Nickel in PDB 1h9u: The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268

The structure of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268, PDB code: 1h9u was solved by J.W.R.Schwabe, J.D.Love, J.T.Gooch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.14 / 2.7
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.886, 106.882, 100.587, 90.00, 122.56, 90.00
R / Rfree (%)	27.3 / 30.6

The structure of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 (pdb code 1h9u). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268, PDB code: 1h9u:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni2 b:31.9 occ:1.00 CL A:CL3 2.0 31.9 1.0 NE2 A:HIS404 2.2 40.8 1.0 ND1 A:HIS402 2.8 52.4 1.0 CE1 A:HIS404 3.1 39.0 1.0 CD2 A:HIS404 3.2 40.4 1.0 CG A:HIS402 3.2 49.7 1.0 CB A:HIS402 3.4 45.9 1.0 CE1 A:HIS402 3.5 52.7 1.0 CD2 A:HIS402 4.0 52.2 1.0 NE2 A:HIS402 4.2 52.4 1.0 ND1 A:HIS404 4.3 41.8 1.0 CG A:HIS404 4.3 42.9 1.0 CA A:HIS402 4.9 43.4 1.0 NH2 A:ARG392 5.0 56.3 1.0

Nickel binding site 2 out of 4 in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni2 b:37.7 occ:1.00 CL B:CL3 2.1 38.5 1.0 NE2 B:HIS404 2.3 34.5 1.0 ND1 B:HIS402 2.6 39.8 1.0 CG B:HIS402 3.0 38.7 1.0 CE1 B:HIS404 3.2 36.8 1.0 CB B:HIS402 3.2 38.3 1.0 CD2 B:HIS404 3.3 35.4 1.0 CE1 B:HIS402 3.3 40.1 1.0 CD2 B:HIS402 3.8 41.3 1.0 NE2 B:HIS402 4.0 41.3 1.0 ND1 B:HIS404 4.3 36.9 1.0 CG B:HIS404 4.4 35.1 1.0 CA B:HIS402 4.8 38.4 1.0

Nickel binding site 3 out of 4 in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni2 b:74.7 occ:1.00 NE2 C:HIS404 2.3 54.8 1.0 ND1 C:HIS402 2.6 61.7 1.0 CG C:HIS402 3.0 59.8 1.0 CE1 C:HIS404 3.0 53.8 1.0 CE1 C:HIS402 3.1 60.8 1.0 CB C:HIS402 3.5 56.8 1.0 CD2 C:HIS404 3.5 53.3 1.0 CD2 C:HIS402 3.7 60.9 1.0 NE2 C:HIS402 3.7 61.2 1.0 ND1 C:HIS404 4.2 52.1 1.0 CG C:HIS404 4.5 54.1 1.0 CG1 C:VAL391 4.8 68.1 1.0 CA C:HIS402 5.0 52.6 1.0

Nickel binding site 4 out of 4 in the The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Structure of the Human Retinoid-X-Receptor Beta Ligand Binding Domain in Complex with the Specific Synthetic Agonist LG100268 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni2 b:76.2 occ:1.00 NE2 D:HIS404 2.3 57.2 1.0 ND1 D:HIS402 2.6 57.7 1.0 CE1 D:HIS404 3.0 57.2 1.0 CG D:HIS402 3.0 56.0 1.0 CE1 D:HIS402 3.1 57.7 1.0 CD2 D:HIS404 3.4 56.4 1.0 CB D:HIS402 3.4 54.2 1.0 CD2 D:HIS402 3.6 56.4 1.0 NE2 D:HIS402 3.7 57.8 1.0 ND1 D:HIS404 4.2 56.9 1.0 CG D:HIS404 4.5 55.9 1.0 CG1 D:VAL391 4.7 62.1 1.0 CA D:HIS402 5.0 51.1 1.0

J.D.Love, J.T.Gooch, S.Benko, C.Li, L.Nagy, V.K.K.Chatterjee, R.M.Evans, J.W.R.Schwabe. The Structural Basis For the Specificity of Retinoid-X Receptor-Selective Agonists: New Insights Into the Role of Helix H12 J.Biol.Chem. V. 277 11385 2002.
ISSN: ISSN 0021-9258
PubMed: 11782480
DOI: 10.1074/JBC.M110869200