Nickel in PDB 4ofo: Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form

The structure of Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form, PDB code: 4ofo 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)	47.93 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.230, 144.690, 149.190, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.4

The binding sites of Nickel atom in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form (pdb code 4ofo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form, PDB code: 4ofo:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form


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, Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni501 b:48.2 occ:1.00 OE1 A:GLU105 1.9 34.7 1.0 NE2 B:HIS244 2.0 52.0 1.0 O B:HOH606 2.1 56.9 1.0 O A:HOH606 2.3 21.5 1.0 CE1 B:HIS244 2.5 49.7 1.0 OE2 A:GLU105 2.5 32.3 1.0 NE2 A:HIS115 2.5 36.9 1.0 CD A:GLU105 2.5 31.5 1.0 CD2 A:HIS115 3.2 39.1 1.0 CD2 B:HIS244 3.3 51.4 1.0 CE1 A:HIS115 3.4 35.8 1.0 ND1 B:HIS244 3.7 44.5 1.0 CG A:GLU105 4.0 30.8 1.0 CG B:HIS244 4.1 45.6 1.0 CG A:HIS115 4.3 37.3 1.0 ND1 A:HIS115 4.4 34.9 1.0 NH1 A:ARG113 4.6 44.9 1.0 CB A:GLU105 5.0 31.4 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form


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, Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni501 b:58.7 occ:1.00 OE1 B:GLU105 1.8 49.7 1.0 NE2 A:HIS244 1.9 59.7 1.0 O A:HOH607 2.3 41.5 1.0 CD B:GLU105 2.4 42.5 1.0 OE2 B:GLU105 2.4 34.7 1.0 CE1 A:HIS244 2.4 56.7 1.0 O A:HOH608 2.4 34.5 1.0 NE2 B:HIS115 2.4 46.7 1.0 CD2 A:HIS244 3.2 59.3 1.0 CD2 B:HIS115 3.2 47.4 1.0 CE1 B:HIS115 3.5 48.3 1.0 ND1 A:HIS244 3.6 52.3 1.0 CG B:GLU105 3.8 42.1 1.0 CG A:HIS244 4.0 53.5 1.0 CG B:HIS115 4.4 46.1 1.0 ND1 B:HIS115 4.5 49.8 1.0 NH1 B:ARG113 4.6 42.4 1.0 CB B:GLU105 4.8 39.5 1.0 CD B:ARG113 4.9 37.7 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form


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 Ynta From Yersinia Pestis, Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni501 b:70.1 occ:1.00 NE2 D:HIS244 2.0 69.6 1.0 OE1 C:GLU105 2.1 60.9 1.0 O C:HOH608 2.2 56.1 1.0 O D:HOH601 2.3 38.3 1.0 NE2 C:HIS115 2.3 48.9 1.0 CE1 D:HIS244 2.6 68.4 1.0 OE2 C:GLU105 2.6 50.8 1.0 CD C:GLU105 2.7 53.1 1.0 CD2 C:HIS115 3.2 49.8 1.0 CD2 D:HIS244 3.2 70.2 1.0 CE1 C:HIS115 3.3 48.7 1.0 ND1 D:HIS244 3.8 67.3 1.0 CG D:HIS244 4.1 70.0 1.0 CG C:GLU105 4.2 47.5 1.0 NH1 C:ARG113 4.2 64.3 1.0 CG C:HIS115 4.4 49.0 1.0 ND1 C:HIS115 4.4 48.9 1.0 CD C:ARG113 4.7 50.9 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Ynta From Yersinia Pestis, Unliganded Form


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 Ynta From Yersinia Pestis, Unliganded Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni501 b:63.9 occ:1.00 OE2 D:GLU105 1.8 66.6 1.0 O C:HOH609 2.1 0.8 1.0 NE2 C:HIS244 2.1 58.5 1.0 O D:HOH602 2.2 48.4 1.0 NE2 D:HIS115 2.3 57.8 1.0 CD D:GLU105 2.5 64.3 1.0 OE1 D:GLU105 2.6 62.7 1.0 CE1 C:HIS244 2.6 57.7 1.0 CD2 D:HIS115 3.0 56.8 1.0 CE1 D:HIS115 3.4 54.3 1.0 CD2 C:HIS244 3.4 57.4 1.0 ND1 C:HIS244 3.9 54.8 1.0 CG D:GLU105 3.9 62.4 1.0 CG D:HIS115 4.1 51.9 1.0 CG C:HIS244 4.3 55.1 1.0 ND1 D:HIS115 4.3 50.9 1.0 NH1 D:ARG113 4.7 66.7 1.0 CB D:GLU105 5.0 61.2 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