Nickel in PDB 3tlp: Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)

The structure of Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1), PDB code: 3tlp was solved by P.Filippakopoulos, I.Felletar, S.Picaud, T.Keates, J.Muniz, T.Krojer, C.K.Allerston, S.Latwiel, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.75 / 2.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.431, 60.220, 109.907, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.9

The binding sites of Nickel atom in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) (pdb code 3tlp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1), PDB code: 3tlp:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1 b:41.1 occ:1.00 O A:HOH63 1.9 36.2 1.0 O A:HOH64 1.9 45.5 1.0 O A:HOH68 2.1 38.6 1.0 NE2 A:HIS567 2.1 35.9 1.0 O A:HOH62 2.4 44.1 1.0 CE1 A:HIS567 3.1 30.8 1.0 CD2 A:HIS567 3.1 39.6 1.0 O A:HOH34 4.1 40.0 1.0 O A:HOH65 4.2 41.2 1.0 ND1 A:HIS567 4.2 36.4 1.0 CG A:HIS567 4.3 48.7 1.0 CG2 A:ILE529 4.3 37.3 1.0 O A:ILE529 5.0 35.7 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni3 b:91.6 occ:1.00 NZ A:LYS547 2.1 54.4 1.0 NE2 A:HIS541 2.2 0.4 1.0 CE1 A:HIS541 2.9 71.1 1.0 CE A:LYS547 3.3 78.0 1.0 CD2 A:HIS541 3.3 64.5 1.0 O A:HOH66 3.5 71.5 1.0 ND1 A:HIS541 4.1 63.9 1.0 CG A:HIS541 4.3 82.3 1.0 CD A:LYS547 4.5 57.8 1.0 OD1 A:ASN545 4.6 86.6 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni4 b:82.9 occ:1.00 CE A:LYS584 2.6 86.0 1.0 NZ A:LYS584 2.6 67.8 1.0 NE2 A:HIS580 2.8 65.0 1.0 CD2 A:HIS580 3.2 74.9 1.0 CE1 A:HIS580 4.0 99.9 1.0 CD A:LYS584 4.2 72.5 1.0 CG A:HIS580 4.5 65.1 1.0 ND1 A:HIS580 4.9 88.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of the Fourth Bromodomain of Human Poly-Bromodomain Containing Protein 1 (PB1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2 b:38.4 occ:1.00 NZ B:LYS584 1.9 25.6 1.0 O B:HOH61 2.0 31.5 1.0 O B:HOH67 2.1 45.1 1.0 NE2 B:HIS580 2.1 34.6 1.0 O B:HOH60 2.3 46.0 1.0 CE1 B:HIS580 3.0 28.7 1.0 CE B:LYS584 3.0 40.1 1.0 CD2 B:HIS580 3.2 29.3 1.0 ND1 B:HIS580 4.2 34.0 1.0 CD B:LYS584 4.3 47.2 1.0 CG B:HIS580 4.3 35.1 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