Zinc in PDB 5pza: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 106)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 106), PDB code: 5pza 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)	31.29 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.900, 45.570, 83.680, 90.00, 101.90, 90.00
R / Rfree (%)	17.3 / 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 106) (pdb code 5pza). 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 106), PDB code: 5pza:
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 106)


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 106) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:26.6 occ:1.00 ND1 A:HIS725 2.1 25.5 1.0 SG A:CYS705 2.3 26.9 1.0 SG A:CYS728 2.3 27.8 1.0 SG A:CYS708 2.3 27.9 1.0 CE1 A:HIS725 3.0 31.4 1.0 CB A:CYS705 3.0 26.4 1.0 CG A:HIS725 3.2 31.6 1.0 CB A:CYS728 3.2 24.4 1.0 CB A:CYS708 3.4 26.9 1.0 CB A:HIS725 3.6 30.9 1.0 N A:CYS708 3.8 24.5 1.0 O A:HOH1273 4.1 56.7 1.0 N A:HIS725 4.1 27.9 1.0 NE2 A:HIS725 4.1 31.6 1.0 CA A:CYS708 4.1 26.9 1.0 CD2 A:HIS725 4.2 33.9 1.0 CA A:HIS725 4.4 26.9 1.0 CA A:CYS705 4.5 26.6 1.0 CA A:CYS728 4.6 20.9 1.0 CB A:VAL707 4.7 21.2 1.0 O A:HOH1251 4.7 37.5 1.0 C A:CYS708 4.8 28.8 1.0 C A:VAL707 4.9 25.6 1.0 N A:ASN709 5.0 27.4 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 106)


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 106) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:32.8 occ:1.00 SG A:CYS720 2.3 37.0 1.0 SG A:CYS717 2.3 35.4 1.0 SG A:CYS742 2.3 26.4 1.0 SG A:CYS745 2.4 31.8 1.0 CB A:CYS720 3.3 36.3 1.0 CB A:CYS742 3.3 23.6 1.0 CB A:CYS717 3.3 32.0 1.0 CB A:CYS745 3.4 27.2 1.0 N A:CYS742 3.7 30.1 1.0 N A:CYS720 3.8 34.9 1.0 N A:CYS745 4.0 28.4 1.0 CA A:CYS742 4.0 27.8 1.0 OG1 A:THR719 4.0 40.9 1.0 CA A:CYS720 4.1 34.7 1.0 CA A:CYS745 4.3 28.7 1.0 O A:CYS742 4.4 26.4 1.0 C A:THR719 4.5 38.2 1.0 C A:CYS742 4.5 28.2 1.0 O A:CYS720 4.6 38.1 1.0 C A:CYS720 4.6 32.1 1.0 NH1 A:ARG722 4.7 30.7 1.0 CA A:CYS717 4.7 40.1 1.0 O A:HOH1238 4.7 38.1 1.0 C A:SER741 4.8 26.8 1.0 CB A:PHE744 4.9 27.4 1.0 O A:THR719 5.0 38.0 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 106)


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 106) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:54.3 occ:0.43 OE2 A:GLU756 2.2 63.7 1.0 SG A:CYS754 2.6 42.5 0.6 OE1 A:GLU756 2.7 47.8 1.0 CD A:GLU756 2.8 52.9 1.0 SG A:CYS754 2.9 32.7 0.5 CB A:CYS754 3.2 37.1 0.6 CB A:CYS754 3.4 33.5 0.5 CA A:CYS754 3.4 34.3 0.5 CA A:CYS754 3.4 36.0 0.6 O A:ARG753 4.0 48.3 1.0 CG A:GLU756 4.3 43.5 1.0 C A:CYS754 4.3 35.4 1.0 N A:CYS754 4.5 36.1 1.0 CD A:PRO755 4.5 35.4 1.0 C A:ARG753 4.7 40.6 1.0 O A:HOH1046 4.7 48.4 1.0 N A:PRO755 4.7 33.3 1.0 O A:CYS754 5.0 32.8 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 106)


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 106) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.9 occ:1.00 ND1 B:HIS725 2.2 24.8 1.0 SG B:CYS728 2.3 22.4 1.0 SG B:CYS708 2.3 23.0 1.0 SG B:CYS705 2.4 21.6 1.0 CE1 B:HIS725 3.1 29.1 1.0 CB B:CYS705 3.1 21.8 1.0 CG B:HIS725 3.2 23.4 1.0 CB B:CYS728 3.2 21.7 1.0 CB B:CYS708 3.4 23.5 1.0 CB B:HIS725 3.5 21.7 1.0 N B:CYS708 3.8 22.8 1.0 CA B:CYS708 4.1 23.2 1.0 N B:HIS725 4.2 22.3 1.0 NE2 B:HIS725 4.2 25.6 1.0 CD2 B:HIS725 4.3 24.1 1.0 CA B:HIS725 4.5 19.4 1.0 CA B:CYS705 4.5 21.2 1.0 CA B:CYS728 4.6 20.6 1.0 O B:HOH1207 4.7 30.2 1.0 CB B:VAL707 4.7 19.4 1.0 C B:CYS708 4.9 27.4 1.0 C B:VAL707 4.9 22.8 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 106)


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 106) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:25.1 occ:1.00 SG B:CYS717 2.2 26.3 1.0 SG B:CYS742 2.3 21.6 1.0 SG B:CYS745 2.3 27.0 1.0 SG B:CYS720 2.4 26.2 1.0 CB B:CYS717 3.2 23.7 1.0 CB B:CYS720 3.4 27.3 1.0 CB B:CYS742 3.5 21.2 1.0 CB B:CYS745 3.5 21.8 1.0 N B:CYS720 3.8 30.8 1.0 N B:CYS742 3.8 22.9 1.0 N B:CYS745 4.0 22.3 1.0 CA B:CYS720 4.1 29.3 1.0 OG1 B:THR719 4.1 30.3 1.0 CA B:CYS742 4.1 21.1 1.0 CA B:CYS745 4.3 23.1 1.0 C B:THR719 4.5 30.7 1.0 O B:CYS742 4.5 19.9 1.0 O B:HOH1189 4.5 38.2 1.0 C B:CYS742 4.6 20.2 1.0 NH1 B:ARG722 4.6 29.4 1.0 C B:CYS720 4.6 30.0 1.0 CA B:CYS717 4.6 22.6 1.0 O B:CYS720 4.7 28.7 1.0 CB B:PHE744 4.9 22.6 1.0 N B:THR719 4.9 30.4 1.0 C B:SER741 4.9 25.0 1.0 CB B:ARG722 5.0 25.0 1.0 CA B:THR719 5.0 29.6 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