Zinc in PDB 8qep: Rna Polymerase II Bound to Alu Rna Right Arm

All present enzymatic activity of Rna Polymerase II Bound to Alu Rna Right Arm:
2.7.7.6;

The binding sites of Zinc atom in the Rna Polymerase II Bound to Alu Rna Right Arm (pdb code 8qep). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Rna Polymerase II Bound to Alu Rna Right Arm, PDB code: 8qep:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Rna Polymerase II Bound to Alu Rna Right Arm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Bound to Alu Rna Right Arm within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:71.5 occ:1.00 SG I:CYS17 2.3 41.3 1.0 SG I:CYS42 2.3 54.5 1.0 SG I:CYS39 2.3 54.1 1.0 SG I:CYS20 2.3 47.0 1.0 CB I:CYS17 3.0 31.3 1.0 CB I:CYS39 3.2 41.8 1.0 CB I:CYS42 3.6 47.4 1.0 CB I:CYS20 3.7 35.0 1.0 N I:CYS20 4.1 28.0 1.0 N I:CYS42 4.1 47.2 1.0 CA I:CYS42 4.4 49.0 1.0 CA I:CYS20 4.4 33.7 1.0 CB I:TYR44 4.5 39.7 1.0 CB I:GLU19 4.5 41.0 1.0 CA I:CYS17 4.5 34.5 1.0 CA I:CYS39 4.6 39.9 1.0 C I:ASN41 4.7 48.5 1.0 O I:CYS42 4.8 53.0 1.0 C I:CYS42 4.8 49.1 1.0 C I:GLU19 4.9 38.2 1.0 C I:CYS20 4.9 39.2 1.0 ND2 I:ASN22 4.9 37.6 1.0 CB I:ASN22 5.0 31.1 1.0

Zinc binding site 2 out of 4 in the Rna Polymerase II Bound to Alu Rna Right Arm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Bound to Alu Rna Right Arm within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:74.5 occ:1.00 SG I:CYS89 2.3 50.4 1.0 SG I:CYS119 2.3 49.9 1.0 SG I:CYS114 2.3 28.1 1.0 SG I:CYS86 2.3 50.3 1.0 CB I:CYS114 2.8 17.6 1.0 CB I:CYS86 3.0 41.7 1.0 CB I:CYS119 3.4 39.0 1.0 CB I:CYS89 3.6 48.3 1.0 N I:CYS89 4.1 48.3 1.0 CB I:HIS121 4.2 29.3 1.0 CA I:CYS114 4.3 17.1 1.0 CA I:CYS89 4.4 47.5 1.0 CB I:HIS91 4.5 40.7 1.0 CA I:CYS86 4.5 43.3 1.0 CA I:CYS119 4.8 42.3 1.0 CB I:ALA116 4.8 38.2 1.0 N I:HIS91 4.8 39.3 1.0 N I:HIS121 4.8 34.3 1.0 C I:CYS89 4.9 49.8 1.0

Zinc binding site 3 out of 4 in the Rna Polymerase II Bound to Alu Rna Right Arm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Bound to Alu Rna Right Arm within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:49.3 occ:1.00 SG J:CYS10 2.3 16.4 1.0 SG J:CYS45 2.3 23.6 1.0 SG J:CYS44 2.3 19.9 1.0 SG J:CYS7 2.3 11.8 1.0 CB J:CYS7 3.3 5.3 1.0 N J:CYS45 3.3 14.0 1.0 CB J:CYS10 3.4 8.7 1.0 CB J:CYS45 3.6 11.8 1.0 C J:CYS44 3.6 17.7 1.0 CB J:CYS44 3.7 11.6 1.0 CA J:CYS45 3.7 10.3 1.0 N J:CYS10 3.8 7.6 1.0 O J:CYS44 4.0 15.2 1.0 CA J:CYS10 4.2 5.9 1.0 CA J:CYS44 4.2 10.3 1.0 NE J:ARG42 4.3 20.9 1.0 CB J:THR9 4.5 9.4 1.0 NH2 J:ARG42 4.7 24.3 1.0 CB J:LYS12 4.7 5.8 1.0 CA J:CYS7 4.7 7.3 1.0 C J:CYS10 4.8 15.1 1.0 C J:THR9 4.9 9.8 1.0 CB J:ARG42 4.9 15.2 1.0 N J:GLY11 4.9 12.2 1.0 N J:CYS44 4.9 14.7 1.0

Zinc binding site 4 out of 4 in the Rna Polymerase II Bound to Alu Rna Right Arm


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Bound to Alu Rna Right Arm within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:86.7 occ:1.00 SG L:CYS36 2.3 34.3 1.0 SG L:CYS22 2.3 33.2 1.0 SG L:CYS39 2.3 46.4 1.0 SG L:CYS19 2.3 28.9 1.0 CB L:CYS19 2.9 17.1 1.0 CB L:CYS36 3.2 31.6 1.0 CB L:CYS22 3.5 28.8 1.0 CB L:CYS39 3.5 44.9 1.0 N L:CYS22 3.8 31.8 1.0 OG1 L:THR24 4.0 35.4 1.0 CA L:CYS22 4.2 32.0 1.0 O L:ARG37 4.3 46.5 1.0 CB L:TYR41 4.3 34.8 1.0 CA L:CYS19 4.4 26.3 1.0 CA L:CYS39 4.5 42.0 1.0 N L:CYS39 4.5 41.5 1.0 CA L:CYS36 4.6 35.6 1.0 N L:TYR41 4.6 35.3 1.0 CB L:GLU21 4.8 39.4 1.0 C L:CYS22 4.8 29.1 1.0 C L:CYS39 4.8 38.1 1.0 C L:GLU21 4.9 30.9 1.0 N L:GLY40 4.9 37.0 1.0 N L:HIS23 4.9 21.4 1.0

K.Tluckova, B.Kaczmarek, A.Salmazo, C.Bernecky. Mechanism of Mammalian Transcriptional Repression By Noncoding Rna. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 39762629
DOI: 10.1038/S41594-024-01448-7