Zinc in PDB 5udz: Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element

The structure of Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element, PDB code: 5udz was solved by Y.Nam, L.Wang, P.Sliz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.52 / 2.00
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	76.429, 76.429, 105.615, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20

The binding sites of Zinc atom in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element (pdb code 5udz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element, PDB code: 5udz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn200 b:13.9 occ:1.00 NE2 A:HIS147 2.0 17.0 1.0 SG A:CYS152 2.2 13.1 1.0 SG A:CYS139 2.4 13.2 1.0 SG A:CYS142 2.4 14.3 1.0 CD2 A:HIS147 2.9 16.1 1.0 CE1 A:HIS147 3.0 18.1 1.0 CB A:CYS152 3.1 8.3 1.0 CB A:CYS139 3.2 13.0 1.0 CB A:CYS142 3.3 11.8 1.0 O A:HOH421 3.3 37.5 1.0 N A:CYS142 3.7 12.7 1.0 CA A:CYS152 3.9 17.4 1.0 CA A:CYS142 4.0 7.3 1.0 ND1 A:HIS147 4.1 17.8 1.0 CG A:HIS147 4.1 15.8 1.0 CB A:ASN141 4.4 6.6 1.0 O A:HOH328 4.5 28.0 1.0 C A:ASN141 4.6 11.1 1.0 CA A:CYS139 4.6 13.3 1.0 C A:CYS142 4.7 6.5 1.0 ND2 A:ASN141 4.8 17.5 1.0 CA A:ASN141 4.8 10.1 1.0 N A:ASN141 4.9 11.6 1.0 N A:GLY143 4.9 6.9 1.0 C A:CYS152 4.9 17.1 1.0 N A:GLY144 4.9 12.5 1.0 N A:CYS152 4.9 22.3 1.0 N A:LYS153 5.0 19.9 1.0

Zinc binding site 2 out of 4 in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:9.1 occ:1.00 NE2 A:HIS169 2.0 7.6 1.0 SG A:CYS174 2.3 8.8 1.0 SG A:CYS161 2.3 7.6 1.0 SG A:CYS164 2.4 6.8 1.0 CD2 A:HIS169 3.0 8.6 1.0 CB A:CYS174 3.0 12.4 1.0 CE1 A:HIS169 3.0 6.9 1.0 CB A:CYS161 3.2 8.7 1.0 CB A:CYS164 3.4 8.7 1.0 CA A:CYS174 3.7 7.2 1.0 N A:CYS164 3.8 7.7 1.0 O A:HOH435 3.8 13.1 1.0 CA A:CYS164 4.1 6.8 1.0 ND1 A:HIS169 4.1 10.0 1.0 CG A:HIS169 4.1 7.0 1.0 CB A:SER166 4.6 8.4 1.0 C A:CYS174 4.6 7.2 1.0 CB A:PHE163 4.7 9.8 1.0 CA A:CYS161 4.7 9.2 1.0 CD A:PRO175 4.7 11.8 1.0 C A:PHE163 4.7 9.6 1.0 C A:CYS164 4.8 6.7 1.0 N A:CYS174 4.8 8.9 1.0 N A:PRO175 4.9 7.2 1.0 N A:GLN165 4.9 7.2 1.0 N A:PHE163 5.0 7.3 1.0 N A:SER166 5.0 6.6 1.0

Zinc binding site 3 out of 4 in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:15.6 occ:1.00 NE2 B:HIS147 2.0 10.5 1.0 SG B:CYS142 2.2 14.7 1.0 SG B:CYS139 2.3 12.6 1.0 SG B:CYS152 2.4 21.4 1.0 CE1 B:HIS147 2.9 16.5 1.0 CB B:CYS139 3.0 10.7 1.0 CD2 B:HIS147 3.1 14.0 1.0 CB B:CYS142 3.2 18.8 1.0 CB B:CYS152 3.3 22.6 1.0 N B:CYS142 3.6 14.7 1.0 CA B:CYS142 4.0 11.6 1.0 ND1 B:HIS147 4.1 20.1 1.0 CG B:HIS147 4.2 16.1 1.0 CA B:CYS152 4.2 18.0 1.0 CB B:ASN141 4.5 15.8 1.0 CA B:CYS139 4.5 11.0 1.0 C B:ASN141 4.6 15.6 1.0 C B:CYS142 4.7 11.1 1.0 O B:HOH422 4.7 36.1 1.0 N B:GLY144 4.8 9.5 1.0 N B:GLY143 4.8 13.1 1.0 N B:ASN141 4.8 9.5 1.0 CA B:ASN141 4.8 14.4 1.0 C B:CYS139 5.0 7.9 1.0 ND2 B:ASN141 5.0 11.8 1.0

Zinc binding site 4 out of 4 in the Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human LIN28A in Complex with Let-7F-1 Microrna Pre-Element within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:13.9 occ:1.00 NE2 B:HIS169 2.0 19.8 1.0 SG B:CYS161 2.3 11.9 1.0 SG B:CYS164 2.3 13.4 1.0 SG B:CYS174 2.4 13.8 1.0 CB B:CYS174 3.0 10.4 1.0 CE1 B:HIS169 3.0 14.9 1.0 CD2 B:HIS169 3.0 20.9 1.0 CB B:CYS161 3.1 16.4 1.0 CB B:CYS164 3.3 15.8 1.0 N B:CYS164 3.7 11.9 1.0 CA B:CYS174 3.8 17.4 1.0 O B:HOH419 3.9 27.9 1.0 CA B:CYS164 4.1 7.5 1.0 ND1 B:HIS169 4.1 11.0 1.0 CG B:HIS169 4.2 13.5 1.0 CA B:CYS161 4.6 10.7 1.0 CB B:SER166 4.6 16.2 1.0 C B:CYS174 4.6 14.9 1.0 CB B:PHE163 4.6 9.2 1.0 C B:PHE163 4.7 8.0 1.0 C B:CYS164 4.7 10.8 1.0 CD B:PRO175 4.9 21.4 1.0 N B:SER166 4.9 17.2 1.0 N B:GLN165 4.9 12.3 1.0 N B:PRO175 4.9 18.3 1.0 N B:CYS174 4.9 17.1 1.0 N B:PHE163 4.9 12.1 1.0 CA B:PHE163 5.0 7.4 1.0

L.Wang, Y.Nam, A.K.Lee, C.Yu, K.Roth, C.Chen, E.M.Ransey, P.Sliz. LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce Let-7 Oligouridylation. Cell Rep V. 18 2664 2017.
ISSN: ESSN 2211-1247
PubMed: 28297670
DOI: 10.1016/J.CELREP.2017.02.044