG A:CYS720 2.2 36.3 1.0 SG A:CYS717 2.3 39.5 1.0 SG A:CYS745 2.3 39.2 1.0 SG A:CYS742 2.5 30.9 1.0 CB A:CYS720 3.3 43.1 1.0 CB A:CYS717 3.3 42.2 1.0 CB A:CYS742 3.5 26.7 1.0 CB A:CYS745 3.5 32.3 1.0 N A:CYS742 3.8 31.7 1.0 N A:CYS720 3.9 41.8 1.0 N A:CYS745 4.0 33.6 1.0 OG1 A:THR719 4.0 42.1 1.0 CA A:CYS720 4.1 41.6 1.0 CA A:CYS742 4.2 32.5 1.0 CA A:CYS745 4.3 34.7 1.0 O A:HOH1232 4.4 49.6 1.0 O A:CYS742 4.5 25.4 1.0 C A:THR719 4.5 45.0 1.0 C A:CYS742 4.6 28.8 1.0 C A:CYS720 4.6 31.6 1.0 O A:CYS720 4.6 41.5 1.0 NH1 A:ARG722 4.6 33.7 1.0 CA A:CYS717 4.7 46.9 1.0 CB A:PHE744 4.9 31.6 1.0 C A:SER741 4.9 32.2 1.0 N A:THR719 4.9 46.5 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 100)


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 100) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:82.7 occ:0.43 OE2 A:GLU756 2.5 78.0 1.0 SG A:CYS754 3.2 71.2 0.6 CD A:GLU756 3.4 67.9 1.0 OE1 A:GLU756 3.4 71.8 1.0 SG A:CYS754 3.7 37.7 0.5 CB A:CYS754 3.7 50.3 0.6 CA A:CYS754 3.9 46.2 0.6 CA A:CYS754 3.9 40.9 0.5 CB A:CYS754 3.9 39.2 0.5 O A:ARG753 3.9 56.5 1.0 C A:ARG753 4.8 51.8 1.0 N A:CYS754 4.8 42.3 1.0 C A:CYS754 4.8 40.5 1.0 CG A:GLU756 4.8 58.8 1.0 CD A:PRO755 4.9 42.9 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 100)


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 100) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:25.8 occ:1.00 ND1 B:HIS725 2.2 32.5 1.0 SG B:CYS705 2.3 24.2 1.0 SG B:CYS728 2.3 28.0 1.0 SG B:CYS708 2.3 26.6 1.0 CB B:CYS705 3.0 27.7 1.0 CE1 B:HIS725 3.1 32.9 1.0 CB B:CYS728 3.2 23.6 1.0 CG B:HIS725 3.2 29.6 1.0 CB B:CYS708 3.4 25.5 1.0 CB B:HIS725 3.6 24.5 1.0 N B:CYS708 3.8 26.2 1.0 CA B:CYS708 4.1 25.9 1.0 NE2 B:HIS725 4.2 34.1 1.0 N B:HIS725 4.2 22.5 1.0 CD2 B:HIS725 4.3 31.3 1.0 CA B:CYS705 4.5 26.4 1.0 CA B:HIS725 4.5 22.5 1.0 CA B:CYS728 4.7 23.1 1.0 CB B:VAL707 4.7 23.3 1.0 O B:HOH1210 4.7 32.3 1.0 C B:CYS708 4.8 28.9 1.0 C B:VAL707 4.9 27.2 1.0 C B:CYS705 5.0 27.0 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 100)


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 100) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:30.5 occ:1.00 SG B:CYS717 2.2 30.4 1.0 SG B:CYS720 2.4 30.0 1.0 SG B:CYS745 2.4 32.3 1.0 SG B:CYS742 2.4 26.9 1.0 CB B:CYS717 3.2 33.4 1.0 CB B:CYS720 3.2 31.8 1.0 CB B:CYS742 3.5 26.0 1.0 CB B:CYS745 3.5 30.1 1.0 N B:CYS720 3.8 38.2 1.0 N B:CYS742 3.8 28.2 1.0 CA B:CYS720 4.1 32.3 1.0 N B:CYS745 4.1 25.0 1.0 OG1 B:THR719 4.1 36.5 1.0 CA B:CYS742 4.2 25.1 1.0 CA B:CYS745 4.4 26.6 1.0 C B:THR719 4.5 35.8 1.0 NH1 B:ARG722 4.5 32.9 1.0 CA B:CYS717 4.6 34.3 1.0 O B:CYS742 4.6 25.0 1.0 C B:CYS742 4.6 24.0 1.0 O B:HOH1194 4.7 38.2 1.0 C B:CYS720 4.7 32.7 1.0 O B:CYS720 4.8 31.6 1.0 N B:THR719 4.8 43.5 1.0 C B:SER741 4.9 33.2 1.0 CB B:PHE744 4.9 25.9 1.0 CA B:THR719 5.0 36.8 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