Zinc in PDB 6iw6: Crystal Structure of the LIN28-Interacting Module of Human TUT4

All present enzymatic activity of Crystal Structure of the LIN28-Interacting Module of Human TUT4:
2.7.7.52;

The structure of Crystal Structure of the LIN28-Interacting Module of Human TUT4, PDB code: 6iw6 was solved by S.Yamashita, K.Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.40
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	113.270, 127.830, 168.800, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.7

The binding sites of Zinc atom in the Crystal Structure of the LIN28-Interacting Module of Human TUT4 (pdb code 6iw6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the LIN28-Interacting Module of Human TUT4, PDB code: 6iw6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the LIN28-Interacting Module of Human TUT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the LIN28-Interacting Module of Human TUT4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:66.6 occ:1.00 ND1 A:HIS328 2.1 82.8 1.0 NE2 A:HIS322 2.3 68.5 1.0 SG A:CYS306 2.3 66.9 1.0 SG A:CYS309 2.4 75.6 1.0 CE1 A:HIS328 3.0 80.0 1.0 CD2 A:HIS322 3.1 68.8 1.0 CG A:HIS328 3.1 79.0 1.0 CB A:CYS309 3.3 74.6 1.0 CE1 A:HIS322 3.3 68.7 1.0 CB A:HIS328 3.5 76.9 1.0 CB A:CYS306 3.5 66.2 1.0 N A:CYS309 3.7 73.4 1.0 CA A:HIS328 4.0 77.8 1.0 NE2 A:HIS328 4.1 81.4 1.0 CB A:LEU308 4.1 71.3 1.0 CA A:CYS309 4.2 74.9 1.0 CD2 A:LEU308 4.2 73.7 1.0 CD2 A:HIS328 4.2 81.3 1.0 CG A:HIS322 4.3 70.7 1.0 ND1 A:HIS322 4.4 70.0 1.0 CG A:LEU308 4.5 70.4 1.0 N A:HIS328 4.6 77.9 1.0 C A:LEU308 4.7 72.3 1.0 CA A:CYS306 4.9 68.9 1.0 CA A:LEU308 4.9 71.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the LIN28-Interacting Module of Human TUT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the LIN28-Interacting Module of Human TUT4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:39.2 occ:1.00 ND1 A:HIS726 2.1 57.2 1.0 NE2 A:HIS730 2.1 55.8 1.0 NE2 A:HIS728 2.2 49.0 1.0 SG A:CYS507 2.3 38.9 1.0 CE1 A:HIS726 3.0 55.1 1.0 CD2 A:HIS730 3.0 51.4 1.0 CE1 A:HIS730 3.1 51.8 1.0 CE1 A:HIS728 3.1 45.0 1.0 CG A:HIS726 3.1 59.5 1.0 CD2 A:HIS728 3.2 49.1 1.0 CB A:CYS507 3.4 30.6 1.0 CB A:HIS726 3.5 67.3 1.0 NE2 A:HIS726 4.2 57.1 1.0 ND1 A:HIS730 4.2 52.3 1.0 CG A:HIS730 4.2 52.1 1.0 CD1 A:TYR502 4.2 36.5 1.0 CD2 A:HIS726 4.2 57.9 1.0 ND1 A:HIS728 4.2 48.6 1.0 CG A:HIS728 4.3 50.0 1.0 CE2 A:TYR508 4.4 40.4 1.0 CD2 A:TYR508 4.5 37.8 1.0 CA A:CYS507 4.6 33.6 1.0 CE1 A:TYR502 4.7 33.5 1.0 C A:CYS507 4.8 37.6 1.0 CA A:HIS726 5.0 76.0 1.0 N A:TYR508 5.0 37.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the LIN28-Interacting Module of Human TUT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the LIN28-Interacting Module of Human TUT4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:0.1 occ:1.00 ND1 B:HIS328 2.2 96.0 1.0 SG B:CYS306 2.3 0.3 1.0 NE2 B:HIS322 2.4 90.8 1.0 SG B:CYS309 2.5 0.0 1.0 CE1 B:HIS328 3.1 94.2 1.0 CB B:CYS309 3.3 0.7 1.0 CG B:HIS328 3.3 98.8 1.0 CE1 B:HIS322 3.4 92.8 1.0 CD2 B:HIS322 3.4 89.6 1.0 CB B:CYS306 3.5 0.6 1.0 N B:CYS309 3.6 0.5 1.0 CB B:HIS328 3.7 0.1 1.0 CA B:HIS328 4.0 0.0 1.0 CA B:CYS309 4.1 0.1 1.0 CB B:LEU308 4.2 0.3 1.0 NE2 B:HIS328 4.3 94.7 1.0 CD2 B:HIS328 4.4 96.6 1.0 O B:HOH1107 4.4 97.8 1.0 ND1 B:HIS322 4.5 93.8 1.0 CG B:HIS322 4.5 93.2 1.0 N B:HIS328 4.7 0.1 1.0 C B:LEU308 4.7 0.6 1.0 CA B:CYS306 4.9 0.4 1.0 CA B:LEU308 4.9 0.4 1.0 O B:ASP287 5.0 89.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the LIN28-Interacting Module of Human TUT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the LIN28-Interacting Module of Human TUT4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:41.1 occ:1.00 NE2 B:HIS730 2.0 51.1 1.0 ND1 B:HIS726 2.1 53.6 1.0 NE2 B:HIS728 2.1 46.4 1.0 SG B:CYS507 2.3 38.1 1.0 CE1 B:HIS730 2.9 47.0 1.0 CE1 B:HIS728 3.0 40.9 1.0 CD2 B:HIS730 3.0 47.3 1.0 CE1 B:HIS726 3.0 49.8 1.0 CG B:HIS726 3.1 56.3 1.0 CD2 B:HIS728 3.2 46.4 1.0 CB B:HIS726 3.4 62.9 1.0 CB B:CYS507 3.5 33.1 1.0 ND1 B:HIS730 4.0 48.4 1.0 CG B:HIS730 4.1 48.0 1.0 NE2 B:HIS726 4.2 51.8 1.0 ND1 B:HIS728 4.2 45.2 1.0 CD2 B:HIS726 4.2 54.3 1.0 CG B:HIS728 4.3 48.1 1.0 CE1 B:TYR508 4.3 43.5 1.0 CD1 B:TYR502 4.3 31.0 1.0 CD1 B:TYR508 4.5 41.3 1.0 CA B:CYS507 4.7 35.5 1.0 C B:CYS507 4.8 38.2 1.0 CE1 B:TYR502 4.9 29.0 1.0 CA B:HIS726 5.0 71.9 1.0

S.Yamashita, T.Nagaike, K.Tomita. Crystal Structure of the LIN28-Interacting Module of Human Terminal Uridylyltransferase That Regulates Let-7 Expression. Nat Commun V. 10 1960 2019.
ISSN: ESSN 2041-1723
PubMed: 31036859
DOI: 10.1038/S41467-019-09966-5