Iodine in PDB 3a4m: Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase

The structure of Crystal Structure of Archaeal O-Phosphoseryl-Trna(Sec) Kinase, PDB code: 3a4m 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)	46.50 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.156, 74.524, 64.817, 90.00, 113.37, 90.00
R / Rfree (%)	20.9 / 25.3

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 3a4m). 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: 3a4m:
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:29.9 occ:1.00 O A:HOH283 3.4 22.9 1.0 NH1 A:ARG223 3.7 25.3 1.0 NH1 A:ARG199 3.7 35.9 1.0 CD A:ARG223 4.0 20.2 1.0 CB A:LYS131 4.0 25.5 1.0 CG A:LYS131 4.1 34.5 1.0 CG A:ARG199 4.1 22.0 1.0 CG2 A:VAL128 4.2 22.0 1.0 CG1 A:VAL220 4.2 31.6 1.0 CZ A:ARG223 4.2 23.7 1.0 CG1 A:VAL128 4.3 18.9 1.0 NE A:ARG223 4.3 19.6 1.0 CA A:VAL128 4.5 20.2 1.0 CB A:ARG199 4.5 19.6 1.0 CB A:VAL128 4.5 20.9 1.0 CD A:ARG199 4.5 28.9 1.0 CG2 A:VAL220 4.6 29.1 1.0 CG1 A:VAL202 4.8 30.2 1.0 CA A:ARG199 4.8 17.7 1.0 CB A:VAL220 4.8 29.9 1.0 CZ A:ARG199 4.8 35.8 1.0 O A:VAL128 4.9 22.5 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:29.4 occ:1.00 CD B:LYS131 3.0 40.6 1.0 NZ B:LYS131 3.4 27.4 1.0 NE B:ARG199 3.4 23.5 0.5 NH2 B:ARG199 3.7 23.8 0.5 NH1 B:ARG223 3.7 25.4 1.0 CE B:LYS131 3.8 40.6 1.0 CZ B:ARG199 3.9 26.4 0.5 CD B:ARG223 4.0 22.8 1.0 CB B:LYS131 4.2 28.1 1.0 CG B:LYS131 4.2 36.8 1.0 CG B:ARG199 4.3 22.0 0.5 CG2 B:VAL128 4.3 26.3 1.0 CZ B:ARG223 4.3 26.5 1.0 CG1 B:VAL128 4.3 23.6 1.0 CG B:ARG199 4.3 22.0 0.5 NE B:ARG223 4.4 20.2 1.0 CD B:ARG199 4.4 22.5 0.5 CG2 B:VAL220 4.4 32.7 1.0 CG1 B:VAL220 4.4 28.4 1.0 CG1 B:VAL202 4.5 26.2 1.0 CD B:ARG199 4.6 22.5 0.5 CB B:ARG199 4.6 20.7 0.5 CA B:VAL128 4.6 25.7 1.0 CB B:ARG199 4.7 20.7 0.5 CB B:VAL128 4.7 21.9 1.0 CA B:ARG199 4.8 21.1 0.5 CA B:ARG199 4.8 21.1 0.5 CB B:VAL220 4.9 30.4 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