Nickel in PDB 4ofl: Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2

The structure of Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2, PDB code: 4ofl was solved by H.Lebrette, C.Cavazza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.45 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.040, 213.830, 52.870, 90.00, 102.72, 90.00
R / Rfree (%)	19.3 / 23.4

The binding sites of Nickel atom in the Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2 (pdb code 4ofl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2, PDB code: 4ofl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Ynta From Yersinia Pestis 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 Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:38.1 occ:1.00 O A:HIS503 1.8 65.9 0.9 ND1 A:HIS503 1.8 61.5 0.9 N A:HIS502 2.0 25.1 1.0 ND1 A:HIS502 2.2 24.5 1.0 NE2 A:HIS482 2.2 37.4 1.0 OXT A:HIS502 2.3 31.3 1.0 CE1 A:HIS503 2.5 61.3 0.9 CA A:HIS502 2.8 23.8 1.0 C A:HIS503 2.9 63.2 0.9 C A:HIS502 2.9 26.5 1.0 CE1 A:HIS482 3.0 36.1 1.0 CG A:HIS503 3.0 61.7 0.9 CE1 A:HIS502 3.1 23.3 1.0 CG A:HIS502 3.2 25.5 1.0 CD2 A:HIS482 3.4 35.4 1.0 CB A:HIS502 3.6 22.5 1.0 CA A:HIS503 3.6 61.5 0.9 CB A:HIS503 3.6 61.2 0.9 NE2 A:HIS503 3.7 63.5 0.9 OXT A:HIS503 3.8 61.0 0.9 CD2 A:HIS503 4.0 62.4 0.9 O A:HIS502 4.1 26.9 1.0 O A:GLY384 4.1 25.3 1.0 ND1 A:HIS482 4.2 35.0 1.0 NE2 A:HIS502 4.3 23.7 1.0 CD2 A:HIS502 4.3 24.8 1.0 CG A:HIS482 4.4 33.6 1.0 CZ2 A:TRP369 4.8 24.1 1.0 NH2 A:ARG344 5.0 40.9 1.0 N A:HIS503 5.0 59.3 0.9

Nickel binding site 2 out of 2 in the Crystal Structure of Ynta From Yersinia Pestis 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 Crystal Structure of Ynta From Yersinia Pestis in Complex with Ni(L- His)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:62.3 occ:1.00 N B:HIS502 1.9 44.3 1.0 ND1 B:HIS503 2.0 87.7 0.9 O B:HIS503 2.1 73.8 0.9 OXT B:HIS502 2.1 58.8 1.0 ND1 B:HIS502 2.3 47.1 1.0 NE2 B:HIS482 2.5 54.3 1.0 CE1 B:HIS503 2.6 89.3 0.9 CA B:HIS502 2.7 46.2 1.0 C B:HIS502 2.7 52.7 1.0 C B:HIS503 3.1 75.2 0.9 CG B:HIS502 3.2 45.6 1.0 CE1 B:HIS502 3.2 48.0 1.0 CG B:HIS503 3.3 85.1 0.9 CE1 B:HIS482 3.3 53.2 1.0 CB B:HIS502 3.5 44.4 1.0 CD2 B:HIS482 3.5 52.8 1.0 NE2 B:HIS503 3.9 88.8 0.9 CB B:HIS503 3.9 81.7 0.9 O B:HIS502 3.9 50.0 1.0 CA B:HIS503 3.9 79.1 0.9 OXT B:HIS503 4.0 73.4 0.9 CD2 B:HIS503 4.2 87.3 0.9 NE2 B:HIS502 4.3 46.1 1.0 CD2 B:HIS502 4.4 44.9 1.0 O B:GLY384 4.4 40.4 1.0 ND1 B:HIS482 4.5 53.1 1.0 CG B:HIS482 4.6 51.2 1.0 NH2 B:ARG344 4.9 53.2 1.0 CZ2 B:TRP369 4.9 40.6 1.0

H.Lebrette, C.Brochier-Armanet, B.Zambelli, H.De Reuse, E.Borezee-Durant, S.Ciurli, C.Cavazza. Promiscuous Nickel Import in Human Pathogens: Structure, Thermodynamics, and Evolution of Extracytoplasmic Nickel-Binding Proteins. Structure 2014.
ISSN: ISSN 0969-2126
PubMed: 25199691
DOI: 10.1016/J.STR.2014.07.012