Zinc in PDB 3hmf: Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)

The structure of Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1), PDB code: 3hmf was solved by P.Filippakopoulos, S.Picaud, T.Keates, J.Muniz, F.Von Delft, C.H.Arrowsmith, A.Edwards, J.Weigelt, C.Bountra, S.Knapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.18 / 1.63
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.810, 49.360, 33.610, 90.00, 97.91, 90.00
R / Rfree (%)	17.1 / 19.9

The structure of Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) (pdb code 3hmf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1), PDB code: 3hmf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


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 the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:12.6 occ:1.00 NE2 A:HIS289 2.0 11.4 1.0 CL A:CL294 2.2 20.8 1.0 CL A:CL293 2.2 15.1 1.0 CD2 A:HIS289 3.0 10.1 1.0 CE1 A:HIS289 3.0 9.2 1.0 ND1 A:HIS289 4.1 9.3 1.0 C2 A:EDO292 4.2 13.0 1.0 CG A:HIS289 4.2 7.5 1.0 O A:HOH321 4.2 41.5 1.0 C1 A:EDO292 4.5 17.3 1.0 O1 A:EDO292 4.8 20.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


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 the Second Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:13.9 occ:1.00 OXT A:GLU291 2.0 15.3 1.0 ND1 A:HIS290 2.1 13.9 1.0 CE1 A:HIS290 2.9 20.3 1.0 C A:GLU291 3.0 16.5 1.0 N A:GLU291 3.0 12.3 1.0 CG A:HIS290 3.2 12.9 1.0 CA A:GLU291 3.4 12.8 1.0 C A:HIS290 3.5 9.8 1.0 CB A:HIS290 3.6 12.6 1.0 CA A:HIS290 4.1 11.0 1.0 O A:GLU291 4.1 14.9 1.0 NE2 A:HIS290 4.1 22.4 1.0 O A:HIS290 4.1 12.9 1.0 CD2 A:HIS290 4.2 17.6 1.0 CB A:GLU291 4.9 14.4 1.0

P.Filippakopoulos, S.Picaud, M.Mangos, T.Keates, J.P.Lambert, D.Barsyte-Lovejoy, I.Felletar, R.Volkmer, S.Muller, T.Pawson, A.C.Gingras, C.H.Arrowsmith, S.Knapp. Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family. Cell(Cambridge,Mass.) V. 149 214 2012.
ISSN: ISSN 0092-8674
PubMed: 22464331
DOI: 10.1016/J.CELL.2012.02.013