Nickel in PDB 8ji6: Crystal Structure of Aetd in Complex with L-Tryptophan

The structure of Crystal Structure of Aetd in Complex with L-Tryptophan, PDB code: 8ji6 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)	24.59 / 1.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	65.289, 65.289, 116.145, 90, 90, 90
R / Rfree (%)	17.4 / 22.7

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

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Aetd in Complex with L-Tryptophan (pdb code 8ji6). 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 L-Tryptophan, PDB code: 8ji6:
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 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 L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:22.1 occ:1.00 O A:HOH483 2.1 20.7 1.0 O A:HOH503 2.1 15.6 1.0 O A:HOH545 2.1 27.4 1.0 ND1 A:HIS72 2.2 21.1 1.0 O1 A:TRS306 2.2 19.2 1.0 N A:TRS306 2.3 25.3 1.0 C1 A:TRS306 3.0 22.6 1.0 CE1 A:HIS72 3.0 22.0 1.0 C A:TRS306 3.1 24.5 1.0 CG A:HIS72 3.3 21.6 1.0 C2 A:TRS306 3.6 26.9 1.0 CB A:HIS72 3.7 19.4 1.0 OD1 A:ASP76 4.0 24.3 1.0 O A:GLU176 4.0 23.5 1.0 CA A:HIS72 4.1 19.3 1.0 OD2 A:ASP76 4.2 26.5 1.0 O2 A:TRS306 4.2 26.8 1.0 NE2 A:HIS72 4.2 20.7 1.0 CD2 A:HIS72 4.3 22.1 1.0 O A:HIS72 4.4 17.5 1.0 O A:HOH582 4.4 34.0 1.0 C3 A:TRS306 4.4 25.7 1.0 OE1 A:GLU75 4.5 47.3 1.0 CG A:ASP76 4.5 26.5 1.0 C A:HIS72 4.7 18.4 1.0 O A:HOH477 4.8 20.5 1.0 OD1 A:ASN185 4.9 34.2 1.0

Nickel binding site 2 out of 5 in the Crystal Structure of Aetd in Complex with 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 L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:33.0 occ:1.00 O A:HOH505 2.1 25.4 1.0 ND1 A:HIS179 2.2 31.3 1.0 O A:HIS179 2.4 36.9 1.0 O A:HOH557 2.5 29.3 1.0 CE1 A:HIS179 3.1 30.8 1.0 CG A:HIS179 3.3 32.1 1.0 C A:HIS179 3.3 33.4 1.0 CB A:HIS179 3.7 32.7 1.0 CA A:HIS179 4.1 31.0 1.0 NE2 A:HIS179 4.2 33.5 1.0 CD2 A:HIS179 4.3 35.1 1.0 N A:HIS179 4.9 31.4 1.0

Nickel binding site 3 out of 5 in the Crystal Structure of Aetd in Complex with 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 L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:39.2 occ:1.00 O B:HOH418 2.0 53.3 1.0 NE2 B:HIS125 2.2 26.4 1.0 O A:HOH431 2.2 34.0 1.0 NE2 A:HIS125 2.3 32.8 1.0 O A:HOH571 2.3 35.9 1.0 O B:HOH537 2.4 42.8 1.0 CD2 B:HIS125 3.1 25.9 1.0 CD2 A:HIS125 3.2 32.2 1.0 CE1 B:HIS125 3.2 25.9 1.0 CE1 A:HIS125 3.3 33.2 1.0 O B:HOH560 3.9 37.0 1.0 OD2 A:ASP126 4.0 40.0 1.0 ND1 B:HIS125 4.3 24.1 1.0 O A:HOH475 4.3 29.8 1.0 CG B:HIS125 4.3 22.2 1.0 O A:HOH445 4.3 40.4 1.0 CG A:HIS125 4.4 30.2 1.0 ND1 A:HIS125 4.4 31.8 1.0 OD2 B:ASP126 4.4 36.9 1.0 CB B:ASP126 4.4 31.1 1.0 CG A:ASP126 4.5 36.9 1.0 OD1 A:ASP126 4.7 41.3 1.0 O A:VAL122 4.7 24.4 1.0 CG B:ASP126 4.8 35.4 1.0

Nickel binding site 4 out of 5 in the Crystal Structure of Aetd in Complex with 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 L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:67.2 occ:1.00 O B:HOH518 2.1 39.6 1.0 ND1 B:HIS72 2.4 53.2 1.0 O B:HOH426 2.4 41.0 1.0 CE1 B:HIS72 3.2 53.8 1.0 CG B:HIS72 3.4 48.4 1.0 CB B:HIS72 3.7 38.7 1.0 O B:HOH541 4.0 34.0 1.0 O B:GLU176 4.2 49.7 1.0 CA B:HIS72 4.2 35.3 1.0 NE2 B:HIS72 4.3 49.7 1.0 CD2 B:HIS72 4.4 50.0 1.0 OD2 B:ASP76 4.5 37.5 1.0 O B:GLY178 4.6 44.0 1.0 O B:HIS72 4.6 33.6 1.0 C B:HIS72 4.9 33.7 1.0 OE1 B:GLU140 5.0 39.5 1.0 O B:VAL175 5.0 43.2 1.0

Nickel binding site 5 out of 5 in the Crystal Structure of Aetd in Complex with 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 L-Tryptophan within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:38.1 occ:1.00 O B:HOH491 2.0 26.9 1.0 NE2 B:HIS228 2.1 22.5 1.0 O B:HOH512 2.2 45.7 1.0 O B:HOH565 2.2 31.9 1.0 O B:HOH508 2.3 25.5 1.0 O B:HOH561 2.9 34.4 1.0 CE1 B:HIS228 3.1 23.2 1.0 CD2 B:HIS228 3.1 20.5 1.0 O B:HOH499 3.9 33.9 1.0 ND1 B:HIS228 4.2 20.6 1.0 CG B:HIS228 4.2 21.3 1.0 CE1 B:TYR224 4.4 14.9 1.0 O B:HOH551 4.6 38.0 1.0 OH B:TYR224 4.6 18.0 1.0 CZ B:TYR224 4.9 16.0 1.0 O B:HOH573 4.9 47.0 1.0

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