Zinc in PDB 6g5p: Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine

The structure of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine, PDB code: 6g5p was solved by R.P.H.Talon, T.Krojer, C.Tallant, G.Nunez-Alonso, M.Fairhead, A.Szykowska, P.Collins, N.M.Pearce, J.Ng, E.Maclean, N.Wright, A.Douangamath, J.Brandao-Neto, N.Burgess-Brown, K.Huber, S.Knapp, P.E.Brennan, C.H.Arrowsmith, A.M.Edwards, C.Bountra, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.59 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.855, 45.429, 83.715, 90.00, 101.77, 90.00
R / Rfree (%)	13.8 / 17.4

The structure of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine (pdb code 6g5p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine, PDB code: 6g5p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:22.5 occ:1.00 ND1 A:HIS725 2.1 22.9 1.0 SG A:CYS728 2.3 22.0 1.0 SG A:CYS708 2.3 23.1 1.0 SG A:CYS705 2.3 20.6 1.0 CE1 A:HIS725 3.0 22.1 1.0 CB A:CYS705 3.0 23.3 1.0 CG A:HIS725 3.2 22.2 1.0 CB A:CYS728 3.2 20.6 1.0 CB A:CYS708 3.3 20.8 1.0 CB A:HIS725 3.5 22.4 1.0 N A:CYS708 3.8 19.8 1.0 O A:HOH1246 4.1 49.0 1.0 N A:HIS725 4.1 25.1 1.0 CA A:CYS708 4.1 21.1 1.0 NE2 A:HIS725 4.2 24.5 1.0 CD2 A:HIS725 4.3 24.4 1.0 CA A:HIS725 4.4 24.9 1.0 CA A:CYS705 4.5 23.9 1.0 CA A:CYS728 4.7 18.9 1.0 CB A:VAL707 4.7 18.5 1.0 O A:HOH1221 4.7 36.5 1.0 O A:HOH1239 4.8 49.2 1.0 C A:CYS708 4.9 22.3 1.0 C A:VAL707 4.9 17.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:30.2 occ:1.00 SG A:CYS717 2.3 33.5 1.0 SG A:CYS720 2.3 31.9 1.0 SG A:CYS742 2.3 24.6 1.0 SG A:CYS745 2.4 29.6 1.0 CB A:CYS717 3.2 31.3 1.0 CB A:CYS720 3.3 33.4 1.0 CB A:CYS742 3.4 23.8 1.0 CB A:CYS745 3.5 27.4 1.0 N A:CYS720 3.7 34.7 1.0 N A:CYS742 3.7 25.2 1.0 CA A:CYS720 4.0 34.2 1.0 N A:CYS745 4.0 22.6 1.0 CA A:CYS742 4.1 23.9 1.0 OG1 A:THR719 4.1 34.9 1.0 CA A:CYS745 4.3 24.3 1.0 C A:THR719 4.4 37.4 1.0 O A:CYS742 4.5 22.9 1.0 C A:CYS720 4.5 34.1 1.0 O A:HOH1181 4.5 41.1 1.0 C A:CYS742 4.5 22.2 1.0 O A:CYS720 4.6 36.8 1.0 NH1 A:ARG722 4.6 31.8 1.0 CA A:CYS717 4.7 31.4 1.0 C A:SER741 4.8 26.8 1.0 CB A:PHE744 4.9 21.7 1.0 N A:THR719 4.9 37.0 1.0 CB A:ARG722 5.0 30.9 1.0 O A:THR719 5.0 39.1 1.0 CA A:THR719 5.0 35.8 1.0 CD A:ARG722 5.0 27.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:20.2 occ:0.99 ND1 B:HIS725 2.1 21.1 1.0 SG B:CYS728 2.3 19.8 1.0 SG B:CYS708 2.3 21.7 1.0 SG B:CYS705 2.4 19.2 1.0 CE1 B:HIS725 3.1 22.3 1.0 CB B:CYS705 3.1 22.2 1.0 CG B:HIS725 3.2 19.9 1.0 CB B:CYS728 3.2 17.8 1.0 CB B:CYS708 3.3 21.3 1.0 CB B:HIS725 3.5 20.7 1.0 N B:CYS708 3.8 19.5 1.0 CA B:CYS708 4.1 20.5 1.0 N B:HIS725 4.2 19.6 1.0 NE2 B:HIS725 4.2 24.2 1.0 CD2 B:HIS725 4.3 22.6 1.0 CA B:HIS725 4.5 18.1 1.0 CA B:CYS705 4.6 22.4 1.0 O B:HOH1184 4.6 29.4 1.0 CA B:CYS728 4.7 17.1 1.0 CB B:VAL707 4.7 17.2 1.0 O B:HOH1206 4.8 45.9 1.0 C B:CYS708 4.9 21.1 1.0 C B:VAL707 4.9 17.4 1.0 N B:ASN709 5.0 21.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human SP100 in Complex with Bromodomain-Focused Fragment FM009493B 2,3-Dimethoxy-2,3-Dimethyl-2,3-Dihydro-1,4- Benzodioxin-6-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:23.1 occ:1.00 SG B:CYS717 2.3 24.6 1.0 SG B:CYS742 2.3 19.3 1.0 SG B:CYS720 2.3 26.6 1.0 SG B:CYS745 2.4 24.1 1.0 CB B:CYS717 3.2 23.2 1.0 CB B:CYS720 3.3 26.9 1.0 CB B:CYS742 3.4 20.7 1.0 CB B:CYS745 3.5 21.5 1.0 N B:CYS720 3.8 31.1 1.0 N B:CYS742 3.8 20.5 1.0 N B:CYS745 4.0 19.9 1.0 CA B:CYS720 4.1 29.6 1.0 OG1 B:THR719 4.1 26.8 1.0 CA B:CYS742 4.1 19.4 1.0 CA B:CYS745 4.3 19.4 1.0 C B:THR719 4.4 29.3 1.0 O B:CYS742 4.5 18.0 1.0 O B:HOH1165 4.6 36.9 1.0 C B:CYS742 4.6 19.2 1.0 C B:CYS720 4.6 30.3 1.0 CA B:CYS717 4.6 23.4 1.0 NH1 B:ARG722 4.7 27.0 1.0 O B:CYS720 4.7 28.9 1.0 N B:THR719 4.8 29.0 1.0 CB B:PHE744 4.9 18.6 1.0 C B:SER741 4.9 21.0 1.0 CA B:THR719 4.9 30.6 1.0 CB B:ARG722 5.0 21.1 1.0

R.P.H.Talon, D.Bowkett, C.Tallant, C.Schofield, F.Von Delft, S.Knapp, G.Bruton, P.E.Brennan. Identifying Small Molecule Binding Sites For Epigenetic Proteins at Domain-Domain Interfaces Biorxiv 2018.
DOI: 10.1101/283069