Zinc in PDB 5pwd: Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B, PDB code: 5pwd 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 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.688, 45.389, 83.411, 90.00, 102.16, 90.00
R / Rfree (%)	18 / 21.1

The structure of Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B (pdb code 5pwd). 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 N09600B, PDB code: 5pwd:
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 N09600B


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 N09600B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.3 occ:1.00 ND1 A:HIS725 2.2 22.2 1.0 SG A:CYS728 2.3 22.4 1.0 SG A:CYS708 2.3 23.5 1.0 SG A:CYS705 2.3 21.2 1.0 CE1 A:HIS725 3.0 25.5 1.0 CB A:CYS705 3.0 21.9 1.0 CG A:HIS725 3.2 26.1 1.0 CB A:CYS728 3.3 21.0 1.0 CB A:CYS708 3.4 25.1 1.0 CB A:HIS725 3.6 26.7 1.0 N A:CYS708 3.8 23.8 1.0 O A:HOH1234 3.8 53.4 1.0 N A:HIS725 4.1 25.0 1.0 CA A:CYS708 4.2 23.9 1.0 NE2 A:HIS725 4.2 26.5 1.0 CD2 A:HIS725 4.3 26.3 1.0 CA A:HIS725 4.5 23.1 1.0 O A:HOH1210 4.5 35.5 1.0 CA A:CYS705 4.5 21.0 1.0 CB A:VAL707 4.7 16.0 1.0 CA A:CYS728 4.7 18.4 1.0 C A:VAL707 4.9 23.8 1.0 C A:CYS708 4.9 26.1 1.0 N A:ASN709 5.0 24.6 1.0 C A:CYS705 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 N09600B


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 N09600B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:32.5 occ:1.00 SG A:CYS717 2.2 30.5 1.0 SG A:CYS742 2.2 24.6 1.0 SG A:CYS720 2.4 33.3 1.0 SG A:CYS745 2.4 30.1 1.0 CB A:CYS717 3.2 31.1 1.0 CB A:CYS742 3.3 19.2 1.0 CB A:CYS720 3.4 34.5 1.0 CB A:CYS745 3.5 26.8 1.0 N A:CYS742 3.7 25.1 1.0 N A:CYS720 3.9 34.5 1.0 CA A:CYS742 4.0 23.4 1.0 N A:CYS745 4.0 25.2 1.0 OG1 A:THR719 4.1 34.8 1.0 CA A:CYS720 4.1 34.6 1.0 CA A:CYS745 4.3 28.3 1.0 O A:CYS742 4.3 21.9 1.0 C A:CYS742 4.5 25.7 1.0 C A:THR719 4.5 36.2 1.0 CA A:CYS717 4.6 34.8 1.0 NH1 A:ARG722 4.6 28.8 1.0 O A:CYS720 4.6 35.2 1.0 C A:CYS720 4.6 31.8 1.0 C A:SER741 4.8 25.0 1.0 O A:HOH1197 4.8 46.7 1.0 CB A:PHE744 4.9 23.2 1.0 CB A:ARG722 4.9 25.5 1.0 CD A:ARG722 5.0 26.8 1.0 N A:THR719 5.0 40.4 1.0

Zinc binding site 3 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B


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 N09600B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:21.3 occ:1.00 ND1 B:HIS725 2.1 22.9 1.0 SG B:CYS728 2.3 19.5 1.0 SG B:CYS708 2.3 22.1 1.0 SG B:CYS705 2.4 18.8 1.0 CB B:CYS705 3.1 19.2 1.0 CE1 B:HIS725 3.1 24.0 1.0 CG B:HIS725 3.2 21.2 1.0 CB B:CYS728 3.2 18.8 1.0 CB B:CYS708 3.4 20.7 1.0 CB B:HIS725 3.5 22.3 1.0 N B:CYS708 3.8 19.6 1.0 CA B:CYS708 4.1 21.4 1.0 N B:HIS725 4.2 20.6 1.0 NE2 B:HIS725 4.2 23.9 1.0 CD2 B:HIS725 4.3 20.6 1.0 CA B:HIS725 4.5 18.3 1.0 CA B:CYS705 4.5 21.4 1.0 O B:HOH1170 4.6 28.3 1.0 CA B:CYS728 4.6 17.4 1.0 CB B:VAL707 4.7 16.7 1.0 C B:CYS708 4.8 22.9 1.0 C B:VAL707 4.9 21.8 1.0 N B:ASN709 4.9 21.4 0.6 N B:ASN709 5.0 22.2 0.4

Zinc binding site 4 out of 4 in the Pandda Analysis Group Deposition -- Crystal Structure of SP100 in Complex with N09600B


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 N09600B within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:25.9 occ:1.00 SG B:CYS717 2.3 23.8 1.0 SG B:CYS742 2.3 21.3 1.0 SG B:CYS720 2.4 25.1 1.0 SG B:CYS745 2.4 24.8 1.0 CB B:CYS717 3.2 22.1 1.0 CB B:CYS720 3.3 25.4 1.0 CB B:CYS742 3.4 18.7 1.0 CB B:CYS745 3.5 19.5 1.0 N B:CYS742 3.8 21.4 1.0 N B:CYS720 3.8 28.7 1.0 N B:CYS745 4.0 19.4 1.0 CA B:CYS720 4.1 27.5 1.0 CA B:CYS742 4.1 19.8 1.0 OG1 B:THR719 4.1 27.4 1.0 CA B:CYS745 4.3 20.3 1.0 C B:THR719 4.5 26.5 1.0 O B:CYS742 4.5 18.3 1.0 C B:CYS742 4.6 18.0 1.0 CA B:CYS717 4.6 21.6 1.0 NH1 B:ARG722 4.6 26.3 1.0 C B:CYS720 4.6 27.2 1.0 O B:CYS720 4.7 27.8 1.0 O B:HOH1164 4.7 37.9 1.0 C B:SER741 4.9 23.5 1.0 N B:THR719 4.9 27.8 1.0 CB B:ARG722 4.9 21.8 1.0 CB B:PHE744 4.9 18.6 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