Erbium in PDB 5nj8: Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation

The structure of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation, PDB code: 5nj8 was solved by O.Daumke, K.W.Schulte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.83 / 3.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.321, 91.321, 464.914, 90.00, 90.00, 120.00
R / Rfree (%)	29.2 / 33.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Erbium atom in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation (pdb code 5nj8). This binding sites where shown within 5.0 Angstroms radius around Erbium atom.
In total 12 binding sites of Erbium where determined in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation, PDB code: 5nj8:
Jump to Erbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Erbium binding site 1 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 1 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ A:Er301 b:95.7 occ:1.00 OE2 A:GLU165 2.7 0.3 1.0 OE1 A:GLU165 2.7 0.7 1.0 CD A:GLU165 2.9 0.7 1.0 HH22 A:ARG223 4.0 74.1 1.0 CG A:GLU165 4.2 0.6 1.0 HG2 A:GLU165 4.3 0.5 1.0 HH12 A:ARG223 4.5 0.3 1.0 HG3 A:GLU165 4.7 0.5 1.0 NH2 A:ARG223 4.8 61.8 1.0 HE2 A:HIS163 4.8 95.4 1.0

Erbium binding site 2 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 2 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ B:Er401 b:57.1 occ:1.00 OD1 B:ASP161 2.6 0.8 1.0 O A:LEU112 2.7 0.5 1.0 OD2 B:ASP161 2.7 0.9 1.0 OXT B:ACT405 2.8 95.2 1.0 CG B:ASP161 3.0 96.2 1.0 OE1 A:GLU116 3.2 1.0 1.0 HA A:LEU112 3.3 0.9 1.0 HB3 A:LEU112 3.4 1.0 1.0 C A:LEU112 3.4 0.8 1.0 OE2 A:GLU116 3.6 0.8 1.0 CA A:LEU112 3.7 0.8 1.0 C B:ACT405 3.7 86.4 1.0 CD A:GLU116 3.8 95.1 1.0 H A:GLY115 4.0 74.5 1.0 HD22 A:LEU112 4.0 0.8 1.0 CB A:LEU112 4.1 96.7 1.0 H B:ASP161 4.1 0.4 1.0 O B:ACT405 4.2 57.6 1.0 H A:GLU116 4.3 87.4 1.0 HD23 A:LEU112 4.3 0.8 1.0 HA3 A:GLY115 4.4 82.9 1.0 CB B:ASP161 4.4 87.1 1.0 HG B:SER157 4.5 0.5 1.0 N A:GLN113 4.5 75.4 1.0 CD2 A:LEU112 4.6 98.2 1.0 N B:ASP161 4.7 83.7 1.0 HA A:GLN113 4.7 90.7 1.0 N A:GLY115 4.7 62.0 1.0 HB2 A:LEU112 4.8 1.0 1.0 H1 B:ACT405 4.8 37.5 1.0 CH3 B:ACT405 4.8 31.2 1.0 HB3 B:ASP161 4.9 0.5 1.0 HB2 B:ASP161 4.9 0.5 1.0 HA B:THR160 5.0 0.2 1.0 CG A:LEU112 5.0 0.1 1.0

Erbium binding site 3 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 3 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ B:Er402 b:0.5 occ:1.00 HB2 B:GLU203 2.1 0.4 1.0 HB3 B:GLU203 2.3 0.4 1.0 CB B:GLU203 2.6 0.1 1.0 OE1 B:GLU203 2.7 0.5 1.0 HA B:GLU203 3.4 0.0 1.0 CD B:GLU203 3.6 0.2 1.0 CA B:GLU203 3.6 0.0 1.0 CG B:GLU203 3.7 1.0 1.0 HG3 B:GLU203 4.2 0.6 1.0 HG2 B:GLU203 4.3 0.6 1.0 O B:GLU203 4.4 0.4 1.0 HE22 B:GLN212 4.6 0.5 1.0 C B:GLU203 4.6 0.7 1.0 N B:GLU203 4.7 0.3 1.0 OE2 B:GLU203 4.8 0.1 1.0 H B:GLU203 4.8 0.1 1.0 HB2 B:SER207 4.9 0.8 1.0

Erbium binding site 4 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 4 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ B:Er403 b:0.2 occ:1.00 OD2 B:ASP173 2.6 94.1 1.0 OD1 B:ASP173 2.6 0.8 1.0 HZ2 A:LYS242 2.9 0.4 1.0 CG B:ASP173 3.0 1.0 1.0 HD2 A:LYS242 3.3 0.9 1.0 NZ A:LYS242 3.7 0.9 1.0 HZ3 A:LYS242 3.8 0.4 1.0 CD A:LYS242 4.1 0.6 1.0 OE2 A:GLU217 4.2 0.5 1.0 HZ1 A:LYS242 4.3 0.4 1.0 HD3 A:LYS242 4.3 0.9 1.0 O B:GLU170 4.4 61.9 1.0 CE A:LYS242 4.5 1.0 1.0 CB B:ASP173 4.5 54.7 1.0 HE3 A:LYS242 4.7 0.6 1.0 HB2 A:LYS242 4.8 0.1 1.0 HB3 B:ASP173 4.9 65.6 1.0 HB2 B:ASP173 4.9 65.6 1.0

Erbium binding site 5 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 5 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ B:Er404 b:0.3 occ:1.00 OE1 B:GLU87 2.7 0.4 1.0 OE2 B:GLU87 2.7 0.2 1.0 CD B:GLU87 3.0 0.4 1.0 HH12 B:ARG91 3.3 0.3 1.0 NH1 B:ARG91 3.9 0.6 1.0 HH11 B:ARG91 4.2 0.3 1.0 CG B:GLU87 4.4 0.3 1.0 HH22 B:ARG91 4.5 0.7 1.0 HG3 B:GLU87 4.6 0.8 1.0 HH21 B:ARG88 4.7 0.6 1.0 CZ B:ARG91 4.8 0.8 1.0 HG2 B:GLU87 4.9 0.8 1.0 NH2 B:ARG91 5.0 0.4 1.0

Erbium binding site 6 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 6 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ C:Er301 b:0.4 occ:1.00 OE1 C:GLU169 2.7 0.7 1.0 OE2 C:GLU169 2.8 0.8 1.0 CD C:GLU169 2.8 0.3 1.0 O C:GLU165 3.3 0.3 1.0 HB2 C:GLU169 3.4 0.4 1.0 HA C:ASP166 3.5 0.3 1.0 C C:GLU165 3.9 1.0 1.0 CG C:GLU169 4.0 0.3 1.0 CB C:GLU169 4.1 0.5 1.0 H C:GLU169 4.3 0.4 1.0 CA C:ASP166 4.4 0.2 1.0 HG2 C:GLU169 4.4 0.8 1.0 N C:ASP166 4.4 0.9 1.0 CB C:GLU165 4.6 0.9 1.0 HB3 C:GLU169 4.7 0.4 1.0 HG3 C:GLU169 4.7 0.8 1.0 CA C:GLU165 4.8 0.8 1.0 HA C:GLU165 4.9 0.0 1.0

Erbium binding site 7 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 7 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ C:Er302 b:0.5 occ:1.00 OE1 C:GLU116 2.6 59.4 1.0 OD1 D:ASP161 2.6 0.4 1.0 O C:LEU112 2.7 0.8 1.0 OE2 C:GLU116 2.7 98.9 1.0 OD2 D:ASP161 2.7 0.0 1.0 OD1 B:ASP326 2.8 57.4 1.0 CD C:GLU116 3.0 59.4 1.0 CG D:ASP161 3.0 0.6 1.0 HB3 B:ASP326 3.3 0.5 1.0 HA C:GLN113 3.4 0.2 1.0 H B:ASP326 3.4 0.9 1.0 HA B:ASP325 3.6 0.8 1.0 CG B:ASP326 3.6 96.0 1.0 N B:ASP326 3.7 0.4 1.0 C C:LEU112 3.8 93.9 1.0 H C:GLU116 3.9 0.9 1.0 CB B:ASP326 3.9 92.1 1.0 HA3 C:GLY115 4.1 0.8 1.0 CA C:GLN113 4.2 98.5 1.0 H C:GLY115 4.2 0.3 1.0 C B:ASP325 4.2 1.0 1.0 CA B:ASP326 4.3 0.7 1.0 CA B:ASP325 4.4 0.1 1.0 O B:ASP324 4.4 0.6 1.0 N C:GLN113 4.5 91.4 1.0 CB D:ASP161 4.5 95.0 1.0 HA B:ASP326 4.5 0.6 1.0 CG C:GLU116 4.5 0.5 1.0 N C:GLU116 4.6 0.6 1.0 C C:GLN113 4.6 94.7 1.0 N C:GLY115 4.7 0.6 1.0 HB3 D:ASP161 4.7 0.0 1.0 OD2 B:ASP326 4.7 0.7 1.0 CA C:GLY115 4.8 0.0 1.0 HB2 B:ASP326 4.8 0.5 1.0 HA C:LEU112 4.8 0.7 1.0 HG2 C:GLU116 4.9 0.5 1.0 HG3 C:GLU116 4.9 0.5 1.0 O C:GLN113 4.9 0.3 1.0 HD3 B:PRO327 4.9 63.2 1.0 HB3 C:LEU112 4.9 0.4 1.0 CA C:LEU112 5.0 94.7 1.0

Erbium binding site 8 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 8 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ D:Er401 b:0.5 occ:1.00 OD2 D:ASP173 1.8 0.3 1.0 CG D:ASP173 3.0 0.6 1.0 OD1 D:ASP173 3.5 0.6 1.0 HB2 D:ASP173 4.1 0.8 1.0 CB D:ASP173 4.2 0.6 1.0 OE2 C:GLU217 4.5 0.0 1.0 O D:ALA171 4.5 98.2 1.0 CB C:LYS242 4.7 0.9 1.0 HB3 D:ASP173 4.8 0.8 1.0 H D:ASP173 4.8 0.3 1.0 N D:ASP173 4.8 0.1 1.0 HA D:ALA172 4.8 0.1 1.0 C D:ALA172 5.0 0.1 1.0

Erbium binding site 9 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 9 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ D:Er402 b:1.0 occ:1.00 OD1 D:ASN93 3.7 0.6 1.0 OE2 D:GLU92 3.8 61.7 1.0 OE2 D:GLU96 4.0 0.8 1.0 CD D:GLU92 4.5 65.2 1.0 OE1 D:GLU92 4.6 67.4 1.0 CG D:ASN93 4.8 56.4 1.0 CD D:GLU96 4.9 74.9 1.0 OE1 D:GLU96 4.9 71.9 1.0

Erbium binding site 10 out of 12 in the Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation


Mono view


Stereo pair view

A full contact list of Erbium with other atoms in the Er binding site number 10 of Structural Basis For Aryl Hydrocarbon Receptor Mediated Gene Activation within 5.0Å range: probe atom residue distance (Å) B Occ E:Er101 b:0.7 occ:1.00 OP1 E:DT3 2.7 90.3 1.0 OD2 A:ASP65 2.8 0.3 1.0 H5'' E:DT3 3.5 81.6 1.0 CG A:ASP65 3.8 0.6 1.0 P E:DT3 3.9 83.5 1.0 HB3 A:ASP65 3.9 93.6 1.0 O3' E:DG2 3.9 67.3 1.0 HB2 A:ASP65 4.1 93.6 1.0 HD23 A:LEU67 4.1 0.9 1.0 CB A:ASP65 4.2 78.0 1.0 H5' E:DT3 4.2 81.6 1.0 C5' E:DT3 4.2 68.0 1.0 HB2 A:LEU67 4.4 73.8 1.0 OG A:SER68 4.5 0.0 1.0 HG A:SER68 4.5 0.0 1.0 O5' E:DT3 4.5 68.0 1.0 OD1 A:ASP65 4.9 81.3 1.0

K.W.Schulte, E.Green, A.Wilz, M.Platten, O.Daumke. Structural Basis For Aryl Hydrocarbon Receptor-Mediated Gene Activation. Structure V. 25 1025 2017.
ISSN: ISSN 1878-4186
PubMed: 28602820
DOI: 10.1016/J.STR.2017.05.008