Zinc in PDB 9w4s: Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2

All present enzymatic activity of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2:
2.7.7.52;

The binding sites of Zinc atom in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2 (pdb code 9w4s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2, PDB code: 9w4s:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2001 b:337.8 occ:1.00 NE2 A:HIS322 2.0 273.0 1.0 ND1 A:HIS328 2.0 252.1 1.0 SG A:CYS306 2.3 250.3 1.0 SG A:CYS309 2.3 258.9 1.0 CG A:HIS328 2.6 252.1 1.0 CB A:HIS328 2.9 252.1 1.0 CE1 A:HIS328 2.9 252.1 1.0 CD2 A:HIS322 3.0 273.0 1.0 CE1 A:HIS322 3.0 273.0 1.0 CB A:CYS306 3.3 250.3 1.0 CB A:CYS309 3.4 258.9 1.0 CA A:HIS328 3.5 252.1 1.0 CD2 A:HIS328 3.5 252.1 1.0 NE2 A:HIS328 3.7 252.1 1.0 N A:CYS309 3.9 258.9 1.0 ND1 A:HIS322 4.1 273.0 1.0 CG A:HIS322 4.1 273.0 1.0 OD1 A:ASN331 4.1 245.6 1.0 CA A:CYS309 4.2 258.9 1.0 N A:HIS328 4.3 252.1 1.0 CB A:LEU308 4.4 231.5 1.0 CB A:ASN331 4.6 245.6 1.0 C A:HIS328 4.7 252.1 1.0 CA A:CYS306 4.7 250.3 1.0 C A:LEU308 4.8 231.5 1.0 CG A:ASN331 4.8 245.6 1.0 O A:HIS328 4.9 252.1 1.0 O A:HIS288 5.0 257.4 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:358.3 occ:1.00 ND1 B:HIS147 2.0 325.2 1.0 SG B:CYS152 2.3 350.9 1.0 SG B:CYS142 2.3 328.6 1.0 SG B:CYS139 2.3 315.3 1.0 CB B:CYS139 2.5 315.3 1.0 CE1 B:HIS147 2.5 325.2 1.0 CB B:CYS152 2.6 350.9 1.0 CG B:HIS147 3.2 325.2 1.0 CB B:CYS142 3.5 328.6 1.0 NE2 B:HIS147 3.6 325.2 1.0 CB B:HIS147 4.0 325.2 1.0 CA B:CYS139 4.0 315.3 1.0 CD2 B:HIS147 4.0 325.2 1.0 N B:CYS142 4.0 328.6 1.0 CA B:CYS152 4.1 350.9 1.0 CA B:CYS142 4.3 328.6 1.0 N B:GLY144 4.4 325.2 1.0 O B:GLY144 4.4 325.2 1.0 O B:CYS139 4.4 315.3 1.0 C B:CYS139 4.5 315.3 1.0 O B:HIS148 4.6 312.8 1.0 CA B:GLY144 4.6 325.2 1.0 C B:HIS147 4.6 325.2 1.0 O B:HIS147 4.7 325.2 1.0 N B:CYS139 4.7 315.3 1.0 CA B:HIS147 4.8 325.2 1.0 C B:CYS142 4.8 328.6 1.0 O B:CYS152 4.9 350.9 1.0 C B:ASN141 4.9 309.6 1.0 CB B:ASN141 4.9 309.6 1.0 N B:CYS152 4.9 350.9 1.0 N B:GLY143 5.0 327.8 1.0 C B:GLY144 5.0 325.2 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of HTUT4_MINI:HLIN28A:Pre-Let-7G MIRNA_UUU, Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:460.2 occ:1.00 NE2 B:HIS169 2.0 361.4 1.0 SG B:CYS161 2.3 353.8 1.0 SG B:CYS164 2.3 388.9 1.0 SG B:CYS174 2.3 306.0 1.0 CE1 B:HIS169 2.5 361.4 1.0 CB B:CYS174 3.1 306.0 1.0 CD2 B:HIS169 3.3 361.4 1.0 CB B:CYS161 3.3 353.8 1.0 ND1 B:HIS169 3.7 361.4 1.0 CB B:CYS164 3.8 388.9 1.0 N B:CYS164 3.9 388.9 1.0 CG B:HIS169 4.1 361.4 1.0 CA B:CYS174 4.2 306.0 1.0 CB B:PHE163 4.3 340.2 1.0 CA B:CYS164 4.5 388.9 1.0 CA B:CYS161 4.6 353.8 1.0 C B:PHE163 4.8 340.2 1.0 N B:PHE163 4.8 340.2 1.0 C B:CYS161 4.8 353.8 1.0 O B:MET170 4.8 330.2 1.0 CA B:PHE163 4.9 340.2 1.0 O B:CYS161 4.9 353.8 1.0

X.Han, S.Yamashita, K.Tomita. Structural Basis of LIN28-Dependent Pre-Let-7 Oligo-Uridylylation By TUT4 To Be Published.