Zinc in PDB 5pwc: Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B, PDB code: 5pwc 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)	28.44 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.740, 45.415, 83.292, 90.00, 102.23, 90.00
R / Rfree (%)	18 / 21

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B (pdb code 5pwc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B, PDB code: 5pwc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B


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 in Complex with E48115B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.3 occ:1.00 ND1 A:HIS725 2.1 22.3 1.0 SG A:CYS728 2.3 22.4 1.0 SG A:CYS708 2.3 23.3 1.0 SG A:CYS705 2.3 20.9 1.0 CB A:CYS705 3.0 23.8 1.0 CE1 A:HIS725 3.0 24.4 1.0 CG A:HIS725 3.2 24.8 1.0 CB A:CYS728 3.2 19.1 1.0 CB A:CYS708 3.4 21.7 1.0 CB A:HIS725 3.5 25.2 1.0 N A:CYS708 3.8 22.4 1.0 O A:HOH1249 4.0 47.4 1.0 N A:HIS725 4.1 23.4 1.0 CA A:CYS708 4.2 23.9 1.0 NE2 A:HIS725 4.2 25.9 1.0 CD2 A:HIS725 4.3 25.8 1.0 CA A:HIS725 4.4 22.0 1.0 CA A:CYS705 4.5 22.1 1.0 O A:HOH1222 4.6 35.8 1.0 CB A:VAL707 4.6 18.2 1.0 CA A:CYS728 4.7 18.1 1.0 C A:CYS708 4.9 26.3 1.0 C A:VAL707 4.9 21.9 1.0 N A:ASN709 5.0 24.8 1.0

Zinc binding site 2 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B


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 in Complex with E48115B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:31.3 occ:1.00 SG A:CYS717 2.2 29.1 1.0 SG A:CYS742 2.3 23.9 1.0 SG A:CYS745 2.4 29.4 1.0 SG A:CYS720 2.4 30.5 1.0 CB A:CYS717 3.2 29.4 1.0 CB A:CYS742 3.3 18.7 1.0 CB A:CYS720 3.4 33.6 1.0 CB A:CYS745 3.5 28.0 1.0 N A:CYS742 3.7 24.8 1.0 N A:CYS720 3.9 33.3 1.0 CA A:CYS742 4.0 22.8 1.0 N A:CYS745 4.1 23.9 1.0 OG1 A:THR719 4.1 35.8 1.0 CA A:CYS720 4.1 33.5 1.0 CA A:CYS745 4.3 27.7 1.0 O A:CYS742 4.4 22.9 1.0 C A:THR719 4.5 34.1 1.0 C A:CYS742 4.5 25.2 1.0 CA A:CYS717 4.6 34.3 1.0 O A:CYS720 4.6 31.0 1.0 O A:HOH1206 4.6 42.1 1.0 C A:CYS720 4.6 29.6 1.0 NH1 A:ARG722 4.6 28.6 1.0 C A:SER741 4.8 25.1 1.0 CB A:PHE744 4.9 24.9 1.0 CB A:ARG722 4.9 26.7 1.0 N A:THR719 4.9 33.6 1.0 O A:THR719 5.0 38.9 1.0

Zinc binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B


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 in Complex with E48115B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.5 occ:1.00 ND1 B:HIS725 2.1 21.5 1.0 SG B:CYS728 2.3 20.1 1.0 SG B:CYS708 2.3 21.7 1.0 SG B:CYS705 2.4 18.6 1.0 CE1 B:HIS725 3.1 22.9 1.0 CB B:CYS705 3.1 19.5 1.0 CG B:HIS725 3.2 20.6 1.0 CB B:CYS728 3.2 18.0 1.0 CB B:CYS708 3.4 20.4 1.0 CB B:HIS725 3.5 19.1 1.0 N B:CYS708 3.8 20.6 1.0 O B:HOH1206 4.1 49.0 1.0 CA B:CYS708 4.1 21.4 1.0 N B:HIS725 4.2 18.1 1.0 NE2 B:HIS725 4.2 22.9 1.0 CD2 B:HIS725 4.3 22.0 1.0 CA B:HIS725 4.5 17.6 1.0 O B:HOH1190 4.5 44.6 1.0 CA B:CYS705 4.5 21.4 1.0 CA B:CYS728 4.6 17.2 1.0 O B:HOH1181 4.6 29.5 1.0 CB B:VAL707 4.7 18.1 1.0 C B:CYS708 4.8 24.7 1.0 C B:VAL707 4.9 22.3 1.0

Zinc binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with E48115B


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 in Complex with E48115B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:25.0 occ:1.00 SG B:CYS742 2.3 20.7 1.0 SG B:CYS717 2.3 22.8 1.0 SG B:CYS720 2.3 24.9 1.0 SG B:CYS745 2.4 24.9 1.0 CB B:CYS717 3.2 20.1 1.0 CB B:CYS720 3.3 23.6 1.0 CB B:CYS742 3.4 19.2 1.0 CB B:CYS745 3.5 21.5 1.0 N B:CYS742 3.8 20.7 1.0 N B:CYS720 3.8 27.9 1.0 N B:CYS745 4.0 20.1 1.0 CA B:CYS720 4.1 26.3 1.0 OG1 B:THR719 4.1 26.5 1.0 CA B:CYS742 4.1 20.1 1.0 CA B:CYS745 4.3 22.6 1.0 C B:THR719 4.4 27.4 1.0 O B:CYS742 4.5 19.1 1.0 NH1 B:ARG722 4.6 25.2 1.0 C B:CYS742 4.6 19.4 1.0 C B:CYS720 4.6 25.2 1.0 CA B:CYS717 4.6 20.3 1.0 O B:HOH1163 4.7 35.2 1.0 O B:CYS720 4.7 25.5 1.0 CB B:PHE744 4.8 19.5 1.0 C B:SER741 4.9 23.3 1.0 N B:THR719 4.9 27.7 1.0 CB B:ARG722 4.9 20.8 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