Nickel in PDB 8ji4: Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan

The structure of Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan, PDB code: 8ji4 was solved by H.Li, L.Dai, H.B.Zheng, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.39 / 1.67
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	65.417, 65.417, 116.617, 90, 90, 90
R / Rfree (%)	17.2 / 20.7

The structure of Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan also contains other interesting chemical elements:

Bromine	(Br)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Nickel atom in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan (pdb code 8ji4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan, PDB code: 8ji4:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan


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 Aetd in Complex with 5-Bromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:31.8 occ:1.00 O A:HOH449 2.1 33.3 1.0 O A:HOH484 2.1 29.8 1.0 O3 A:TRS306 2.2 28.6 1.0 ND1 A:HIS72 2.2 34.9 1.0 O A:HOH529 2.2 34.8 1.0 N A:TRS306 2.3 33.0 1.0 C3 A:TRS306 2.9 30.7 1.0 C A:TRS306 3.0 28.8 1.0 CE1 A:HIS72 3.0 38.4 1.0 CG A:HIS72 3.3 33.2 1.0 C1 A:TRS306 3.7 33.2 1.0 CB A:HIS72 3.7 31.4 1.0 OD1 A:ASP76 4.0 32.8 1.0 O A:GLU176 4.0 33.4 1.0 CA A:HIS72 4.2 28.7 1.0 O1 A:TRS306 4.2 35.5 1.0 NE2 A:HIS72 4.2 34.7 1.0 OD2 A:ASP76 4.2 32.8 1.0 O A:HOH540 4.3 47.2 1.0 C2 A:TRS306 4.3 35.3 1.0 CD2 A:HIS72 4.4 35.5 1.0 O A:HIS72 4.4 27.4 1.0 CG A:ASP76 4.5 35.0 1.0 O A:HOH454 4.7 36.0 1.0 C A:HIS72 4.7 30.9 1.0 OD1 A:ASN185 4.8 44.8 1.0

Nickel binding site 2 out of 5 in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan


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 Aetd in Complex with 5-Bromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:48.2 occ:1.00 NE2 A:HIS228 2.1 34.2 1.0 CD2 A:HIS228 2.8 37.2 1.0 CE1 A:HIS228 3.3 31.1 1.0 O A:HOH558 3.3 40.4 1.0 CG A:HIS228 4.0 32.0 1.0 ND1 A:HIS228 4.2 35.0 1.0 OE1 A:GLU231 4.4 59.6 1.0 OH A:TYR224 4.6 42.0 1.0

Nickel binding site 3 out of 5 in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan


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 Aetd in Complex with 5-Bromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:38.1 occ:1.00 NE2 A:HIS125 2.0 36.1 1.0 NE2 B:HIS125 2.1 31.0 1.0 O A:HOH515 2.1 32.5 1.0 O B:HOH405 2.2 42.9 1.0 O B:HOH512 2.2 45.9 1.0 O A:HOH417 2.2 39.7 1.0 O B:HOH547 2.9 52.3 1.0 CD2 A:HIS125 3.0 35.3 1.0 CE1 A:HIS125 3.0 41.6 1.0 CE1 B:HIS125 3.0 33.5 1.0 CD2 B:HIS125 3.1 33.5 1.0 O B:HOH542 3.9 54.6 1.0 N A:TRS307 4.0 36.8 1.0 OD2 B:ASP126 4.0 43.0 1.0 OD2 A:ASP126 4.1 43.6 1.0 ND1 A:HIS125 4.1 36.0 1.0 CG A:HIS125 4.1 37.2 1.0 ND1 B:HIS125 4.2 30.2 1.0 CG B:HIS125 4.2 26.8 1.0 O A:HOH414 4.3 38.7 1.0 CB B:ASP126 4.5 33.8 1.0 CG A:ASP126 4.5 42.5 1.0 O A:VAL122 4.6 32.5 1.0 CG B:ASP126 4.6 38.1 1.0 OD1 A:ASP126 4.7 40.5 1.0

Nickel binding site 4 out of 5 in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan


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 Aetd in Complex with 5-Bromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:53.1 occ:1.00 NE2 B:HIS72 2.2 55.0 1.0 OE1 B:GLU140 2.2 54.0 1.0 O B:HOH419 2.2 40.8 1.0 O B:HOH404 2.3 43.2 1.0 OD2 B:ASP76 2.3 39.7 1.0 O B:HOH488 2.5 41.2 1.0 CD2 B:HIS72 2.9 55.0 1.0 CG B:ASP76 3.0 38.3 1.0 OD1 B:ASP76 3.0 37.4 1.0 CE1 B:HIS72 3.0 60.4 1.0 CD B:GLU140 3.3 52.3 1.0 O B:HOH414 3.7 52.0 1.0 OE2 B:GLU140 3.8 59.8 1.0 CG B:HIS72 3.9 49.6 1.0 ND1 B:HIS72 3.9 54.4 1.0 O B:GLU176 4.1 51.2 1.0 O B:HOH533 4.4 60.1 1.0 CB B:ASP76 4.5 29.3 1.0 OE1 B:GLU176 4.5 48.3 1.0 O B:HOH401 4.5 43.6 1.0 CG B:GLU140 4.6 43.3 1.0 O B:HOH502 4.6 42.5 1.0 O B:HIS72 4.7 37.0 1.0 CA B:GLU176 4.9 48.5 1.0 C B:GLU176 5.0 52.8 1.0

Nickel binding site 5 out of 5 in the Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:44.5 occ:1.00 O B:HOH492 2.0 38.3 1.0 NE2 B:HIS228 2.1 32.3 1.0 O B:HOH507 2.1 46.9 1.0 O B:HOH520 2.2 46.8 1.0 O B:HOH552 2.3 43.5 1.0 O B:HOH519 2.5 42.2 1.0 CE1 B:HIS228 3.0 33.6 1.0 CD2 B:HIS228 3.1 34.4 1.0 O B:HOH517 4.0 42.7 1.0 ND1 B:HIS228 4.1 25.4 1.0 CG B:HIS228 4.2 29.5 1.0 CE2 B:TYR224 4.4 26.0 1.0 OH B:TYR224 4.5 32.4 1.0 O B:HOH538 4.6 47.3 1.0 O B:HOH518 4.7 53.4 1.0 CZ B:TYR224 4.8 28.8 1.0

H.Li, L.Dai, H.B.Zheng, C.-C.Chen, R.-T.Guo. Crystal Structure of Aetd in Complex with 5-Bromo-L-Tryptophan To Be Published.