Nickel in PDB 2bj9: Nikr with Bound Nickel and Phosphate

The structure of Nikr with Bound Nickel and Phosphate, PDB code: 2bj9 was solved by T.H.Tahirov, P.T.Chivers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.13 / 3.0
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.536, 108.536, 78.818, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 23.2

The binding sites of Nickel atom in the Nikr with Bound Nickel and Phosphate (pdb code 2bj9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Nikr with Bound Nickel and Phosphate, PDB code: 2bj9:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Nikr with Bound Nickel and Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nikr with Bound Nickel and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1134 b:42.8 occ:1.00 ND1 A:HIS91 2.0 38.9 1.0 NE2 A:HIS89 2.1 31.9 1.0 SG A:CYS97 2.3 47.8 1.0 CE1 A:HIS91 2.8 40.5 1.0 CE1 A:HIS89 2.8 37.1 1.0 CG A:HIS91 3.1 36.7 1.0 CD2 A:HIS89 3.2 34.2 1.0 CB A:CYS97 3.3 31.4 1.0 CA A:HIS91 3.6 40.9 1.0 CB A:HIS91 3.6 32.6 1.0 NE2 A:HIS91 4.0 36.0 1.0 CA A:CYS97 4.0 32.4 1.0 ND1 A:HIS89 4.0 40.1 1.0 CD2 A:HIS91 4.1 40.7 1.0 N A:HIS91 4.2 38.8 1.0 CG A:HIS89 4.2 37.2 1.0 O A:VAL90 4.6 45.9 1.0 C A:VAL90 4.6 39.0 1.0 O A:ASN96 4.6 43.9 1.0 N A:CYS97 4.8 34.5 1.0 ND1 A:HIS64 4.9 46.8 1.0 C A:HIS91 4.9 41.1 1.0

Nickel binding site 2 out of 5 in the Nikr with Bound Nickel and Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nikr with Bound Nickel and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1135 b:82.7 occ:1.00 OE1 B:GLU32 2.2 46.4 1.0 OD1 B:ASP36 2.7 70.4 1.0 O A:LEU120 2.9 47.6 1.0 O A:VAL123 2.9 60.2 1.0 OD2 B:ASP36 3.1 63.2 1.0 O A:LEU118 3.2 44.0 1.0 CG B:ASP36 3.3 62.9 1.0 CD B:GLU32 3.4 62.8 1.0 O A:SER119 3.7 46.0 1.0 C A:LEU120 3.9 48.6 1.0 C A:SER119 3.9 39.0 1.0 C A:VAL123 4.0 46.3 1.0 CG B:GLU32 4.1 58.7 1.0 O1 B:PO41142 4.2 0.5 1.0 N A:VAL123 4.3 41.6 1.0 CB A:VAL123 4.3 36.2 1.0 C A:LEU118 4.3 40.4 1.0 CA A:SER119 4.3 39.0 1.0 OE2 B:GLU32 4.4 66.2 1.0 CA A:VAL123 4.4 38.2 1.0 CA A:LYS121 4.5 53.4 1.0 N A:LEU120 4.5 39.5 1.0 NH2 B:ARG39 4.6 69.6 1.0 N A:LYS121 4.6 53.3 1.0 N A:GLY122 4.7 52.9 1.0 N A:SER119 4.8 40.0 1.0 CB B:ASP36 4.8 45.0 1.0 CA A:LEU120 4.9 41.7 1.0 CE2 B:TYR27 4.9 65.0 1.0 C A:LYS121 5.0 53.8 1.0

Nickel binding site 3 out of 5 in the Nikr with Bound Nickel and Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nikr with Bound Nickel and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1139 b:40.3 occ:1.00 ND1 B:HIS91 1.9 37.0 1.0 NE2 B:HIS89 2.2 44.2 1.0 SG B:CYS97 2.5 51.2 1.0 CE1 B:HIS91 2.6 44.0 1.0 CE1 B:HIS89 3.0 43.8 1.0 CG B:HIS91 3.1 43.4 1.0 CB B:CYS97 3.2 45.4 1.0 CD2 B:HIS89 3.2 37.8 1.0 CB B:HIS91 3.7 43.4 1.0 NE2 B:HIS91 3.8 37.3 1.0 CA B:HIS91 3.8 49.6 1.0 CA B:CYS97 4.0 40.3 1.0 CD2 B:HIS91 4.0 43.2 1.0 ND1 B:HIS89 4.1 49.2 1.0 CG B:HIS89 4.3 38.8 1.0 N B:HIS91 4.3 47.3 1.0 O B:VAL90 4.3 50.1 1.0 C B:VAL90 4.5 41.7 1.0 N B:CYS97 4.8 44.6 1.0 O B:ASN96 4.8 47.9 1.0

Nickel binding site 4 out of 5 in the Nikr with Bound Nickel and Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nikr with Bound Nickel and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1140 b:99.5 occ:1.00 NE2 B:HIS64 2.2 58.0 1.0 OD2 B:ASP65 2.3 57.0 1.0 OD1 B:ASP65 2.7 47.6 1.0 CG B:ASP65 2.9 59.0 1.0 CE1 B:HIS64 3.0 59.4 1.0 CD2 B:HIS64 3.2 57.1 1.0 ND1 B:HIS64 4.1 58.1 1.0 O B:GLU94 4.3 68.5 1.0 CG B:HIS64 4.3 56.3 1.0 CB B:ASP65 4.4 58.2 1.0

Nickel binding site 5 out of 5 in the Nikr with Bound Nickel and Phosphate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Nikr with Bound Nickel and Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1141 b:70.1 occ:1.00 OD2 B:ASP75 2.4 62.5 1.0 CG B:ASP75 3.3 60.9 1.0 NZ B:LYS71 3.9 0.4 1.0 OD1 B:ASP75 4.0 66.7 1.0 CA B:ASP75 4.2 49.0 1.0 CB B:ASP75 4.2 55.8 1.0 N B:ASP75 4.6 44.4 1.0

P.T.Chivers, T.H.Tahirov. Structure of Pyrococcus Horikoshii Nikr: Nickel Sensing and Implications For the Regulation of Dna Recognition J.Mol.Biol. V. 348 597 2005.
ISSN: ISSN 0022-2836
PubMed: 15826657
DOI: 10.1016/J.JMB.2005.03.017