Iodine in PDB 5w0m: Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna

All present enzymatic activity of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna:
2.7.7.52;

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna, PDB code: 5w0m was solved by C.R.Faehnle, J.Walleshauser, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	98.17 / 2.30
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	135.472, 135.472, 179.268, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 22.9

The structure of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iodine atom in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna (pdb code 5w0m). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna, PDB code: 5w0m:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:I1404 b:58.7 occ:0.75 HG1 A:THR1174 2.5 38.9 1.0 HZ1 A:LYS1152 2.7 85.2 1.0 HD21 A:ASN1050 2.7 42.0 1.0 HA A:TYR1171 3.3 39.5 1.0 OG1 A:THR1174 3.3 32.4 1.0 HE3 A:LYS1152 3.3 57.2 1.0 NZ A:LYS1152 3.4 71.0 1.0 HZ2 A:LYS1152 3.4 85.2 1.0 ND2 A:ASN1050 3.5 35.0 1.0 HB2 A:PHE1052 3.5 44.3 1.0 HD2 A:PHE1052 3.7 45.2 1.0 HB A:THR1174 3.8 42.3 1.0 HB3 A:SER1047 3.8 61.7 1.0 HG21 A:THR1174 3.8 46.4 1.0 CE A:LYS1152 3.8 47.6 1.0 HD22 A:ASN1050 3.8 42.0 1.0 HD23 A:LEU1134 3.9 41.2 1.0 CB A:THR1174 4.0 35.3 1.0 O A:SER1170 4.1 33.6 1.0 OG A:SER1170 4.1 62.7 1.0 CA A:TYR1171 4.1 32.9 1.0 HE2 A:LYS1152 4.1 57.2 1.0 HZ3 A:LYS1152 4.1 85.2 1.0 N A:TYR1171 4.1 31.0 1.0 HG A:SER1170 4.1 75.3 1.0 C A:SER1170 4.2 41.8 1.0 HB2 A:SER1170 4.3 39.7 1.0 CB A:PHE1052 4.3 36.9 1.0 HD1 A:TYR1171 4.3 41.2 1.0 HB3 A:PHE1052 4.4 44.3 1.0 CG2 A:THR1174 4.4 38.7 1.0 CD2 A:PHE1052 4.4 37.7 1.0 CG A:ASN1050 4.5 40.6 1.0 HB2 A:TYR1171 4.5 48.6 1.0 HB2 A:SER1047 4.5 61.7 1.0 HA A:SER1047 4.5 53.6 1.0 H A:TYR1171 4.5 37.2 1.0 CB A:SER1047 4.5 51.4 1.0 OD1 A:ASN1050 4.6 52.1 1.0 HD21 A:LEU1134 4.6 41.2 1.0 CD2 A:LEU1134 4.6 34.3 1.0 CB A:SER1170 4.7 33.1 1.0 HD22 A:LEU1134 4.8 41.2 1.0 CG A:PHE1052 4.8 34.4 1.0 CB A:TYR1171 4.9 40.5 1.0 O3' H:U4 4.9 44.7 1.0 HG23 A:THR1174 4.9 46.4 1.0 O A:HOH1539 5.0 36.0 1.0 CA A:SER1047 5.0 44.6 1.0

Iodine binding site 2 out of 4 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:I1402 b:45.8 occ:0.75 HG1 B:THR1174 2.5 47.6 1.0 HZ3 B:LYS1152 2.7 69.1 1.0 HD21 B:ASN1050 2.7 39.3 1.0 HA B:TYR1171 3.2 52.2 1.0 HZ1 B:LYS1152 3.2 69.1 1.0 OG1 B:THR1174 3.3 39.7 1.0 HE3 B:LYS1152 3.3 50.0 1.0 NZ B:LYS1152 3.3 57.5 1.0 ND2 B:ASN1050 3.5 32.7 1.0 HB2 B:PHE1052 3.5 40.5 1.0 HB B:THR1174 3.8 54.9 1.0 CE B:LYS1152 3.8 41.7 1.0 HD22 B:ASN1050 3.8 39.3 1.0 HD23 B:LEU1134 3.9 73.7 1.0 HG21 B:THR1174 3.9 84.6 1.0 HB3 B:SER1047 3.9 45.5 1.0 HD2 B:PHE1052 3.9 53.0 1.0 CA B:TYR1171 4.0 43.5 1.0 CB B:THR1174 4.0 45.8 1.0 HZ2 B:LYS1152 4.0 69.1 1.0 O B:SER1170 4.1 45.8 1.0 OG B:SER1170 4.1 75.9 1.0 N B:TYR1171 4.1 48.0 1.0 HG B:SER1170 4.1 91.0 1.0 HE2 B:LYS1152 4.1 50.0 1.0 HB2 B:SER1170 4.2 0.5 1.0 C B:SER1170 4.2 42.8 1.0 HD1 B:TYR1171 4.3 71.3 1.0 HB2 B:TYR1171 4.3 46.2 1.0 CB B:PHE1052 4.4 33.7 1.0 HB3 B:PHE1052 4.4 40.5 1.0 CG B:ASN1050 4.4 58.4 1.0 H B:TYR1171 4.5 57.6 1.0 CG2 B:THR1174 4.5 70.5 1.0 OD1 B:ASN1050 4.5 36.0 1.0 HA B:SER1047 4.6 80.2 1.0 HD21 B:LEU1134 4.6 73.7 1.0 CD2 B:LEU1134 4.6 61.4 1.0 CB B:SER1170 4.6 88.0 1.0 CD2 B:PHE1052 4.6 44.2 1.0 O3 B:SO41401 4.6 72.3 1.0 HB2 B:SER1047 4.6 45.5 1.0 CB B:SER1047 4.7 37.9 1.0 CB B:TYR1171 4.7 38.5 1.0 HD22 B:LEU1134 4.7 73.7 1.0 O3' I:U4 4.8 42.1 1.0 CG B:PHE1052 4.9 40.3 1.0 H B:THR1174 4.9 45.3 1.0 HG23 B:THR1174 5.0 84.6 1.0 O B:PHE1052 5.0 46.5 1.0 O B:HOH1534 5.0 49.4 1.0

Iodine binding site 3 out of 4 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:I1403 b:68.5 occ:0.73 HG C:SER1293 2.4 70.2 1.0 OG C:SER1293 3.0 58.5 1.0 HB2 C:PRO1342 3.0 58.3 1.0 H C:ASP1344 3.0 64.0 1.0 HB2 C:ASP1344 3.2 81.2 1.0 HG3 C:ARG1345 3.2 94.7 1.0 H C:ARG1345 3.4 60.7 1.0 HB2 C:MET1296 3.4 64.6 1.0 O C:HOH1568 3.5 58.9 1.0 O C:HOH1526 3.6 48.0 1.0 HE2 C:MET1296 3.7 80.5 1.0 N C:ASP1344 3.7 53.3 1.0 HG2 C:PRO1342 3.8 72.0 1.0 HB3 C:SER1293 3.8 76.0 1.0 HD2 C:ARG1345 3.8 0.8 1.0 HD3 C:ARG1345 3.9 0.8 1.0 CB C:PRO1342 3.9 48.6 1.0 HB2 C:LYS1295 4.0 64.7 1.0 CB C:SER1293 4.0 63.3 1.0 H C:MET1296 4.0 64.6 1.0 CG C:ARG1345 4.1 79.0 1.0 CB C:ASP1344 4.1 67.7 1.0 N C:ARG1345 4.1 50.6 1.0 O C:PRO1342 4.1 56.2 1.0 CD C:ARG1345 4.1 95.7 1.0 C C:PRO1342 4.2 60.3 1.0 CG C:PRO1342 4.3 60.0 1.0 CB C:MET1296 4.3 53.9 1.0 CA C:ASP1344 4.4 56.9 1.0 HB2 C:SER1293 4.4 76.0 1.0 HA C:ASN1343 4.4 66.1 1.0 N C:ASN1343 4.4 55.1 1.0 HB2 C:ARG1345 4.5 82.9 1.0 HB3 C:PRO1342 4.6 58.3 1.0 HB3 C:MET1296 4.6 64.6 1.0 N C:MET1296 4.6 53.8 1.0 H C:SER1293 4.6 60.4 1.0 C C:ASN1343 4.6 58.5 1.0 HG3 C:PRO1342 4.6 72.0 1.0 CE C:MET1296 4.6 67.1 1.0 OD2 C:ASP1344 4.6 0.8 1.0 CG C:ASP1344 4.6 98.7 1.0 CA C:ASN1343 4.7 55.1 1.0 CA C:PRO1342 4.7 53.0 1.0 C C:ASP1344 4.7 64.3 1.0 CB C:ARG1345 4.7 69.1 1.0 H C:ASN1343 4.8 66.1 1.0 HG2 C:ARG1345 4.8 94.7 1.0 HB3 C:ASP1344 4.8 81.2 1.0 HD3 C:LYS1295 4.8 0.1 1.0 CB C:LYS1295 4.9 53.9 1.0 HE3 C:MET1296 4.9 80.5 1.0 HB3 C:LYS1295 4.9 64.7 1.0 CA C:MET1296 4.9 43.4 1.0

Iodine binding site 4 out of 4 in the Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Human TUT7 Catalytic Module (Cm) in Complex with U5 Rna within 5.0Å range: probe atom residue distance (Å) B Occ C:I1404 b:59.1 occ:0.75 HG1 C:THR1174 2.5 56.2 1.0 HZ1 C:LYS1152 2.7 51.1 1.0 HD21 C:ASN1050 2.7 36.4 1.0 OG1 C:THR1174 3.3 46.9 1.0 HE3 C:LYS1152 3.3 77.8 1.0 HA C:TYR1171 3.3 42.5 1.0 NZ C:LYS1152 3.3 42.5 1.0 HZ2 C:LYS1152 3.4 51.1 1.0 HB2 C:PHE1052 3.4 38.1 1.0 ND2 C:ASN1050 3.5 30.3 1.0 HD2 C:PHE1052 3.7 54.3 1.0 CE C:LYS1152 3.8 64.9 1.0 HB C:THR1174 3.8 37.6 1.0 HG21 C:THR1174 3.8 43.1 1.0 HD22 C:ASN1050 3.8 36.4 1.0 HD23 C:LEU1134 3.9 52.0 1.0 HB3 C:SER1047 4.0 43.6 1.0 O C:SER1170 4.0 38.3 1.0 CB C:THR1174 4.0 31.3 1.0 HZ3 C:LYS1152 4.1 51.1 1.0 HE2 C:LYS1152 4.1 77.8 1.0 OG C:SER1170 4.1 43.8 1.0 CA C:TYR1171 4.1 35.4 1.0 C C:SER1170 4.1 25.9 1.0 N C:TYR1171 4.2 30.9 1.0 HB2 C:SER1170 4.2 48.0 1.0 HG C:SER1170 4.2 52.5 1.0 CB C:PHE1052 4.2 31.8 1.0 HB3 C:PHE1052 4.2 38.1 1.0 CD2 C:PHE1052 4.4 45.2 1.0 HD1 C:TYR1171 4.4 49.1 1.0 CG2 C:THR1174 4.4 35.9 1.0 CG C:ASN1050 4.4 42.3 1.0 HA C:SER1047 4.5 69.9 1.0 HB2 C:TYR1171 4.5 67.0 1.0 H C:TYR1171 4.5 37.1 1.0 OD1 C:ASN1050 4.6 35.0 1.0 HB2 C:SER1047 4.6 43.6 1.0 CB C:SER1170 4.6 40.0 1.0 CD2 C:LEU1134 4.6 43.3 1.0 HD21 C:LEU1134 4.6 52.0 1.0 CB C:SER1047 4.6 36.4 1.0 CG C:PHE1052 4.7 38.0 1.0 O1 C:SO41401 4.7 53.4 1.0 HD22 C:LEU1134 4.8 52.0 1.0 O C:HOH1544 4.9 25.6 1.0 O3' J:U4 4.9 35.1 1.0 CB C:TYR1171 4.9 55.9 1.0 HG23 C:THR1174 4.9 43.1 1.0

C.R.Faehnle, J.Walleshauser, L.Joshua-Tor. Multi-Domain Utilization By TUT4 and TUT7 in Control of Let-7 Biogenesis. Nat. Struct. Mol. Biol. V. 24 658 2017.
ISSN: ESSN 1545-9985
PubMed: 28671666
DOI: 10.1038/NSMB.3428