Iodine in PDB 3gqu: Pyrococcus Horikoshii NOP5 Rna Binding Domain

The structure of Pyrococcus Horikoshii NOP5 Rna Binding Domain, PDB code: 3gqu was solved by F.E.Reyes, J.W.Hardin, R.T.Batey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.68 / 2.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.604, 73.604, 114.279, 90.00, 90.00, 90.00
R / Rfree (%)	29.9 / 33.4

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Pyrococcus Horikoshii NOP5 Rna Binding Domain (pdb code 3gqu). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the Pyrococcus Horikoshii NOP5 Rna Binding Domain, PDB code: 3gqu:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I1 b:72.6 occ:1.00 O A:HOH36 2.5 52.9 1.0 I A:IOD2 3.0 0.7 1.0 O A:HOH32 3.8 58.4 1.0 O A:LYS265 4.1 38.7 1.0 CA A:LEU266 4.1 37.2 1.0 OE1 A:GLN315 4.1 85.0 1.0 CB A:ARG269 4.2 44.6 1.0 N A:LEU266 4.2 32.9 1.0 NE2 A:GLN315 4.3 70.0 1.0 C A:LYS265 4.3 39.0 1.0 CG A:ARG269 4.4 44.5 1.0 CD1 A:LEU266 4.4 25.9 1.0 CD A:GLN315 4.5 74.6 1.0 CB A:LEU266 4.6 28.1 1.0 CD A:ARG269 4.6 44.8 1.0 O A:HOH58 4.7 72.9 1.0 CB A:LYS265 4.9 43.3 1.0

Iodine binding site 2 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I2 b:0.7 occ:1.00 I A:IOD1 3.0 72.6 1.0 O A:HOH44 3.1 43.1 1.0 NE2 A:GLN315 3.4 70.0 1.0 CB A:LEU266 3.7 28.1 1.0 CD A:GLN315 3.8 74.6 1.0 CD1 A:LEU266 4.1 25.9 1.0 CB A:GLN315 4.1 46.8 1.0 O A:HOH58 4.1 72.9 1.0 OE1 A:GLN315 4.2 85.0 1.0 O A:HOH31 4.2 59.3 1.0 CG A:LEU266 4.3 34.7 1.0 CA A:LEU266 4.3 37.2 1.0 O A:HOH19 4.3 34.4 1.0 CD2 A:LEU266 4.3 36.5 1.0 N A:LEU266 4.5 32.9 1.0 CG A:GLN315 4.5 50.1 1.0 O A:VAL312 5.0 44.2 1.0

Iodine binding site 3 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I3 b:1.0 occ:1.00 O A:HOH27 2.8 52.6 1.0 CA A:GLU244 3.9 40.9 1.0 I A:IOD4 4.0 0.6 1.0 CB A:GLU244 4.0 39.8 1.0 CD1 A:ILE247 4.0 63.5 1.0 CG A:GLU244 4.2 56.6 1.0 N A:GLU244 4.4 42.0 1.0 O A:HOH399 4.6 52.5 1.0 CD1 A:LEU243 4.8 43.9 1.0 CB A:ILE247 4.8 54.0 1.0 O A:HOH37 4.8 57.0 1.0 CG1 A:ILE247 4.9 51.1 1.0 CB A:LYS265 5.0 43.3 1.0 CG2 A:ILE247 5.0 54.6 1.0

Iodine binding site 4 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I4 b:0.6 occ:1.00 O A:HOH26 2.8 60.4 1.0 CB A:GLU244 3.7 39.8 1.0 N A:GLU244 3.9 42.0 1.0 I A:IOD3 4.0 1.0 1.0 CB A:LEU243 4.0 48.3 1.0 CD1 A:LEU243 4.2 43.9 1.0 CA A:GLU244 4.3 40.9 1.0 CG A:GLU244 4.6 56.6 1.0 CG A:LEU243 4.8 54.5 1.0 C A:LEU243 4.8 48.3 1.0 OE1 A:GLU244 4.9 80.6 1.0 CD A:GLU244 4.9 70.2 1.0 CA A:LEU243 5.0 52.5 1.0

Iodine binding site 5 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I5 b:1.0 occ:1.00 O A:HOH55 3.4 62.8 1.0 ND2 A:ASN320 3.6 45.0 1.0 CA A:PRO317 3.9 53.6 1.0 CB A:PRO317 4.0 50.5 1.0 O A:PRO317 4.4 62.0 1.0 CG A:ASN320 4.6 57.0 1.0 CG A:PRO317 4.6 47.7 1.0 C A:PRO317 4.6 56.5 1.0 CB A:ASN320 4.6 54.7 1.0 N A:PRO317 4.9 41.3 1.0

Iodine binding site 6 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I6 b:63.6 occ:1.00 I A:IOD7 3.4 0.7 1.0 N A:LEU277 3.5 30.3 1.0 CG1 A:VAL254 3.7 49.2 1.0 CB A:LEU277 3.8 44.6 1.0 CA A:LEU277 4.3 46.5 1.0 CA A:GLY276 4.4 44.0 1.0 C A:GLY276 4.5 47.8 1.0 CG2 A:ILE271 4.5 43.9 1.0

Iodine binding site 7 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I7 b:0.7 occ:1.00 I A:IOD6 3.4 63.6 1.0 N A:LYS278 3.7 41.5 1.0 CB A:LEU277 3.9 44.6 1.0 N A:LEU277 4.0 30.3 1.0 CE1 A:TYR346 4.3 49.5 1.0 CB A:LYS278 4.3 46.7 1.0 CA A:LEU277 4.3 46.5 1.0 C A:LEU277 4.5 48.5 1.0 CA A:LYS278 4.6 52.5 1.0 OE2 A:GLU279 4.8 51.6 1.0 CD1 A:TYR346 4.8 39.0 1.0 C A:GLY276 4.8 47.8 1.0

Iodine binding site 8 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I8 b:0.3 occ:1.00 CA A:ALA333 3.8 38.7 1.0 CB A:ALA333 3.9 29.9 1.0 I A:IOD9 4.1 0.8 1.0 N A:ALA333 4.2 33.8 1.0 C A:ARG332 4.8 35.6 1.0

Iodine binding site 9 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I9 b:0.8 occ:1.00 NZ A:LYS337 3.1 67.2 1.0 CE A:LYS337 3.3 61.8 1.0 CD A:LYS337 3.8 62.4 1.0 CB A:ALA362 3.9 52.5 1.0 I A:IOD8 4.1 0.3 1.0 CB A:ALA333 4.4 29.9 1.0 O A:ALA333 4.6 56.5 1.0 O A:LYS358 4.6 66.8 1.0 CA A:GLU359 4.7 55.3 1.0 CA A:ALA333 4.9 38.7 1.0 C A:LYS358 4.9 58.0 1.0 OE2 A:GLU359 4.9 57.2 1.0

Iodine binding site 10 out of 12 in the Pyrococcus Horikoshii NOP5 Rna Binding Domain


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Pyrococcus Horikoshii NOP5 Rna Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:I10 b:0.3 occ:1.00 CA A:GLU366 4.3 64.6 1.0 N A:GLU366 4.4 65.6 1.0 O A:HOH53 4.5 69.6 1.0 CB A:GLU366 4.6 60.1 1.0 CB A:LYS365 4.8 61.3 1.0 C A:LYS365 4.9 57.8 1.0

J.W.Hardin, F.E.Reyes, R.T.Batey. Analysis of A Critical Interaction Within the Archaeal Box C/D Small Ribonucleoprotein Complex J.Biol.Chem. V. 284 15317 2009.
ISSN: ISSN 0021-9258
PubMed: 19336398
DOI: 10.1074/JBC.M901368200