Iodine in PDB 3a4l: Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4l was solved by Y.Araiso, R.Ishitani, D.Soll, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.37 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.134, 74.452, 64.698, 90.00, 113.64, 90.00
R / Rfree (%)	21 / 24.9

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iodine atom in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase (pdb code 3a4l). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4l:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:29.2 occ:1.00 O A:HOH291 3.5 22.1 1.0 NH1 A:ARG223 3.7 22.5 1.0 CD A:ARG223 3.9 18.5 1.0 CG2 A:VAL128 4.1 22.1 1.0 CZ A:ARG223 4.1 22.9 1.0 CB A:LYS131 4.1 28.3 1.0 CG A:ARG199 4.2 18.9 1.0 NE A:ARG223 4.2 16.1 1.0 CG1 A:VAL128 4.3 19.2 1.0 CG1 A:VAL220 4.3 30.6 1.0 CG A:LYS131 4.3 31.5 1.0 CG2 A:VAL220 4.4 30.4 1.0 CD A:ARG199 4.4 22.6 1.0 CA A:VAL128 4.5 19.7 1.0 CB A:VAL128 4.5 21.6 1.0 CB A:ARG199 4.6 20.0 1.0 CA A:ARG199 4.8 19.4 1.0 CB A:VAL220 4.8 28.2 1.0 CG1 A:VAL202 4.8 25.8 1.0 O A:VAL128 4.9 20.5 1.0 NH2 A:ARG223 5.0 23.0 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase within 5.0Å range: probe atom residue distance (Å) B Occ B:I402 b:30.3 occ:1.00 O B:HOH295 3.5 28.5 1.0 NH1 B:ARG223 3.8 27.0 1.0 CG B:LYS131 3.9 37.3 1.0 CD B:ARG223 4.0 24.7 1.0 CG2 B:VAL128 4.1 28.3 1.0 CB B:LYS131 4.2 29.7 1.0 CZ B:ARG223 4.3 27.7 1.0 CG1 B:VAL128 4.3 25.2 1.0 NE B:ARG223 4.4 21.1 1.0 CG B:ARG199 4.4 20.8 1.0 CG2 B:VAL220 4.5 35.3 1.0 CG1 B:VAL220 4.5 36.1 1.0 CB B:VAL128 4.6 27.8 1.0 CA B:VAL128 4.6 25.7 1.0 CD B:ARG199 4.7 24.8 1.0 CB B:ARG199 4.7 20.9 1.0 CG1 B:VAL202 4.7 28.9 1.0 CA B:ARG199 4.8 23.5 1.0 CB B:VAL220 5.0 30.3 1.0

Y.Araiso, R.L.Sherrer, R.Ishitani, J.M.L.Ho, D.Soll, O.Nureki. Structure of A Trna-Dependent Kinase Essential For Selenocysteine Decoding Proc.Natl.Acad.Sci.Usa V. 106 16215 2009.
ISSN: ISSN 0027-8424
PubMed: 19805283
DOI: 10.1073/PNAS.0908861106