Iodine in PDB 6l7v: Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions.

The structure of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions., PDB code: 6l7v was solved by N.Kuwabara, K.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.266, 67.266, 76.820, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 26.1

The structure of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Iodine atom in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. (pdb code 6l7v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions., PDB code: 6l7v:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide 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 CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:0.4 occ:1.00 NH1 A:ARG46 3.5 90.0 1.0 CD A:ARG156 3.6 66.1 1.0 CZ A:ARG46 3.9 85.1 1.0 NE A:ARG46 4.0 72.9 1.0 CG A:ARG156 4.1 54.0 1.0 CB A:ALA158 4.2 40.3 1.0 NH1 A:ARG156 4.7 84.2 1.0 CG1 A:VAL143 4.8 56.7 1.0 NH2 A:ARG46 4.8 89.4 1.0 NE A:ARG156 4.9 71.6 1.0 CG2 A:VAL143 4.9 62.1 1.0

Iodine binding site 2 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide 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 CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:0.7 occ:1.00 O A:HOH405 3.2 37.6 1.0 CE A:MET235 3.6 44.3 1.0 CD2 A:LEU231 4.4 43.2 1.0 O A:VAL147 4.8 43.1 1.0 CG A:LEU231 4.9 41.4 1.0

Iodine binding site 3 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide 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 CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:0.6 occ:1.00 NE2 A:GLN49 3.6 53.4 1.0 CA A:SER84 3.9 48.6 1.0 N A:SER84 4.1 43.7 1.0 O A:VAL83 4.1 43.5 1.0 C A:VAL83 4.2 41.3 1.0 O A:HOH414 4.2 69.0 1.0 SG A:CYS82 4.3 68.5 1.0 CB A:SER84 4.3 50.5 1.0 CD A:GLN49 4.6 56.0 1.0 OE1 A:GLN49 4.9 63.9 1.0

Iodine binding site 4 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:0.4 occ:1.00 N A:LEU222 3.9 69.9 1.0 OE1 A:GLN221 4.2 99.7 1.0 CB A:LEU222 4.3 57.9 1.0 CB A:PHE215 4.3 58.9 1.0 CA A:GLN221 4.5 84.4 1.0 CD A:GLN221 4.7 99.9 1.0 C A:GLN221 4.7 74.5 1.0 CA A:LEU222 4.7 61.6 1.0 CB A:GLN221 4.8 90.3 1.0

Iodine binding site 5 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:0.5 occ:1.00 O A:HOH425 4.1 47.7 1.0 CA A:TRP226 4.2 45.7 1.0 CD1 A:TRP226 4.3 48.0 1.0 CE1 A:PHE192 4.3 43.3 1.0 CZ A:PHE192 4.5 43.4 1.0 N A:TRP226 4.5 51.2 1.0 CB A:TRP226 4.6 46.4 1.0 O A:SER225 4.7 45.2 1.0 CB A:GLU229 4.7 51.2 1.0 C A:SER225 4.8 50.3 1.0 CG A:TRP226 4.8 47.7 1.0

Iodine binding site 6 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I308 b:0.2 occ:1.00 OG1 A:THR239 3.5 40.2 1.0 CA A:ARG236 3.8 34.0 1.0 O A:HOH402 3.8 44.5 1.0 NH1 A:ARG236 3.8 45.4 1.0 O A:MET235 3.9 43.1 1.0 N A:ARG236 4.0 34.7 1.0 C A:MET235 4.1 38.4 1.0 CB A:ARG236 4.5 39.6 1.0 CZ A:ARG236 4.6 46.1 1.0 CB A:MET235 4.7 39.5 1.0 CB A:THR239 4.7 41.2 1.0 CD A:ARG236 4.8 49.9 1.0 CG A:MET235 4.8 48.2 1.0 CG2 A:THR239 4.9 41.2 1.0 C A:ARG236 5.0 34.4 1.0 NE A:ARG236 5.0 51.2 1.0

Iodine binding site 7 out of 7 in the Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions.


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of CET1 From Trypanosoma Cruzi in Complex with Tripolyphosphate, Manganese and Iodide Ions. within 5.0Å range: probe atom residue distance (Å) B Occ A:I309 b:0.9 occ:1.00 CB A:ASP111 3.6 83.2 1.0 N A:VAL112 3.9 82.6 1.0 C A:ASP111 4.0 80.7 1.0 CA A:VAL112 4.0 86.6 1.0 C A:VAL112 4.3 87.2 1.0 O A:ASP111 4.3 81.9 1.0 CB A:ARG180 4.3 76.3 1.0 CA A:ASP111 4.5 74.9 1.0 N A:ARG180 4.5 93.1 1.0 CG A:ASP111 4.7 88.2 1.0 CA A:THR179 4.8 0.5 1.0 C A:THR179 4.8 0.7 1.0 N A:THR179 4.9 0.0 1.0 OD2 A:ASP111 4.9 88.0 1.0

Y.Takagi, N.Kuwabara, T.T.Dang, K.Furukawa, C.K.Ho. Crystal Structures of the Rna Triphosphatase From Trypanosoma Cruzi Provide Insights Into How It Recognizes the 5' End of the Rna Substrate. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 32381506
DOI: 10.1074/JBC.RA119.011811