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

Protein crystallography data

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

Nickel Binding Sites:

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 1h9u

Go back to Nickel Binding Sites List in 1h9u
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 1h9u

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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 1h9u

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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 1h9u

Go back to Nickel Binding Sites List in 1h9u
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

Reference:

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
Page generated: Fri Sep 25 07:54:04 2020
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