Magnesium in PDB 2bj3: Nikr-Apo

The structure of Nikr-Apo, PDB code: 2bj3 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)	29.25 / 2.2
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.783, 54.322, 77.276, 90.00, 116.06, 90.00
R / Rfree (%)	21.8 / 26.8

The structure of Nikr-Apo also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Nikr-Apo (pdb code 2bj3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Nikr-Apo, PDB code: 2bj3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Nikr-Apo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nikr-Apo within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1139 b:92.9 occ:1.00 O A:HOH2028 2.1 89.7 1.0 O B:HOH2005 2.1 93.5 1.0 O A:HOH2027 2.1 93.4 1.0 O B:HOH2006 2.1 92.5 1.0 O A:HOH2026 2.1 90.9 1.0 O B:HOH2004 2.1 93.1 1.0 O B:ILE25 3.5 64.6 1.0 OD1 A:ASP115 4.0 62.6 1.0 OD2 A:ASP115 4.3 67.2 1.0 O B:GLU24 4.5 66.8 1.0 C B:ILE25 4.5 64.3 1.0 CG A:ASP115 4.6 57.4 1.0 OE2 A:GLU48 4.7 57.3 1.0 CA B:ILE25 4.9 64.5 1.0

Magnesium binding site 2 out of 2 in the Nikr-Apo


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nikr-Apo within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1134 b:79.7 occ:1.00 O D:HOH2023 2.1 77.8 1.0 O C:HOH2001 2.1 84.4 1.0 O C:HOH2002 2.1 77.2 1.0 O D:HOH2014 2.1 80.5 1.0 O D:HOH2025 2.1 76.5 1.0 O D:HOH2024 2.1 74.3 1.0 OE2 D:GLU48 3.9 55.3 1.0 OD1 D:ASP115 4.1 79.0 1.0 OD2 D:ASP115 4.1 81.6 1.0 O C:GLU24 4.5 57.6 1.0 CG D:ASP115 4.5 73.5 1.0 O C:ILE25 4.7 50.8 1.0 CD D:LYS111 4.8 33.4 1.0 CB D:LYS111 4.8 38.3 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