Nickel in PDB 3de9: Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination

The structure of Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination, PDB code: 3de9 was solved by E.N.Salgado, R.A.Lewis, A.L.Rheingold, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.52 / 2.04
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	51.042, 51.042, 121.971, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 27.8

The structure of Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Nickel atom in the Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination (pdb code 3de9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination, PDB code: 3de9:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination


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 A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni107 b:29.3 occ:0.33 NE2 A:HIS63 2.1 30.8 1.0 NE2 A:HIS59 2.2 30.9 1.0 CE1 A:HIS63 3.0 31.2 1.0 CD2 A:HIS63 3.1 29.0 1.0 CD2 A:HIS59 3.2 29.4 1.0 CE1 A:HIS59 3.2 35.1 1.0 ND1 A:HIS63 4.1 29.4 1.0 CG A:HIS63 4.2 27.2 1.0 CG A:HIS59 4.3 31.6 1.0 ND1 A:HIS59 4.3 35.1 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination


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 A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni108 b:18.4 occ:0.33 NE2 A:HIS77 2.2 12.7 1.0 NE2 A:HIS73 2.2 8.2 1.0 CE1 A:HIS77 3.1 17.4 1.0 CE1 A:HIS73 3.1 15.8 1.0 CD2 A:HIS77 3.2 16.8 1.0 CD2 A:HIS73 3.2 13.0 1.0 ND1 A:HIS77 4.3 19.1 1.0 ND1 A:HIS73 4.3 14.1 1.0 CG A:HIS77 4.3 17.3 1.0 CG A:HIS73 4.4 13.6 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination


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 A Trimeric Cytochrome CB562 Assembly Induced By Nickel Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni109 b:67.0 occ:1.00 O A:ALA1 2.0 36.1 1.0 N A:ALA1 2.0 36.6 1.0 OD2 A:ASP39 2.6 30.5 1.0 C A:ALA1 2.8 36.5 1.0 CA A:ALA1 3.0 36.9 1.0 OD1 A:ASP39 3.1 26.6 1.0 NZ A:LYS42 3.1 33.8 1.0 CG A:ASP39 3.1 27.6 1.0 N A:ASP2 4.1 36.8 1.0 CB A:ALA1 4.1 37.4 1.0 CE A:LYS42 4.1 34.9 1.0 ND2 A:ASN6 4.3 30.3 1.0 CD A:LYS42 4.3 33.4 1.0 CB A:ASP39 4.5 26.3 1.0 O A:ASP39 4.6 28.3 1.0 CG A:LYS42 4.7 33.3 1.0 CA A:ASP2 4.8 37.1 1.0

E.N.Salgado, R.A.Lewis, S.Mossin, A.L.Rheingold, F.A.Tezcan. Control of Protein Oligomerization Symmetry By Metal Coordination: C2 and C3 Symmetrical Assemblies Through Cu(II) and Ni(II) Coordination. Inorg.Chem. V. 48 2726 2009.
ISSN: ISSN 0020-1669
PubMed: 19267481
DOI: 10.1021/IC9001237