Bromine in PDB 6qgn: Crystal Structure of APT1 Bound to 2-Bromopalmitate

The structure of Crystal Structure of APT1 Bound to 2-Bromopalmitate, PDB code: 6qgn was solved by M.J.Marcaida, M.Audagnotto, S.Ho, F.Pojer, G.Van Der Goot, M.Dal Peraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.900, 109.616, 174.713, 90.00, 90.00, 90.00
R / Rfree (%)	23 / 27.3

The binding sites of Bromine atom in the Crystal Structure of APT1 Bound to 2-Bromopalmitate (pdb code 6qgn). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of APT1 Bound to 2-Bromopalmitate, PDB code: 6qgn:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of APT1 Bound to 2-Bromopalmitate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of APT1 Bound to 2-Bromopalmitate within 5.0Å range: probe atom residue distance (Å) B Occ A:Br301 b:30.0 occ:0.16 BR A:J1W301 0.0 30.0 0.2 C15 A:J1W301 1.9 33.8 1.0 H151 A:J1W301 2.4 40.5 1.0 H142 A:J1W301 2.5 40.8 1.0 C14 A:J1W301 2.8 34.0 1.0 C17 A:J1W301 2.9 27.3 1.0 O A:HOH417 3.1 25.3 1.0 O18 A:J1W301 3.3 23.8 1.0 H141 A:J1W301 3.4 40.8 1.0 CD1 A:LEU176 3.6 26.4 1.0 H131 A:J1W301 3.8 35.7 1.0 NE2 A:HIS208 3.8 23.1 1.0 C13 A:J1W301 3.9 29.7 1.0 O19 A:J1W301 4.0 29.4 1.0 CD2 A:LEU30 4.0 25.7 1.0 CB A:LEU30 4.0 22.2 1.0 OG A:SER119 4.2 22.9 1.0 H132 A:J1W301 4.3 35.7 1.0 CB A:LEU176 4.3 26.7 1.0 CD2 A:HIS208 4.3 21.9 1.0 CG A:LEU176 4.4 31.9 1.0 OD1 C:ASN64 4.5 23.9 1.0 CD2 A:LEU176 4.5 31.8 1.0 CE1 A:HIS208 4.6 24.0 1.0 CG A:LEU30 4.6 24.3 1.0 CG C:ASN64 4.7 30.9 1.0 ND2 C:ASN64 4.8 30.1 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of APT1 Bound to 2-Bromopalmitate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of APT1 Bound to 2-Bromopalmitate within 5.0Å range: probe atom residue distance (Å) B Occ B:Br301 b:33.4 occ:0.27 BR B:J1W301 0.0 33.4 0.3 C15 B:J1W301 1.9 37.1 1.0 H151 B:J1W301 2.4 44.6 1.0 HD13 B:LEU176 2.7 36.5 1.0 C17 B:J1W301 2.8 29.4 1.0 H132 B:J1W301 2.8 42.8 1.0 C14 B:J1W301 2.9 33.2 1.0 O18 B:J1W301 3.0 26.9 1.0 H131 B:J1W301 3.0 42.8 1.0 C13 B:J1W301 3.1 35.6 1.0 HG B:SER119 3.2 33.8 1.0 H142 B:J1W301 3.3 39.9 1.0 HB3 B:LEU176 3.3 35.1 1.0 O D:HOH428 3.3 26.6 1.0 OG B:SER119 3.5 28.1 1.0 NE2 B:HIS208 3.6 31.2 1.0 H141 B:J1W301 3.7 39.9 1.0 CD1 B:LEU176 3.7 30.4 1.0 HB3 B:LEU30 3.8 35.8 1.0 HD12 B:LEU176 3.9 36.5 1.0 HD22 B:LEU176 4.0 40.5 1.0 HG23 B:VAL177 4.0 34.9 1.0 O19 B:J1W301 4.0 35.4 1.0 CB B:LEU176 4.1 29.2 1.0 HD22 B:LEU30 4.1 35.1 1.0 HB2 B:LEU176 4.2 35.1 1.0 CD2 B:HIS208 4.2 28.2 1.0 HD23 B:LEU30 4.2 35.1 1.0 CE1 B:HIS208 4.2 28.4 1.0 HD11 B:LEU176 4.3 36.5 1.0 HB2 B:LEU30 4.3 35.8 1.0 HD2 B:HIS208 4.3 33.9 1.0 CG B:LEU176 4.3 32.3 1.0 HE1 B:HIS208 4.4 34.1 1.0 CB B:LEU30 4.5 29.8 1.0 C12 B:J1W301 4.6 36.1 1.0 CD2 B:LEU30 4.6 29.3 1.0 CD2 B:LEU176 4.6 33.8 1.0 CG2 B:VAL177 4.7 29.1 1.0 H B:LEU30 4.7 25.9 1.0 CB B:SER119 4.7 26.0 1.0 HG21 B:VAL177 4.7 34.9 1.0 HG22 B:VAL177 4.7 34.9 1.0 HB3 B:SER119 4.8 31.2 1.0 OD1 D:ASN64 4.8 28.3 1.0 H122 B:J1W301 4.9 43.4 1.0 HZ3 B:TRP145 5.0 30.1 1.0 HB2 B:SER119 5.0 31.2 1.0 H121 B:J1W301 5.0 43.4 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of APT1 Bound to 2-Bromopalmitate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of APT1 Bound to 2-Bromopalmitate within 5.0Å range: probe atom residue distance (Å) B Occ C:Br301 b:35.5 occ:0.29 BR C:J1W301 0.0 35.5 0.3 C15 C:J1W301 1.9 34.9 1.0 H151 C:J1W301 2.4 41.8 1.0 H132 C:J1W301 2.7 43.2 1.0 H131 C:J1W301 2.8 43.2 1.0 C14 C:J1W301 2.9 34.0 1.0 C17 C:J1W301 2.9 31.3 1.0 C13 C:J1W301 3.0 36.0 1.0 O18 C:J1W301 3.0 30.3 1.0 NE2 C:HIS208 3.3 21.9 1.0 H141 C:J1W301 3.4 40.8 1.0 O C:HOH420 3.5 25.5 1.0 H142 C:J1W301 3.6 40.8 1.0 OG C:SER119 3.6 30.9 1.0 CB C:LEU176 3.9 29.9 1.0 CE1 C:HIS208 4.0 23.8 1.0 CD1 C:LEU176 4.0 20.6 1.0 O19 C:J1W301 4.1 34.2 1.0 CD2 C:HIS208 4.1 22.3 1.0 CG C:LEU176 4.3 22.4 1.0 CD2 C:LEU176 4.4 20.7 1.0 C12 C:J1W301 4.5 38.5 1.0 CD2 C:LEU30 4.6 26.9 1.0 CB C:LEU30 4.7 23.7 1.0 CG2 C:VAL177 4.7 27.0 1.0 CB C:SER119 4.7 25.2 1.0 OD1 A:ASN64 4.8 28.6 1.0 H121 C:J1W301 4.9 46.2 1.0 H122 C:J1W301 4.9 46.2 1.0 ND1 C:HIS208 4.9 20.5 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of APT1 Bound to 2-Bromopalmitate


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of APT1 Bound to 2-Bromopalmitate within 5.0Å range: probe atom residue distance (Å) B Occ D:Br301 b:30.4 occ:0.20 BR D:J1W301 0.0 30.4 0.2 C15 D:J1W301 1.9 35.2 1.0 H151 D:J1W301 2.5 42.3 1.0 H142 D:J1W301 2.6 42.5 1.0 C14 D:J1W301 2.8 35.4 1.0 C17 D:J1W301 2.8 25.5 1.0 O18 D:J1W301 3.1 30.8 1.0 O B:HOH457 3.2 27.0 1.0 H141 D:J1W301 3.4 42.5 1.0 NE2 D:HIS208 3.6 25.2 1.0 OG D:SER119 3.7 26.2 1.0 CD1 D:LEU176 3.8 33.3 1.0 O19 D:J1W301 3.8 29.9 1.0 C13 D:J1W301 3.9 34.1 1.0 H131 D:J1W301 3.9 41.0 1.0 H132 D:J1W301 4.1 41.0 1.0 CD2 D:HIS208 4.2 24.3 1.0 CB D:LEU30 4.2 19.7 1.0 CB D:LEU176 4.3 28.4 1.0 OD1 B:ASN64 4.3 24.0 1.0 CD2 D:LEU30 4.3 33.2 1.0 CE1 D:HIS208 4.4 28.6 1.0 CG D:LEU176 4.4 27.1 1.0 CD2 D:LEU176 4.5 29.8 1.0 CB D:SER119 4.8 28.1 1.0 CG2 D:VAL177 4.9 20.2 1.0 CG B:ASN64 4.9 35.8 1.0 CG D:LEU30 5.0 28.1 1.0

M.Audagnotto, S.Ho, L.Abrami, M.J.Marcaida, G.Fonti, F.Pojer, G.Van Der Goot, M.Dal Peraro. Insights Into the Molecular Mechanism of Depalmitoylation By Human Acyl-Protein Thioesterases To Be Published.