Nickel in PDB 4i8c: X-Ray Structure of Nika in Complex with Ni-(L-His)2

The structure of X-Ray Structure of Nika in Complex with Ni-(L-His)2, PDB code: 4i8c was solved by H.Lebrette, M.Iannello, J.C.Fontecilla-Camps, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.50 / 2.50
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	158.630, 158.630, 135.820, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 23.4

The structure of X-Ray Structure of Nika in Complex with Ni-(L-His)2 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the X-Ray Structure of Nika in Complex with Ni-(L-His)2 (pdb code 4i8c). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the X-Ray Structure of Nika in Complex with Ni-(L-His)2, PDB code: 4i8c:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the X-Ray Structure of Nika in Complex with Ni-(L-His)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of X-Ray Structure of Nika in Complex with Ni-(L-His)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni603 b:55.8 occ:1.00 OXT A:HIS601 2.0 48.9 1.0 N A:HIS601 2.2 45.5 1.0 ND1 A:HIS601 2.2 49.8 1.0 N A:HIS602 2.4 54.4 0.7 NE2 A:HIS416 2.4 58.6 1.0 ND1 A:HIS602 2.5 58.5 0.7 C A:HIS601 2.7 44.2 1.0 CA A:HIS601 2.8 41.0 1.0 CG A:HIS601 3.1 47.1 1.0 CE1 A:HIS416 3.2 55.0 1.0 CE1 A:HIS601 3.2 38.8 1.0 CG A:HIS602 3.3 64.5 0.7 CE1 A:HIS602 3.4 59.0 0.7 CB A:HIS601 3.4 47.0 1.0 CA A:HIS602 3.5 59.1 0.7 CD2 A:HIS416 3.6 57.8 1.0 CB A:HIS602 3.6 63.5 0.7 O A:HIS601 3.9 38.5 1.0 CD2 A:HIS601 4.2 44.3 1.0 NE2 A:HIS601 4.2 41.6 1.0 ND1 A:HIS416 4.4 60.5 1.0 O A:HOH729 4.4 49.4 1.0 NE2 A:HIS602 4.4 70.1 0.7 CD2 A:HIS602 4.4 69.8 0.7 NH2 A:ARG137 4.6 40.5 1.0 CZ2 A:TRP398 4.6 39.0 1.0 CG A:HIS416 4.6 59.6 1.0 CE2 A:TRP398 4.8 38.7 1.0 C A:HIS602 4.8 73.0 0.7 NE1 A:TRP398 4.8 38.7 1.0

Nickel binding site 2 out of 3 in the X-Ray Structure of Nika in Complex with Ni-(L-His)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of X-Ray Structure of Nika in Complex with Ni-(L-His)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni603 b:39.5 occ:1.00 N B:HIS602 1.9 39.7 0.9 OXT B:HIS601 2.0 38.1 1.0 NE2 B:HIS416 2.0 41.7 1.0 N B:HIS601 2.2 38.7 1.0 ND1 B:HIS601 2.3 42.4 1.0 ND1 B:HIS602 2.3 45.5 0.9 C B:HIS601 2.8 39.1 1.0 CE1 B:HIS416 2.9 43.7 1.0 CA B:HIS602 2.9 47.4 0.9 CA B:HIS601 2.9 37.0 1.0 CG B:HIS602 3.1 45.9 0.9 CD2 B:HIS416 3.1 50.4 1.0 CE1 B:HIS601 3.1 35.3 1.0 CB B:HIS602 3.2 49.6 0.9 CG B:HIS601 3.3 42.7 1.0 CE1 B:HIS602 3.4 52.4 0.9 CB B:HIS601 3.7 39.1 1.0 O B:HIS601 4.0 35.9 1.0 ND1 B:HIS416 4.1 46.6 1.0 CG B:HIS416 4.2 45.5 1.0 C B:HIS602 4.2 56.5 0.9 CD2 B:HIS602 4.3 58.1 0.9 NE2 B:HIS601 4.3 34.5 1.0 O B:HOH754 4.4 49.6 1.0 NE2 B:HIS602 4.4 57.5 0.9 NH2 B:ARG137 4.4 38.4 1.0 CD2 B:HIS601 4.4 44.1 1.0 OXT B:HIS602 4.5 61.6 0.9 CZ2 B:TRP398 4.6 39.8 1.0 CE2 B:TRP398 4.9 40.0 1.0 CH2 B:TRP398 4.9 32.8 1.0

Nickel binding site 3 out of 3 in the X-Ray Structure of Nika in Complex with Ni-(L-His)2


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of X-Ray Structure of Nika in Complex with Ni-(L-His)2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni603 b:56.1 occ:1.00 N C:HIS601 2.0 51.7 1.0 N C:HIS602 2.0 56.3 0.8 OXT C:HIS601 2.1 57.1 1.0 ND1 C:HIS602 2.1 61.2 0.8 NE2 C:HIS416 2.2 54.8 1.0 ND1 C:HIS601 2.2 54.6 1.0 C C:HIS601 2.7 51.8 1.0 CA C:HIS601 2.8 53.4 1.0 CA C:HIS602 3.1 60.0 0.8 CG C:HIS602 3.1 63.7 0.8 CE1 C:HIS602 3.1 66.9 0.8 CE1 C:HIS416 3.1 48.5 1.0 CE1 C:HIS601 3.2 48.3 1.0 CD2 C:HIS416 3.2 53.2 1.0 CG C:HIS601 3.2 59.5 1.0 CB C:HIS602 3.4 63.7 0.8 CB C:HIS601 3.5 53.7 1.0 O C:HIS601 3.9 47.0 1.0 NE2 C:HIS602 4.2 72.7 0.8 CD2 C:HIS602 4.2 70.5 0.8 ND1 C:HIS416 4.2 56.5 1.0 NE2 C:HIS601 4.3 57.8 1.0 CG C:HIS416 4.3 54.2 1.0 CD2 C:HIS601 4.3 55.2 1.0 C C:HIS602 4.4 68.5 0.8 O C:HOH711 4.5 56.8 1.0 CZ2 C:TRP398 4.6 54.6 1.0 NH2 C:ARG137 4.6 55.8 1.0 OXT C:HIS602 4.7 78.9 0.8 CE2 C:TRP398 4.8 56.7 1.0

H.Lebrette, M.Iannello, J.C.Fontecilla-Camps, C.Cavazza. The Binding Mode of Ni-((L)-His)(2) in Nika Revealed By X-Ray Crystallography. J.Inorg.Biochem. V.121C 16 2012.
ISSN: ISSN 0162-0134
PubMed: 23314594
DOI: 10.1016/J.JINORGBIO.2012.12.010