Nickel in PDB 2bj1: Nikr in Open Conformation and Nickel Bound to High-Affinity Sites

The structure of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites, PDB code: 2bj1 was solved by T.H.Tahirov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.64 / 3.0
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.893, 99.893, 97.978, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 28.1

The structure of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Nickel atom in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites (pdb code 2bj1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites, PDB code: 2bj1:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1133 b:83.0 occ:1.00 ND1 A:HIS91 1.9 73.8 1.0 NE2 A:HIS89 2.1 74.5 1.0 SG A:CYS97 2.1 87.8 1.0 CE1 A:HIS91 2.6 76.0 1.0 CE1 A:HIS89 2.9 69.3 1.0 CG A:HIS91 3.2 72.4 1.0 CD2 A:HIS89 3.3 69.3 1.0 CB A:CYS97 3.5 75.0 1.0 CA A:HIS91 3.8 75.5 1.0 CB A:HIS91 3.8 71.8 1.0 NE2 A:HIS91 3.8 70.6 1.0 ND1 A:HIS89 4.1 68.0 1.0 CD2 A:HIS91 4.1 74.6 1.0 CA A:CYS97 4.1 78.1 1.0 O A:VAL90 4.1 65.3 1.0 CG A:HIS89 4.3 69.1 1.0 N A:HIS91 4.4 75.1 1.0 C A:VAL90 4.5 69.6 1.0 O A:ASN96 4.7 84.5 1.0 N A:CYS97 4.8 81.1 1.0 C A:ASN96 5.0 87.0 1.0

Nickel binding site 2 out of 4 in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1133 b:84.2 occ:1.00 ND1 B:HIS91 1.9 70.1 1.0 NE2 B:HIS89 2.1 69.2 1.0 SG B:CYS97 2.3 77.7 1.0 CE1 B:HIS91 2.8 70.7 1.0 CE1 B:HIS89 2.9 70.2 1.0 CG B:HIS91 3.0 65.0 1.0 CD2 B:HIS89 3.2 68.2 1.0 CA B:HIS91 3.5 71.1 1.0 CB B:HIS91 3.5 65.4 1.0 CB B:CYS97 3.6 78.3 1.0 NE2 B:HIS91 4.0 66.3 1.0 N B:HIS91 4.0 73.4 1.0 ND1 B:HIS89 4.0 70.6 1.0 CD2 B:HIS91 4.1 64.2 1.0 CG B:HIS89 4.2 68.1 1.0 CA B:CYS97 4.3 84.6 1.0 C B:VAL90 4.6 67.0 1.0 O B:ASN96 4.7 88.9 1.0 O B:VAL90 4.8 68.5 1.0 C B:HIS91 4.8 71.8 1.0

Nickel binding site 3 out of 4 in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1134 b:0.5 occ:1.00 OD1 B:ASP65 2.3 0.2 1.0 NE2 B:HIS64 2.9 93.7 1.0 CG B:ASP65 3.1 0.1 1.0 OD2 B:ASP65 3.2 99.2 1.0 CD2 B:HIS64 3.5 94.3 1.0 CE1 B:HIS64 3.9 92.7 1.0 O B:GLU94 4.5 93.9 1.0 CB B:ASP65 4.6 0.2 1.0 CG B:HIS64 4.6 93.3 1.0 ND1 B:HIS64 4.8 92.0 1.0

Nickel binding site 4 out of 4 in the Nikr in Open Conformation and Nickel Bound to High-Affinity Sites


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Nikr in Open Conformation and Nickel Bound to High-Affinity Sites within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1135 b:0.9 occ:1.00 OD1 B:ASP75 2.5 0.7 1.0 CG B:ASP75 3.6 0.7 1.0 CA B:ASP75 4.0 89.9 1.0 CB B:ASP75 4.0 96.9 1.0 N B:ASP75 4.5 88.5 1.0 OD2 B:ASP75 4.7 0.3 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