Nickel in PDB 8ji2: Crystal Structure of Aetd in Complex with 5,7-Dibromo-L-Tryptophan

The structure of Crystal Structure of Aetd in Complex with 5,7-Dibromo-L-Tryptophan, PDB code: 8ji2 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)	22.64 / 1.75
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	65.227, 65.227, 116.859, 90, 90, 90
R / Rfree (%)	17.1 / 21.9

The structure of Crystal Structure of Aetd in Complex with 5,7-Dibromo-L-Tryptophan also contains other interesting chemical elements:

Bromine	(Br)	6 atoms
Iron	(Fe)	2 atoms

The binding sites of Nickel atom in the Crystal Structure of Aetd in Complex with 5,7-Dibromo-L-Tryptophan (pdb code 8ji2). 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 5,7-Dibromo-L-Tryptophan, PDB code: 8ji2:
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 5,7-Dibromo-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 5,7-Dibromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:38.5 occ:1.00 O A:HOH440 2.0 40.9 1.0 ND1 A:HIS72 2.2 40.0 1.0 O A:HOH513 2.2 43.7 1.0 O A:HOH466 2.2 36.2 1.0 N A:TRS307 2.2 40.4 1.0 O2 A:TRS307 2.3 35.7 1.0 CE1 A:HIS72 3.0 46.0 1.0 C2 A:TRS307 3.0 37.9 1.0 C A:TRS307 3.1 35.4 1.0 CG A:HIS72 3.3 41.6 1.0 C1 A:TRS307 3.7 37.0 1.0 CB A:HIS72 3.7 37.1 1.0 O A:GLU176 4.0 38.7 1.0 OD1 A:ASP76 4.1 43.8 1.0 CA A:HIS72 4.2 34.9 1.0 NE2 A:HIS72 4.2 40.7 1.0 OD2 A:ASP76 4.3 39.1 1.0 CD2 A:HIS72 4.3 45.0 1.0 C3 A:TRS307 4.4 43.7 1.0 O1 A:TRS307 4.4 41.2 1.0 O A:HIS72 4.5 34.5 1.0 CG A:ASP76 4.6 45.1 1.0 C A:HIS72 4.8 35.0 1.0 ND2 A:ASN185 4.8 38.5 1.0

Nickel binding site 2 out of 5 in the Crystal Structure of Aetd in Complex with 5,7-Dibromo-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 5,7-Dibromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:45.4 occ:1.00 NE2 B:HIS125 2.1 34.9 1.0 O A:HOH503 2.1 43.6 1.0 NE2 A:HIS125 2.2 45.4 1.0 O B:HOH508 2.2 54.7 1.0 O B:HOH402 2.2 46.9 1.0 O A:HOH403 2.2 46.6 1.0 CE1 B:HIS125 3.0 39.1 1.0 CD2 B:HIS125 3.1 37.8 1.0 CD2 A:HIS125 3.1 40.9 1.0 CE1 A:HIS125 3.2 47.9 1.0 OD2 A:ASP126 3.7 56.8 1.0 OD2 B:ASP126 4.1 53.1 1.0 ND1 B:HIS125 4.1 35.5 1.0 CG B:HIS125 4.2 34.8 1.0 ND1 A:HIS125 4.3 41.3 1.0 CG A:HIS125 4.3 43.1 1.0 O A:HOH454 4.3 39.7 1.0 CG A:ASP126 4.4 50.4 1.0 O A:VAL122 4.5 37.6 1.0 CB B:ASP126 4.6 43.3 1.0 CG B:ASP126 4.6 46.3 1.0 O A:HOH417 4.7 54.9 1.0 OD1 A:ASP126 4.7 52.5 1.0

Nickel binding site 3 out of 5 in the Crystal Structure of Aetd in Complex with 5,7-Dibromo-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 5,7-Dibromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni306 b:40.3 occ:1.00 OXT A:67I303 2.1 33.2 1.0 ND1 A:HIS179 2.2 42.0 1.0 O A:HIS179 2.2 44.9 1.0 N A:67I303 2.3 50.5 1.0 C A:67I303 2.8 47.1 1.0 CA A:67I303 3.0 50.7 1.0 CE1 A:HIS179 3.0 42.7 1.0 CG A:HIS179 3.2 46.5 1.0 C A:HIS179 3.3 49.4 1.0 CD1 A:67I303 3.4 78.6 1.0 CB A:HIS179 3.6 44.2 1.0 O A:HOH401 3.7 54.0 1.0 CB A:67I303 3.7 61.7 1.0 CA A:HIS179 3.9 44.6 1.0 O A:67I303 4.0 44.8 1.0 CG A:67I303 4.0 74.1 1.0 NE2 A:HIS179 4.2 42.9 1.0 CD2 A:HIS179 4.3 46.4 1.0 N A:ALA180 4.4 53.0 1.0 NE1 A:67I303 4.4 87.9 1.0 N A:HIS179 4.7 47.3 1.0 CA A:ALA180 4.8 62.4 1.0

Nickel binding site 4 out of 5 in the Crystal Structure of Aetd in Complex with 5,7-Dibromo-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 5,7-Dibromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:69.1 occ:1.00 O B:HOH404 2.1 38.5 1.0 O B:HOH405 2.3 44.2 1.0 O B:HOH530 2.5 55.0 1.0 NE2 B:HIS72 2.6 70.4 1.0 OD2 B:ASP76 2.6 40.8 1.0 OE2 B:GLU140 2.8 74.0 1.0 OD1 B:ASP76 3.0 40.7 1.0 CE1 B:HIS72 3.1 73.3 1.0 CG B:ASP76 3.1 41.0 1.0 CD2 B:HIS72 3.2 63.5 1.0 CD B:GLU140 3.6 61.3 1.0 ND1 B:HIS72 3.8 67.2 1.0 OE1 B:GLU140 3.9 60.5 1.0 CG B:HIS72 3.9 57.9 1.0 OE2 B:GLU176 4.4 57.9 1.0 CB B:ASP76 4.6 31.2 1.0 O B:GLU176 4.6 75.3 1.0 O B:HIS72 4.6 43.8 1.0 CG B:GLU140 4.7 49.1 1.0 O B:HOH420 4.8 51.0 1.0 O B:HOH414 4.8 61.7 1.0

Nickel binding site 5 out of 5 in the Crystal Structure of Aetd in Complex with 5,7-Dibromo-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 5,7-Dibromo-L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:48.3 occ:1.00 O B:HOH489 1.9 42.8 1.0 O B:HOH473 2.0 57.5 1.0 O B:HOH468 2.0 47.5 1.0 NE2 B:HIS228 2.1 39.8 1.0 O B:HOH538 2.2 53.2 1.0 O B:HOH506 2.2 45.0 1.0 CE1 B:HIS228 3.1 37.4 1.0 CD2 B:HIS228 3.1 35.8 1.0 O B:HOH501 4.1 47.4 1.0 O B:HOH544 4.2 56.9 1.0 ND1 B:HIS228 4.2 30.7 1.0 CG B:HIS228 4.2 34.2 1.0 CE1 B:TYR224 4.5 29.4 1.0 OH B:TYR224 4.5 35.9 1.0 O B:HOH549 4.7 62.1 1.0 CZ B:TYR224 4.8 33.5 1.0

H.Li, L.Dai, H.B.Zheng, C.-C.Chen, R.-T.Guo. Crystal Structure of Aetd in Complex with 5,7-Dibromo-L-Tryptophan To Be Published.