Zinc in PDB 5pxw: Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 56)

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 56), PDB code: 5pxw 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)	28.41 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.769, 45.487, 83.076, 90.00, 102.33, 90.00
R / Rfree (%)	21.1 / 26.9

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 After Initial Refinement with No Ligand Modelled (Structure 56) (pdb code 5pxw). 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 56), PDB code: 5pxw:
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 56)


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 56) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:30.1 occ:1.00 SG A:CYS728 2.2 25.3 1.0 ND1 A:HIS725 2.2 39.9 1.0 SG A:CYS705 2.2 34.1 1.0 SG A:CYS708 2.4 29.2 1.0 CB A:CYS705 3.0 33.0 1.0 CE1 A:HIS725 3.0 37.5 1.0 CB A:CYS728 3.1 23.9 1.0 CG A:HIS725 3.3 34.6 1.0 CB A:CYS708 3.4 27.3 1.0 CB A:HIS725 3.8 30.4 1.0 N A:CYS708 3.8 26.0 1.0 CA A:CYS708 4.2 27.6 1.0 N A:HIS725 4.2 28.4 1.0 NE2 A:HIS725 4.2 32.7 1.0 CD2 A:HIS725 4.4 38.7 1.0 CA A:CYS705 4.4 33.7 1.0 O A:HOH1256 4.5 40.0 1.0 CA A:HIS725 4.6 28.7 1.0 CA A:CYS728 4.6 24.1 1.0 CB A:VAL707 4.7 21.0 1.0 C A:VAL707 4.9 25.5 1.0 C A:CYS708 4.9 30.3 1.0 N A:ASN709 5.0 33.3 1.0 C A:CYS705 5.0 33.0 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 56)


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 56) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:36.6 occ:1.00 SG A:CYS717 2.1 44.9 1.0 SG A:CYS720 2.2 39.8 1.0 SG A:CYS745 2.4 41.9 1.0 SG A:CYS742 2.4 30.3 1.0 CB A:CYS720 3.2 42.2 1.0 CB A:CYS717 3.2 48.9 1.0 CB A:CYS742 3.5 29.9 1.0 CB A:CYS745 3.5 36.5 1.0 N A:CYS720 3.7 40.9 1.0 N A:CYS742 3.8 37.2 1.0 CA A:CYS720 4.0 39.6 1.0 N A:CYS745 4.0 35.6 1.0 CA A:CYS742 4.1 34.3 1.0 CA A:CYS745 4.3 42.1 1.0 OG1 A:THR719 4.3 47.7 1.0 C A:THR719 4.4 42.7 1.0 O A:CYS742 4.4 32.3 1.0 C A:CYS742 4.5 32.5 1.0 C A:CYS720 4.5 36.9 1.0 O A:CYS720 4.6 39.3 1.0 NH1 A:ARG722 4.6 33.4 1.0 CA A:CYS717 4.7 53.3 1.0 O A:HOH1224 4.8 42.3 1.0 CB A:PHE744 4.8 29.2 1.0 O A:THR719 4.9 45.6 1.0 C A:SER741 4.9 36.6 1.0 CD A:ARG722 4.9 36.6 1.0 N A:THR719 5.0 52.9 1.0 C A:PHE744 5.0 32.8 1.0 CA A:THR719 5.0 48.1 1.0 CB A:ARG722 5.0 40.8 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 56)


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 56) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:0.9 occ:0.43 OE2 A:GLU756 3.1 76.3 1.0 SG A:CYS754 3.1 79.8 0.6 OE1 A:GLU756 3.4 69.3 1.0 O A:ARG753 3.5 81.7 1.0 CD A:GLU756 3.7 67.7 1.0 CA A:CYS754 3.9 63.1 0.6 CA A:CYS754 4.0 55.5 0.5 CB A:CYS754 4.1 67.5 0.6 SG A:CYS754 4.1 43.3 0.5 CB A:CYS754 4.3 52.0 0.5 C A:ARG753 4.4 63.3 1.0 CD A:PRO755 4.6 58.5 1.0 N A:CYS754 4.7 62.3 1.0 C A:CYS754 4.9 57.6 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 56)


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 56) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:27.3 occ:1.00 ND1 B:HIS725 2.1 35.3 1.0 SG B:CYS705 2.3 27.4 1.0 SG B:CYS728 2.3 22.5 1.0 SG B:CYS708 2.4 28.5 1.0 CB B:CYS705 3.0 27.6 1.0 CE1 B:HIS725 3.0 35.2 1.0 CB B:CYS728 3.2 19.5 1.0 CG B:HIS725 3.3 30.6 1.0 CB B:CYS708 3.4 25.2 1.0 CB B:HIS725 3.7 24.4 1.0 N B:CYS708 3.8 24.7 1.0 N B:HIS725 4.1 27.7 1.0 NE2 B:HIS725 4.2 32.2 1.0 CA B:CYS708 4.2 25.4 1.0 CD2 B:HIS725 4.3 27.9 1.0 CA B:CYS705 4.5 29.2 1.0 CA B:HIS725 4.5 26.7 1.0 CA B:CYS728 4.6 22.1 1.0 O B:HOH1198 4.7 38.9 1.0 CB B:VAL707 4.8 19.5 1.0 C B:CYS708 4.8 27.7 1.0 C B:VAL707 4.9 21.3 1.0 C B:CYS705 5.0 28.4 1.0 N B:ASN709 5.0 30.1 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 56)


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 56) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:31.0 occ:1.00 SG B:CYS717 2.1 30.8 1.0 SG B:CYS745 2.3 35.5 1.0 SG B:CYS720 2.4 36.5 1.0 SG B:CYS742 2.4 25.2 1.0 CB B:CYS720 3.2 37.6 1.0 CB B:CYS717 3.2 33.5 1.0 CB B:CYS742 3.3 27.7 1.0 CB B:CYS745 3.5 32.2 1.0 N B:CYS742 3.7 33.1 1.0 N B:CYS720 3.8 36.5 1.0 OG1 B:THR719 4.0 36.3 1.0 CA B:CYS720 4.0 35.3 1.0 CA B:CYS742 4.1 27.9 1.0 N B:CYS745 4.2 27.9 1.0 C B:THR719 4.4 35.1 1.0 CA B:CYS745 4.4 30.4 1.0 C B:CYS742 4.6 30.7 1.0 O B:CYS742 4.6 32.1 1.0 CA B:CYS717 4.6 35.4 1.0 O B:HOH1186 4.6 38.1 1.0 C B:CYS720 4.7 35.0 1.0 NH1 B:ARG722 4.8 34.2 1.0 N B:THR719 4.9 38.0 1.0 C B:SER741 4.9 38.1 1.0 O B:CYS720 4.9 33.6 1.0 O B:THR719 4.9 35.0 1.0 CB B:ARG722 4.9 36.8 1.0 CB B:PHE744 5.0 24.9 1.0 CA B:THR719 5.0 36.9 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