Iodine in PDB 5hml: Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions

All present enzymatic activity of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions:
3.1.11.3;

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml was solved by C.S.Flemming, M.Feng, S.E.Sedelnikova, J.Zhang, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.60 / 1.48
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.380, 58.380, 59.720, 66.53, 79.48, 73.71
R / Rfree (%)	14.1 / 19.6

The structure of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	13 atoms

The binding sites of Iodine atom in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions (pdb code 5hml). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions, PDB code: 5hml:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:I313 b:17.7 occ:0.80 I B:IOD313 0.0 17.7 0.8 I B:IOD313 2.8 20.6 0.2 CG2 B:VAL73 3.9 12.1 1.0 CG B:ARG125 4.1 13.1 1.0 CA B:GLY126 4.3 8.7 1.0 O B:ARG125 4.4 10.4 1.0 O B:HOH564 4.5 27.0 1.0 N B:GLY126 4.5 10.0 1.0 CD B:ARG125 4.5 14.1 1.0 C B:ARG125 4.6 9.5 1.0 CB B:ARG125 5.0 11.0 1.0

Iodine binding site 2 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


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 T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:I313 b:20.6 occ:0.20 I B:IOD313 0.0 20.6 0.2 I B:IOD313 2.8 17.7 0.8 O B:HOH564 3.0 27.0 1.0 N B:LYS71 3.6 14.5 1.0 O B:LYS71 3.8 26.0 1.0 CA B:GLY126 3.8 8.7 1.0 CA B:GLY70 4.0 15.5 1.0 N B:GLY126 4.0 10.0 1.0 CG B:ARG125 4.1 13.1 1.0 C B:GLY70 4.3 14.9 1.0 CG2 B:VAL73 4.4 12.1 1.0 CA B:LYS71 4.5 15.1 1.0 C B:LYS71 4.6 15.3 1.0 CB B:LYS71 4.7 18.7 1.0 C B:ARG125 4.7 9.5 1.0 CD B:ARG125 4.9 14.1 1.0

Iodine binding site 3 out of 3 in the Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of T5 D15 Protein Co-Crystallized with Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:I314 b:10.8 occ:0.80 O B:HOH482 3.4 17.4 1.0 O A:HOH475 3.5 14.9 1.0 O A:HOH535 3.5 11.8 1.0 CG B:LYS241 3.9 22.9 1.0 CA B:GLY211 3.9 14.7 1.0 ND2 B:ASN245 4.0 13.0 1.0 CA A:GLU251 4.1 10.4 1.0 CB B:LYS241 4.2 14.7 1.0 N B:TYR242 4.3 11.1 1.0 CB A:PHE254 4.4 9.2 1.0 N B:GLY211 4.4 12.9 1.0 OE2 A:GLU250 4.4 16.7 1.0 O B:GLU210 4.5 11.6 1.0 CG A:GLU250 4.5 12.7 1.0 CB B:TYR242 4.5 12.4 1.0 CA B:TYR242 4.6 11.0 1.0 C B:GLU210 4.6 10.8 1.0 CB A:GLU251 4.6 11.7 1.0 CG A:PHE254 4.6 11.1 1.0 N A:GLU251 4.7 9.6 1.0 CD2 A:PHE254 4.7 11.1 1.0 O A:GLU250 4.7 11.0 1.0 C B:LYS241 4.7 11.9 1.0 CD A:GLU250 4.8 14.9 1.0 CG B:GLU210 4.8 20.9 1.0 NH1 B:ARG216 4.8 12.4 1.0 C A:GLU250 4.9 10.1 1.0 CG A:GLU251 4.9 12.5 1.0

F.A.Almalki, C.S.Flemming, J.Zhang, M.Feng, S.E.Sedelnikova, T.Ceska, J.B.Rafferty, J.R.Sayers, P.J.Artymiuk. Direct Observation of Dna Threading in Flap Endonuclease Complexes. Nat.Struct.Mol.Biol. V. 23 640 2016.
ISSN: ESSN 1545-9985
PubMed: 27273516
DOI: 10.1038/NSMB.3241