Zinc in PDB 4ptb: Crystal Structure of Human SP100 Phd-Bromodomain in the Free State

The structure of Crystal Structure of Human SP100 Phd-Bromodomain in the Free State, PDB code: 4ptb was solved by C.Tallant, G.Nunez-Alonso, P.Savitsky, J.Newman, T.Krojer, A.Szykowska, N.Burgess-Brown, P.Filippakopoulos, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.72 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.520, 45.183, 83.188, 90.00, 102.21, 90.00
R / Rfree (%)	17.3 / 19.2

The binding sites of Zinc atom in the Crystal Structure of Human SP100 Phd-Bromodomain in the Free State (pdb code 4ptb). 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 Phd-Bromodomain in the Free State, PDB code: 4ptb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Human SP100 Phd-Bromodomain in the Free State


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 Phd-Bromodomain in the Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:22.6 occ:1.00 ND1 A:HIS725 2.1 20.9 1.0 SG A:CYS708 2.3 22.4 1.0 SG A:CYS728 2.3 23.7 1.0 SG A:CYS705 2.4 20.3 1.0 CE1 A:HIS725 3.0 24.1 1.0 CB A:CYS705 3.1 20.4 1.0 CG A:HIS725 3.2 22.3 1.0 CB A:CYS728 3.2 21.6 1.0 CB A:CYS708 3.3 21.3 1.0 CB A:HIS725 3.6 21.3 1.0 N A:CYS708 3.8 19.8 1.0 CA A:CYS708 4.1 20.9 1.0 NE2 A:HIS725 4.1 23.7 1.0 N A:HIS725 4.2 21.4 1.0 CD2 A:HIS725 4.3 23.3 1.0 CA A:HIS725 4.4 21.3 1.0 CA A:CYS705 4.5 21.3 1.0 CA A:CYS728 4.6 20.6 1.0 CB A:VAL707 4.7 18.8 1.0 C A:CYS708 4.8 22.6 1.0 C A:VAL707 4.9 20.4 1.0 N A:ASN709 5.0 23.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Human SP100 Phd-Bromodomain in the Free State


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 Phd-Bromodomain in the Free State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:27.9 occ:1.00 SG A:CYS742 2.3 21.1 1.0 SG A:CYS717 2.3 26.8 1.0 SG A:CYS745 2.4 28.8 1.0 SG A:CYS720 2.4 30.2 1.0 CB A:CYS717 3.2 27.2 1.0 CB A:CYS742 3.4 20.4 1.0 CB A:CYS720 3.4 31.0 1.0 CB A:CYS745 3.5 25.6 1.0 N A:CYS742 3.8 23.1 1.0 N A:CYS720 3.9 32.9 1.0 N A:CYS745 4.0 22.9 1.0 CA A:CYS742 4.1 21.6 1.0 OG1 A:THR719 4.1 32.9 1.0 CA A:CYS720 4.1 33.2 1.0 CA A:CYS745 4.3 24.2 1.0 O A:CYS742 4.5 20.7 1.0 C A:THR719 4.5 34.0 1.0 C A:CYS742 4.6 21.5 1.0 CA A:CYS717 4.6 27.8 1.0 O A:CYS720 4.6 31.8 1.0 C A:CYS720 4.6 31.4 1.0 NH1 A:ARG722 4.7 29.8 1.0 O A:HOH1112 4.8 45.1 1.0 CB A:PHE744 4.8 21.3 1.0 C A:SER741 4.9 24.6 1.0 CB A:ARG722 4.9 24.3 1.0 N A:THR719 4.9 33.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Human SP100 Phd-Bromodomain in the Free State


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 Phd-Bromodomain in the Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:19.4 occ:1.00 ND1 B:HIS725 2.1 17.1 1.0 SG B:CYS728 2.3 20.3 1.0 SG B:CYS708 2.3 21.1 1.0 SG B:CYS705 2.3 18.2 1.0 CE1 B:HIS725 3.0 19.6 1.0 CB B:CYS705 3.1 18.4 1.0 CG B:HIS725 3.1 17.7 1.0 CB B:CYS728 3.2 18.3 1.0 CB B:CYS708 3.4 20.7 1.0 CB B:HIS725 3.5 16.8 1.0 N B:CYS708 3.8 20.5 1.0 CA B:CYS708 4.1 21.5 1.0 N B:HIS725 4.1 16.6 1.0 NE2 B:HIS725 4.2 19.3 1.0 CD2 B:HIS725 4.2 18.7 1.0 CA B:HIS725 4.5 16.7 1.0 CA B:CYS705 4.5 18.9 1.0 CA B:CYS728 4.6 17.2 1.0 O B:HOH1049 4.7 28.6 1.0 CB B:VAL707 4.7 18.1 1.0 C B:CYS708 4.9 23.4 1.0 C B:VAL707 4.9 20.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Human SP100 Phd-Bromodomain in the Free State


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 Phd-Bromodomain in the Free State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:21.5 occ:1.00 SG B:CYS720 2.3 22.8 1.0 SG B:CYS742 2.3 18.8 1.0 SG B:CYS745 2.3 23.2 1.0 SG B:CYS717 2.4 21.6 1.0 CB B:CYS717 3.2 21.5 1.0 CB B:CYS720 3.3 23.7 1.0 CB B:CYS745 3.5 22.4 1.0 CB B:CYS742 3.5 18.6 1.0 N B:CYS720 3.7 25.4 1.0 N B:CYS742 3.8 19.9 1.0 N B:CYS745 4.0 19.4 1.0 CA B:CYS720 4.0 24.5 1.0 OG1 B:THR719 4.0 26.1 1.0 CA B:CYS742 4.1 18.5 1.0 CA B:CYS745 4.3 21.2 1.0 C B:THR719 4.4 26.5 1.0 NH1 B:ARG722 4.5 24.1 1.0 O B:CYS742 4.6 18.4 1.0 C B:CYS720 4.6 24.7 1.0 C B:CYS742 4.6 18.4 1.0 CA B:CYS717 4.7 22.2 1.0 O B:CYS720 4.7 25.1 1.0 CB B:PHE744 4.8 18.7 1.0 N B:THR719 4.9 27.0 1.0 CB B:ARG722 4.9 20.7 1.0 C B:SER741 4.9 21.1 1.0 CA B:THR719 5.0 26.7 1.0

C.Tallant, G.Nunez-Alonso, P.Savitsky, J.Newman, T.Krojer, A.Szykowska, N.Burgess-Brown, P.Filippakopoulos, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, S.Knapp. Crystal Structure of Human SP100 Phd-Bromodomain in the Free State To Be Published.